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1.  Slow cooling of protein crystals 
Journal of Applied Crystallography  2009;42(Pt 5):944-952.
High-quality, ice-free X-ray diffraction data were continuously collected while cryoprotectant-free thaumatin crystals were cooled at 0.1 K s−1 from 300 to 100 K. This establishes the feasibility of fully temperature controlled studies of protein structure and dynamics, and provides insight into how cooling creates crystal disorder.
Cryoprotectant-free thaumatin crystals have been cooled from 300 to 100 K at a rate of 0.1 K s−1 – 103–104 times slower than in conventional flash cooling – while continuously collecting X-ray diffraction data, so as to follow the evolution of protein lattice and solvent properties during cooling. Diffraction patterns show no evidence of crystalline ice at any temperature. This indicates that the lattice of protein molecules is itself an excellent cryoprotectant, and with sodium potassium tartrate incorporated from the 1.5 M mother liquor ice nucleation rates are at least as low as in a 70% glycerol solution. Crystal quality during slow cooling remains high, with an average mosaicity at 100 K of 0.2°. Most of the mosaicity increase occurs above ∼200 K, where the solvent is still liquid, and is concurrent with an anisotropic contraction of the unit cell. Near 180 K a crossover to solid-like solvent behavior occurs, and on further cooling there is no additional degradation of crystal order. The variation of B factor with temperature shows clear evidence of a protein dynamical transition near 210 K, and at lower temperatures the slope dB/dT is a factor of 3–6 smaller than has been reported for any other protein. These results establish the feasibility of fully temperature controlled studies of protein structure and dynamics between 300 and 100 K.
doi:10.1107/S0021889809023553
PMCID: PMC2746722  PMID: 19798409
protein crystallography; cryocrystallography; X-ray diffraction; slow cooling; temperature control
2.  Purification, crystallization and preliminary X-ray analysis of Enterococcus casseliflavus aminoglycoside-2′′-phosphotransferase-IVa 
Aminoglycoside-2′′-phosphotransferase-IVa [APH(2′′)-IVa] is an enzyme that is responsible for high-level gentamicin resistance in E. casseliflavus isolates. Three different crystals of wild-type substrate-free APH(2′′)-IVa have been prepared and preliminary X-ray diffraction experiments have been undertaken on all three crystal forms.
The deactivation of aminoglycoside antibiotics by chemical modification is one of the major sources of bacterial resistance to this family of therapeutic compounds, which includes the clinically relevant drugs streptomycin, kanamycin and gentamicin. The aminoglycoside phosphotransferases (APHs) form one such family of enzymes responsible for this resistance. The gene encoding one of these enzymes, aminoglycoside-2′′-phosphotransferase-IVa [APH(2′′)-IVa] from Enterococcus casseliflavus, has been cloned and the protein (comprising 306 amino-acid residues) has been expressed in Escherichia coli and purified. The enzyme was crystallized in three substrate-free forms. Two of the crystal forms belonged to the orthorhombic space group P212121 with similar unit-cell parameters, although one of the crystal forms had a unit-cell volume that was approximately 13% smaller than the other and a very low solvent content of around 38%. The third crystal form belonged to the monoclinic space group P21 and preliminary X-ray diffraction analysis was consistent with the presence of two molecules in the asymmetric unit. The orthorhombic crystal forms of apo APH(2′′)-IVa both diffracted to 2.2 Å resolution and the monoclinic crystal form diffracted to 2.4 Å resolution; synchrotron diffraction data were collected from these crystals at SSRL (Stanford, California, USA). Structure determination by molecular replacement using the structure of the related enzyme APH(2′′)-IIa is proceeding.
doi:10.1107/S1744309109050039
PMCID: PMC2805544  PMID: 20057078
aminoglycoside-2′′-phosphotransferase-IVa; Enterococcus casseliflavus; antibiotic resistance
3.  Imperfect pseudo-merohedral twinning in crystals of fungal fatty acid synthase 
A case of imperfect pseudo-merohedral twinning in monoclinic crystals of fungal fatty acid synthase is discussed. A space-group transition during crystal dehydration resulted in a Moiré pattern-like interference of the twinned diffraction patterns.
The recent high-resolution structures of fungal fatty acid synthase (FAS) have provided new insights into the principles of fatty acid biosynthesis by large multifunctional enzymes. The crystallographic phase problem for the 2.6 MDa fungal FAS was initially solved to 5 Å resolution using two crystal forms from Thermomyces lanuginosus. Monoclinic crystals in space group P21 were obtained from orthorhombic crystals in space group P212121 by dehydration. Here, it is shown how this space-group transition induced imperfect pseudo-merohedral twinning in the monoclinic crystal, giving rise to a Moiré pattern-like interference of the two twin-related reciprocal lattices. The strategy for processing the twinned diffraction images and obtaining a quantitative analysis is presented. The twinning is also related to the packing of the molecules in the two crystal forms, which was derived from self-rotation function analysis and molecular-replacement solutions using a low-resolution electron microscopy map as a search model.
doi:10.1107/S0907444909000778
PMCID: PMC2631638  PMID: 19171964
imperfect pseudo-merohedral twinning; fungal fatty acid synthase
4.  The use of trimethylamine N-oxide as a primary precipitating agent and related methylamine osmolytes as cryoprotective agents for macromolecular crystallography 
The stabilizing osmolyte trimethylamine N-oxide (TMAO) is shown to be an efficient primary precipitant for protein crystal growth. In addition to TMAO, two other methylamine osmolytes, sarcosine and betaine, are shown to be effective cryoprotective agents for protein crystal cooling.
Both crystallization and cryoprotection are often bottlenecks for high-resolution X-ray structure determination of macromolecules. Methylamine osmolytes are known stabilizers of protein structure. One such osmolyte, trimethylamine N-oxide (TMAO), has seen occasional use as an additive to improve macromolecular crystal quality and has recently been shown to be an effective cryoprotective agent for low-temperature data collection. Here, TMAO and the related osmolytes sarcosine and betaine are investigated as primary precipitating agents for protein crystal growth. Crystallization experiments were undertaken with 14 proteins. Using TMAO, seven proteins crystallized in a total of 13 crystal forms, including a new tetragonal crystal form of trypsin. The crystals diffracted well, and eight of the 13 crystal forms could be effectively cryo­­cooled as grown with TMAO as an in situ cryoprotective agent. Sarcosine and betaine produced crystals of four and two of the 14 proteins, respectively. In addition to TMAO, sarcosine and betaine were effective post-crystallization cryoprotective agents for two different crystal forms of thermolysin. Precipitation reactions of TMAO with several transition-metal ions (Fe3+, Co2+, Cu2+ and Zn2+) did not occur with sarcosine or betaine and were inhibited for TMAO at lower pH. Structures of proteins from TMAO-grown crystals and from crystals soaked in TMAO, sarcosine or betaine were determined, showing osmolyte binding in five of the 12 crystals tested. When an osmolyte was shown to bind, it did so near the protein surface, interacting with water molecules, side chains and backbone atoms, often at crystal contacts.
doi:10.1107/S0907444911050360
PMCID: PMC3245723  PMID: 22194335
crystallization; cryoprotection; osmolytes; trimethylamine N-oxide; sarcosine; betaine
5.  Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments 
A new crystal-mounting method has been developed that involves a combination of controlled humid air and polymer glue for crystal coating. This method is particularly useful when applied to fragile protein crystals that are known to be sensitive to subtle changes in their physicochemical environment.
Protein crystals are fragile, and it is sometimes difficult to find conditions suitable for handling and cryocooling the crystals before conducting X-ray diffraction experiments. To overcome this issue, a protein crystal-mounting method has been developed that involves a water-soluble polymer and controlled humid air that can adjust the moisture content of a mounted crystal. By coating crystals with polymer glue and exposing them to controlled humid air, the crystals were stable at room temperature and were cryocooled under optimized humidity. Moreover, the glue-coated crystals reproducibly showed gradual transformations of their lattice constants in response to a change in humidity; thus, using this method, a series of isomorphous crystals can be prepared. This technique is valuable when working on fragile protein crystals, including membrane proteins, and will also be useful for multi-crystal data collection.
doi:10.1107/S0907444913018027
PMCID: PMC3760132  PMID: 23999307
cryocrystallography; macromolecular crystallography; crystal mounting
6.  Crystallographic characterization of two novel crystal forms of human insulin induced by chaotropic agents and a shift in pH 
Background
Insulin is a therapeutic protein that is widely used for the treatment of diabetes. Its biological function was discovered more than 80 years ago and it has since then been characterized extensively. Crystallization of the insulin molecule has always been a key activity since the protein is often administered by subcutaneous injections of crystalline insulin formulations. Over the years, insulin has been crystallized and characterized in a number of crystal systems.
Results
Interestingly, we have now discovered two new crystal forms of human insulin. The crystals were obtained when the two chaotropic agents, urea and thiocyanate were present in the crystallization experiments, and their structures were determined by X-ray crystallography. The crystals belong to the orthorhombic and monoclinic crystal systems, with space groups C2221 and C2 respectively. The orthorhombic crystals were obtained at pH 6.5 and contained three insulin hexamers in R6 conformation in the asymmetric unit whilst the monoclinic C2 crystals were obtained at pH 7.0 and contained one R6 hexamer in the asymmetric unit. Common for the two new crystals is a hexamer-hexamer interaction that has not been found in any of the previous crystal forms of insulin. The contacts involve a tight glutamate-glutamate interaction with a distance of 2.3 Å between groups. The short distance suggests a low barrier hydrogen bond. In addition, two tyrosine-tyrosine interactions occupying a known phenol binding pocket contribute to the stabilization of the contacts. Within the crystals, distinct binding sites for urea were found, adding further to the discussion on the role of urea in protein denaturation.
Conclusion
The change in space group from C2221 to C2 was primarily caused by an increase in pH. The fewer number of hexamer-hexamer interactions comprising the short hydrogen bond in the C2 space group suggest that pH is the driving force. In addition, the distance between the two glutamates increases from 2.32 Å in the C2221 crystals to 2.4 Å in the C2 crystals. However, in both cases the low barrier hydrogen bond and the tyrosine-tyrosine interaction should contribute to the stability of the crystals which is crucial when used in pharmaceutical formulations.
doi:10.1186/1472-6807-7-83
PMCID: PMC2241603  PMID: 18093308
7.  Crystallization and preliminary X-ray diffraction analysis of biotin acetyl-CoA carboxylase ligase (BirA) from Mycobacterium tuberculosis  
The cloning, purification, crystallization and preliminary X-ray characterization of the crystals of biotin acetyl-CoA carboxylase ligase from M. tuberculosis are reported.
The gene encoding biotin acetyl-CoA carboxylase ligase (BirA) from Myco­bacterium tuberculosis was cloned and expressed in Escherichia coli with a C-­terminal Strep-tag. PEG 4000 as well as PEG 8000 were used as precipitants at pH 7.5 to crystallize the protein using the vapour-diffusion technique. X-ray characterization of crystals at room temperature indicated that the crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 79.7, b = 62.8, c = 105.8 Å. Assuming the presence of two BirA molecules in the asymmetric unit, the solvent content of the crystals was 44% (V M = 2.2 Å3 Da−1). When transferred to a cryoprotectant, crystals grown in the same drop exhibited a difference in one unit-cell parameter, with a = 60.1, b = 64.0, c = 103.6 Å, but belonged to the same P212121 space group. These crystals, with two molecules of BirA present per asymmetric unit, appeared to have a very low solvent content of 28% (V M = 1.7 Å3 Da−1).
doi:10.1107/S1744309108012475
PMCID: PMC2496853  PMID: 18540066
biotin; biotin protein ligase; Mycobacterium tuberculosis
8.  High-Pressure Synthesis and Characterization of New Actinide Borates, AnB4O8 (An=Th, U) 
New actinide borates ThB4O8 and UB4O8 were synthesized under high-pressure, high-temperature conditions (5.5 GPa/1100 °C for thorium borate, 10.5 GPa/1100 °C for the isotypic uranium borate) in a Walker-type multianvil apparatus from their corresponding actinide oxide and boron oxide. The crystal structure was determined on basis of single-crystal X-ray diffraction data that were collected at room temperature. Both compounds crystallized in the monoclinic space group C2/c (Z=4). Lattice parameters for ThB4O8: a=1611.3(3), b=419.86(8), c=730.6(2) pm; β=114.70(3)°; V=449.0(2) Å3; R1=0.0255, wR2=0.0653 (all data). Lattice parameters for UB4O8: a=1589.7(3), b=422.14(8), c=723.4(2) pm; β=114.13(3)°; V=443.1(2) Å3; R1=0.0227, wR2=0.0372 (all data). The new AnB4O8 (An=Th, U) structure type is constructed from corner-sharing BO4 tetrahedra, which form layers in the bc plane. One of the four independent oxygen atoms is threefold-coordinated. The actinide cations are located between the boron–oxygen layers. In addition to Raman spectroscopic investigations, DFT calculations were performed to support the assignment of the vibrational bands.
doi:10.1002/chem.201302378
PMCID: PMC4068220  PMID: 24123698
actinides; borates; density functional theory; high-pressure chemistry; Raman spectroscopy
9.  Structural disorder and transformation in crystal growth: direct observation of ring-opening isomerization in a metal–organic solid solution 
IUCrJ  2014;1(Pt 5):318-327.
The co-crystallization of cyclic and polymeric isomers in the same crystal in varying ratios with the skeleton frameworks packed in a geometrically compatible and energetically similar fashion gives a chance to rationalize ring-opening isomerization in a crystal growth process.
A rare example is reported in which discrete Ag2 L 2 ring and (AgL)∞ chain motifs [L = N,N′-bis(3-imidazol-1-yl-propyl)-pyromellitic diimide] co-crystallize in the same crystal lattice with varying ratios and degrees of disorder. Crystal structures obtained from representative crystals reveal compatible packing arrangements of the cyclic and polymeric isomers within the crystal lattice, which enables them to co-exist within a crystalline solid solution. A feasible pathway for transformation between the isomers is suggested via facile rotation of the coordinating imidazolyl groups. This chemical system could provide a chance for direct observation of ring-opening isomerization at the crystal surface. Mass spectrometry and 1H NMR titration show a dynamic equilibrium between cyclic and oligomeric species in solution, and a potential crystallization process is suggested involving alignment of precursors directed by aromatic stacking interactions between pyromellitic diimide units, followed by ring-opening isomerization at the interface between the solid and the solution. Both cyclic and oligomeric species can act as precursors, with interconversion between them being facile due to a low energy barrier for rotation of the imidazole rings. Thermogravimetric analysis and variable-temperature powder X-ray diffraction indicate a transition to a different crystalline phase around 120°C, which is associated with loss of solvent from the crystal lattice.
doi:10.1107/S2052252514015966
PMCID: PMC4174874  PMID: 25295173
crystallization; structural transformation; ring-opening isomerism; solid solution; disorder
10.  Expression, purification and crystallization of Trypanosoma cruzi dihydroorotate dehydrogenase complexed with orotate 
The Trypanosoma cruzi dihydroorotate dehydrogenase, a key enzyme in pyrimidine de novo biosynthesis and redox homeostasis, was crystallized in complex with its first reaction product, orotate.
Dihydroorotate dehydrogenase (DHOD) catalyzes the oxidation of dihydroorotate to orotate, the fourth step and the only redox reaction in the de novo biosynthesis of pyrimidine. DHOD from Trypanosoma cruzi (TcDHOD) has been expressed as a recombinant protein in Escherichia coli and purified to homogeneity. Crystals of the TcDHOD–orotate complex were grown at 277 K by the sitting-drop vapour-diffusion technique using polyethylene glycol 3350 as a precipitant. The crystals diffract to better than 1.8 Å resolution using synchrotron radiation (λ = 0.900 Å). X-ray diffraction data were collected at 100 K and processed to 1.9 Å resolution with 98.2% completeness and an overall R merge of 7.8%. The TcDHOD crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 67.87, b = 71.89, c = 123.27 Å. The presence of two molecules in the asymmetric unit (2 × 34 kDa) gives a crystal volume per protein weight (V M) of 2.2 Å3 Da−1 and a solvent content of 44%.
doi:10.1107/S174430910502659X
PMCID: PMC1991314  PMID: 16511183
dihydroorotate dehydrogenase; pyrimidine biosynthesis; Trypanosoma cruzi; fumarate reductase; redox homeostasis; structure-based drug design
11.  Crystal structure of 8-hy­droxy­quinoline: a new monoclinic polymorph 
In an attempt to grow 8-hy­droxy­quinoline–acetamino­phen co-crystals from equimolar amounts of conformers in a chloro­form–ethanol solvent mixture at room temperature, the title compound, C9H7NO, was obtained. The mol­ecule is planar, with the hy­droxy H atom forming an intra­molecular O—H⋯N hydrogen bond. In the crystal, mol­ecules form centrosymmetric dimers via two O—H⋯N hydrogen bonds. Thus, the hy­droxy H atoms are involved in bifurcated O—H⋯N hydrogen bonds, leading to the formation of a central planar four-membered N2H2 ring. The dimers are bound by inter­molecular π–π stacking [the shortest C⋯C distance is 3.2997 (17) Å] and C—H⋯π inter­actions into a three-dimensional framework. The crystal grown represents a new monoclinic polymorph in the space group P21/n. The mol­ecular structure of the present monoclinic polymorph is very similar to that of the ortho­rhom­bic polymorph (space group Fdd2) studied previously [Roychowdhury et al. (1978 ▶). Acta Cryst. B34, 1047–1048; Banerjee & Saha (1986 ▶). Acta Cryst. C42, 1408–1411]. The structures of the two polymorphs are distinguished by the different geometries of the hydrogen-bonded dimers, which in the crystal of the ortho­rhom­bic polymorph possess twofold axis symmetry, with the central N2H2 ring adopting a butterfly conformation.
doi:10.1107/S1600536814016110
PMCID: PMC4186174  PMID: 25309256
8-hy­droxy­quinoline; hydrogen bonds; polymorphism; crystal structure
12.  An evaluation of adhesive sample holders for advanced crystallographic experiments 
Commercially available adhesives have been evaluated for crystal mounting when undertaking complex macromolecular crystallography experiments. Here, their use as tools for advanced sample mounting and cryoprotection is assessed and their suitability for room-temperature data-collection and humidity-controlled studies is investigated.
The hydration state of macromolecular crystals often affects their overall order and, ultimately, the quality of the X-ray diffraction pattern that they produce. Post-crystallization techniques that alter the solvent content of a crystal may induce rearrangement within the three-dimensional array making up the crystal, possibly resulting in more ordered packing. The hydration state of a crystal can be manipulated by exposing it to a stream of air at controlled relative humidity in which the crystal can equilibrate. This approach provides a way of exploring crystal hydration space to assess the diffraction capabilities of existing crystals. A key requirement of these experiments is to expose the crystal directly to the dehydrating environment by having the minimum amount of residual mother liquor around it. This is usually achieved by placing the crystal on a flat porous support (Kapton mesh) and removing excess liquid by wicking. Here, an alternative approach is considered whereby crystals are harvested using adhesives that capture naked crystals directly from their crystallization drop, reducing the process to a one-step procedure. The impact of using adhesives to ease the harvesting of different types of crystals is presented together with their contribution to background scattering and their usefulness in dehydration experiments. It is concluded that adhesive supports represent a valuable tool for mounting macromolecular crystals to be used in humidity-controlled experiments and to improve signal-to-noise ratios in diffraction experiments, and how they can protect crystals from modifications in the sample environment is discussed.
doi:10.1107/S1399004714014370
PMCID: PMC4157448  PMID: 25195752
macromolecular crystallography; humidity control; Crystal Catcher; resolution; crystal packing
13.  Improved crystal orientation and physical properties from single-shot XFEL stills 
X-ray free-electron laser crystallography relies on the collection of still-shot diffraction patterns. New methods are developed for optimal modeling of the crystals’ orientations and mosaic block properties.
X-ray diffraction patterns from still crystals are inherently difficult to process because the crystal orientation is not uniquely determined by measuring the Bragg spot positions. Only one of the three rotational degrees of freedom is directly coupled to spot positions; the other two rotations move Bragg spots in and out of the reflecting condition but do not change the direction of the diffracted rays. This hinders the ability to recover accurate structure factors from experiments that are dependent on single-shot exposures, such as femtosecond diffract-and-destroy protocols at X-ray free-electron lasers (XFELs). Here, additional methods are introduced to optimally model the diffraction. The best orientation is obtained by requiring, for the brightest observed spots, that each reciprocal-lattice point be placed into the exact reflecting condition implied by Bragg’s law with a minimal rotation. This approach reduces the experimental uncertainties in noisy XFEL data, improving the crystallographic R factors and sharpening anomalous differences that are near the level of the noise.
doi:10.1107/S1399004714024134
PMCID: PMC4257623  PMID: 25478847
X-ray free-electron lasers; single-shot exposures
14.  X-RAY AND CRYSTALLOGRAPHIC STUDIES OF PLANT VIRUS PREPARATIONS. III 
The Journal of General Physiology  1941;25(1):147-165.
These papers give an account of an optical and x-ray examination of preparations of plant virus substances isolated by Bawden and Pirie, in particular of those of tobacco mosaic disease. They open with a historical survey of the work, indicating the order in which new phenomena were discovered. The subsequent treatment is divided into three parts: I. Introduction and preparation of specimens. II. Modes of aggregation of virus particles. III. (1) The structure of the particles. (2) Biological implications. Part I, after an historical introduction, describes the method of preparation, from solutions of the virus, of optically oriented specimens of different concentrations. For their examination special x-ray apparatus was developed, in particular cameras working with very low angles and capable of indicating spacings up to 1000 Å. In Part III, Section 1 deals with the x-ray evidence on the internal structure of the particles. Even in solution, they have an inner regularity like that of a crystal. Virus preparations are thus in a sense doubly crystalline. Closer analysis reveals that the x-ray patterns are not directly comparable to those of a crystal as many of the reflections do not obey Bragg's law, but can be understood on the theory of gratings of limited size. The structure seems to consist of sub-units of the dimensions of approximately 11 Å cube, fitted together in a hexagonal or pseudohexagonal lattice of dimensions—a = 87 Å, c = 68 Å. Contrary to what earlier observations seemed to indicate, the particle seems to be virtually unchanged by drying and must therefore contain little water. There are marked resemblances with the structure of both crystalline and fibrous protein, but the virus structure does not belong to any of the classes hitherto studied. There are indications that the inner structure is of a simpler character than that of the molecules of crystalline proteins. Part III, Section 2 contains a comparative study of the optical and x-ray examinations of three strains of tobacco mosaic virus, two of cucumber disease virus, two of potato virus X, and the virus of bushy stunt disease of tomato. In the last case x-ray measurement confirmed the deduction from its cubic crystal habit that it was composed of spherical rather than long particles, and showed that these had a diameter when dry of 276 Å and were arranged in a body-centred cubic close packing. This single example is sufficient to show that the elongated particle form which gives rise to all the anomalous physical properties of the other viruses studied is of no essential biological importance. The similarity and differences observed between the physical properties of these preparations run closely parallel to their clinical and serological classification. Finally, the biological implications of these results are discussed together with possible applications of the new methods of examination to the study of colloid and biological problems.
PMCID: PMC2142028  PMID: 19873256
15.  Improved X-ray diffraction from Bacillus megaterium penicillin G acylase crystals through long cryosoaking dehydration 
Penicillin G acylase from the Gram-positive bacterium B. megaterium was crystallized and X-ray diffraction from these crystals could be substantially improved by slight dehydration through a long cryo-soak.
Penicillin G acylase from Bacillus megaterium (BmPGA) is currently used in the pharmaceutical industry as an alternative to PGA from Escherichia coli (EcPGA) for the hydrolysis of penicillin G to produce 6-aminopenicillanic acid (6-APA), a penam nucleus for semisynthetic penicillins. Despite the significant differences in amino-acid sequence between PGAs from Gram-positive and Gram-negative bacteria, a representative PGA structure of Gram-positive origin has never been reported. In this study, crystallization and diffraction studies of BmPGA are described. Poor diffraction patterns with blurred spots at higher resolution were typical for BmPGA crystals cryocooled after a brief immersion in cryoprotectant solution. Overnight soaking in the same cryo-solution substantially improved both the mosaicity and resolution limit through the establishment of a new crystal-packing equilibrium. A crystal of BmPGA diffracted X-rays to 2.20 Å resolution and belonged to the monoclinic space group P21 with one molecule of BmPGA in the asymmetric unit.
doi:10.1107/S1744309111040462
PMCID: PMC3232142  PMID: 22139169
Bacillus megaterium; crystal dehydration; long cryo-soaking; penicillin G acylase
16.  Four crystal forms of a Bence-Jones protein 
Four crystal forms have been grown and characterized by X-ray diffraction of a Bence-Jones protein collected from the urine of a multiple myeloma patient more than 40 y ago. The trigonal crystal form may shed some light on the formation of fibrils common to certain storage diseases.
Four crystal forms have been grown and characterized by X-ray diffraction of a Bence-Jones protein collected from the urine of a multiple myeloma patient more than 40 years ago. Closely related tetragonal and orthorhombic forms belonging to space groups P43212 and P212121, with unit-cell parameters a = b = 68.7, c = 182.1 and a = 67.7, b = 69.4, c = 87.3 Å, diffract to 1.5 and 1.9 Å, respectively. Two closely related trigonal forms, both belonging to space group P3121 with unit-cell parameters a = b = 154.3 Å but differing by a doubling of the c axis, one 46.9 Å and the other 94.0 Å, diffract to 2.9 and 2.6 Å resolution, respectively. The trigonal crystal of short c-axis length shows a positive indication of twinning. The trigonal crystal of longer c axis, which appeared only after eight months of incubation at room temperature, is likely to be composed of proteolytically degraded molecules and unlike the other crystal forms contains two entire Bence-Jones dimers in the asymmetric unit. This latter crystal form may shed some light on the formation of fibrils common to certain storage diseases.
doi:10.1107/S1744309104028532
PMCID: PMC1952397  PMID: 16508097
storage diseases; multiple myeloma; immunoglobulins; proteolysis; twinning
17.  A look inside epitaxial cobalt-on-fluorite nanoparticles with three-dimensional reciprocal space mapping using GIXD, RHEED and GISAXS 
Journal of Applied Crystallography  2013;46(Pt 4):874-881.
Three-dimensional reciprocal space mapping by X-ray and electron diffraction [namely grazing-incidence X-ray diffraction (GIXD), reflection high-energy electron diffraction (RHEED) and grazing-incidence small-angle X-ray scattering (GISAXS)] was used to explore the internal structure and shape of differently oriented epitaxial Co/CaF2 facetted nanoparticles.
In this work epitaxial growth of cobalt on CaF2(111), (110) and (001) surfaces has been extensively studied. It has been shown by atomic force microscopy that at selected growth conditions stand-alone faceted Co nanoparticles are formed on a fluorite surface. Grazing-incidence X-ray diffraction (GIXD) and reflection high-energy electron diffraction (RHEED) studies have revealed that the particles crystallize in the face-centered cubic lattice structure otherwise non-achievable in bulk cobalt under normal conditions. The particles were found to inherit lattice orientation from the underlying CaF2 layer. Three-dimensional reciprocal space mapping carried out using X-ray and electron diffraction has revealed that there exist long bright 〈111〉 streaks passing through the cobalt Bragg reflections. These streaks are attributed to stacking faults formed in the crystal lattice of larger islands upon coalescence of independently nucleated smaller islands. Distinguished from the stacking fault streaks, crystal truncation rods perpendicular to the {111} and {001} particle facets have been observed. Finally, grazing-incidence small-angle X-ray scattering (GISAXS) has been applied to decouple the shape-related scattering from that induced by the crystal lattice defects. Particle faceting has been verified by modeling the GISAXS patterns. The work demonstrates the importance of three-dimensional reciprocal space mapping in the study of epitaxial nanoparticles.
doi:10.1107/S0021889813008777
PMCID: PMC3769055  PMID: 24046491
cobalt-on-fluorite nanoparticles; grazing-incidence X-ray diffraction (GIXD); reflection high-energy electron diffraction (RHEED); grazing-incidence small-angle X-ray scattering (GISAXS); epitaxial growth; three-dimensional reciprocal space mapping
18.  Structural aspects of intermolecular interactions in the solid state of 1,4-dibenzylpiperazines bearing nitrile or amidine groups 
X-ray diffraction analyses for new pentamidine analogs are presented: 1,4-bis(4-cyanobenzyl)piperazine (1) crystallizes in the triclinic space group () and 1,4-bis(4-amidinobenzyl)piperazine tetrahydrochloride tetrahydrate (2) in the monoclinic space group (P21/n) revealing a complex system of hydrogen bonds for (2).
The crystal structures of the title 1,4-bis(4-cyanobenzyl)piperazine (1) and 1,4-bis(4-amidinobenzyl)piperazine tetrahydrochloride tetrahydrate (2) are reported. Compound (1) crystallizes in the triclinic space group and compound (2) in the monoclinic space group P21 /n. In both (1) and (2) the asymmetric unit contains one half of the molecule because the central piperazine rings were located across a symmetry center. The packing of both molecules was dominated by hydrogen bonds. The crystal lattice of (1) was formed by weak C—H⋯N and C—H⋯π interactions. The crystal structure of (2) was completely different, with cations as well as chloride anions and water molecules taking part in intermolecular interactions. Single-crystal X-ray diffraction studies combined with density functional theory (DFT) calculations allowed the characterization of the intermolecular interactions in those two systems having different types of very strong electrophilic groups: non-ionic nitrile and ionic amidine. Chemical shift data from 13C CP/MAS (Cross Polarization Magic Angle Spinning) NMR spectra were analyzed using the different procedures for the theoretical computation of shielding constants.
doi:10.1107/S2052520614013754
PMCID: PMC4184373  PMID: 25274515
pharmaceuticals; solid-state study; density functional theory; spanning X-ray diffraction
19.  Crystallization and preliminary X-ray diffraction analysis of the β subunit Yke2 of the Gim complex from Saccharomyces cerevisiae  
Crystallization of the prefoldin β subunit Yke2 is reported. This protein is a novel and potentially important target for anti-cancer therapeutics.
The Gim complex (GimC) from Saccharomyces cerevisiae is a heterohexameric protein complex, also known as prefoldin (PFD), which binds and stabilizes unfolded target polypeptides and subsequently delivers them to chaperonins for completion of folding. In this study, the crystallization and preliminary X-ray analysis of one of the β subunits of the Gim complex (Yke2) from S. cerevisiae are described. The purified protein was crystallized by the vapour-diffusion method, producing two types of crystals that belonged to the orthorhombic space group C222 or the primitive monoclinic space group P21. The unit-cell parameters for the C-centred orthorhombic crystal were a = 48.2, b = 168.86, c = 131.81 Å and the unit-cell parameters for the primitive monoclinic crystal were a = 47.83, b = 134.90, c = 81.50 Å, β = 100.71°. The Yke2 crystals diffracted to 4.2 and 3.1 Å resolution, respectively, on a rotating-anode generator under cryoconditions. This is the first report concerning the crystallization of a β subunit of a eukaryotic prefoldin.
doi:10.1107/S1744309108011846
PMCID: PMC2496857  PMID: 18540060
prefoldin; β subunit; Gim complex; Yke2
20.  Crystallization and preliminary X-ray diffraction studies on the human Plk1 Polo-box domain in complex with an unphosphorylated and a phosphorylated target peptide from Cdc25C 
Crystals of the human Plk1 Polo-box domain in complex with a Cdc25C target peptide in an unphosphorylated and a phosphorylated state have been obtained in orthorhombic and monoclinic forms that diffract to 2.1 and 2.85 Å, respectively, using synchrotron radiation.
Polo-like kinase (Plk1) is crucial for cell-cycle progression via mitosis. Members of the Polo-like kinase family are characterized by the presence of a C-terminal domain termed the Polo-box domain (PBD) in addition to the N-terminal kinase domain. The PBD of Plk1 was cloned and overexpressed in Escherichia coli. Crystallization experiments of the protein in complex with an unphosphorylated and a phosphorylated target peptide from Cdc25C yield crystals suitable for X-­ray diffraction analysis. Crystals of the PBD in complex with the phosphorylated peptide belong to the orthorhombic space group P212121, with unit-cell parameters a = 38.23, b = 67.35, c = 88.25 Å, α = γ = β = 90°, and contain one molecule per asymmetric unit. Crystals of the PBD in complex with the unphosphorylated peptide belong to the monoclinic space group P21, with unit-cell parameters a = 40.18, b = 49.17, c = 56.23 Å, α = γ = 90, β = 109.48°, and contain one molecule per asymmetric unit. The crystals diffracted to resolution limits of 2.1 and 2.85 Å using synchrotron radiation at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS), respectively.
doi:10.1107/S1744309106007494
PMCID: PMC2222578  PMID: 16582488
Polo-like kinase; Polo-box domain; Cdc25C
21.  Crystallization and X-ray diffraction studies of cellobiose phosphorylase from Cellulomonas uda  
Preliminary crystallographic studies of recombinant cellobiose phosphorylase from Cellulomonas uda in complex with reaction substrates and products have led to high-quality diffraction data at high resolution, thus enabling structural studies to dissect the structural and mechanistic determinants of disaccharide phosphorylase activity.
Disaccharide phosphorylases are able to catalyze both the synthesis and the breakdown of disaccharides and have thus emerged as attractive platforms for tailor-made sugar synthesis. Cellobiose phosphorylase from Cellulomonas uda (CPCuda) is an enzyme that belongs to glycoside hydrolase family 94 and catalyzes the reversible breakdown of cellobiose [β-d-glucopyranosyl-(1,4)-d-­glucopyranose] to α-d-glucose-1-phosphate and d-glucose. Crystals of ligand-free recombinant CPCuda and of its complexes with substrates and reaction products yielded complete X-ray diffraction data sets to high resolution using synchrotron radiation but suffered from significant variability in diffraction quality. In at least one case an intriguing space-group transition from a primitive monoclinic to a primitive orthorhombic lattice was observed during data collection. The structure of CPCuda was determined by maximum-likelihood molecular replacement, thus establishing a starting point for an investigation of the structural and mechanistic determinants of disaccharide phosphorylase activity.
doi:10.1107/S1744309110002642
PMCID: PMC2833054  PMID: 20208178
cellobiose phosphorylases; GH94; disaccharide phosphorylases; inverting hydrolases
22.  Structural Ordering of Disordered Ligand-Binding Loops of Biotin Protein Ligase into Active Conformations as a Consequence of Dehydration 
PLoS ONE  2010;5(2):e9222.
Mycobacterium tuberculosis (Mtb), a dreaded pathogen, has a unique cell envelope composed of high fatty acid content that plays a crucial role in its pathogenesis. Acetyl Coenzyme A Carboxylase (ACC), an important enzyme that catalyzes the first reaction of fatty acid biosynthesis, is biotinylated by biotin acetyl-CoA carboxylase ligase (BirA). The ligand-binding loops in all known apo BirAs to date are disordered and attain an ordered structure only after undergoing a conformational change upon ligand-binding. Here, we report that dehydration of Mtb-BirA crystals traps both the apo and active conformations in its asymmetric unit, and for the first time provides structural evidence of such transformation. Recombinant Mtb-BirA was crystallized at room temperature, and diffraction data was collected at 295 K as well as at 120 K. Transfer of crystals to paraffin and paratone-N oil (cryoprotectants) prior to flash-freezing induced lattice shrinkage and enhancement in the resolution of the X-ray diffraction data. Intriguingly, the crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensued structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration resulted in a shift of ∼3.5 Å in the flexible loop L6, a proline-rich loop unique to Mtb complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein (BCCP) domain of ACCA3. This is contrary to the involvement of loop L14 observed in Pyrococcus horikoshii BirA-BCCP complex. Another interesting feature that emerges from this dehydrated structure is that the two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively. In-depth analyses of the sequence and the structure also provide answers to the reported lower affinities of Mtb-BirA toward ATP and biotin substrates. This dehydrated crystal structure not only provides key leads to the understanding of the structure/function relationships in the protein in the absence of any ligand-bound structure, but also demonstrates the merit of dehydration of crystals as an inimitable technique to have a glance at proteins in action.
doi:10.1371/journal.pone.0009222
PMCID: PMC2821413  PMID: 20169168
23.  Crystallization and preliminary X-ray diffraction analysis of the wild-type haloalkane dehalogenase DhaA and its variant DhaA13 complexed with different ligands 
Crystals of the wild-type haloalkane dehalogenase DhaA derived from R. rhodochrous NCIMB 13064 and of its catalytically inactive variant DhaA13 were grown in the presence of various ligands and diffraction data were collected to high and atomic resolution.
Haloalkane dehalogenases make up an important class of hydrolytic enzymes which catalyse the cleavage of carbon–halogen bonds in halogenated aliphatic compounds. There is growing interest in these enzymes owing to their potential use in environmental and industrial applications. The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 can slowly detoxify the industrial pollutant 1,2,3-trichloropropane (TCP). Structural analysis of this enzyme complexed with target ligands was conducted in order to obtain detailed information about the structural limitations of its catalytic properties. In this study, the crystallization and preliminary X-ray analysis of complexes of wild-type DhaA with 2-propanol and with TCP and of complexes of the catalytically inactive variant DhaA13 with the dye coumarin and with TCP are described. The crystals of wild-type DhaA were plate-shaped and belonged to the triclinic space group P1, while the variant DhaA13 can form prism-shaped crystals belonging to the orthorhombic space group P212121 as well as plate-shaped crystals belonging to the triclinic space group P1. Diffraction data for crystals of wild-type DhaA grown from crystallization solutions with different concentrations of 2-propanol were collected to 1.70 and 1.26 Å resolution, respectively. A prism-shaped crystal of DhaA13 complexed with TCP and a plate-shaped crystal of the same variant complexed with the dye coumarin diffracted X-rays to 1.60 and 1.33 Å resolution, respectively. A crystal of wild-type DhaA and a plate-shaped crystal of DhaA13, both complexed with TCP, diffracted to atomic resolutions of 1.04 and 0.97 Å, respectively.
doi:10.1107/S1744309110051286
PMCID: PMC3034621  PMID: 21301099
haloalkane dehalogenases; DhaA; Rhodococcus rhodochrous; microseeding; atomic resolution
24.  High-Pressure Synthesis and Characterization of the Actinide Borate Phosphate U2[BO4][PO4] 
European Journal of Inorganic Chemistry  2013;2013(30):5247-5252.
A new actinide borate phosphate, U2[BO4][PO4], was synthesized in a Walker-type multianvil apparatus at 12.5 GPa and 1000 °C. The crystal structure was determined from single-crystal X-ray diffraction data collected at room temperature. U2[BO4][PO4] crystallizes in the monoclinic space group P21/c with four formula units per unit cell and the lattice parameters a = 854.6(2), b = 775.3(2), c = 816.3(2) pm, and β = 102.52(3)°. The structure consists of double layers of linked uranium–oxygen polyhedra parallel to [100]. The borate tetrahedra are located between the uranium–oxygen layers inside the double layer. The phosphate groups link the double layers.
doi:10.1002/ejic.201300662
PMCID: PMC3939824  PMID: 24611029
Actinides; Uranium; High-pressure chemistry; Borate phosphates
25.  Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of a 12R-LOX–chaperone complex 
Cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of a 12R-LOX–chaperone complex are reported. The crystals belonged to the space group P21 and diffracted to 4 Å resolution.
Lipoxygenases are a family of nonheme iron-containing dioxygenases. An Escherichia coli expression system producing the bacterial chaperones GroES and GroEL was engineered and successfully used to produce large quantities of recombinant human 12R-LOX (LOXR; MW 80.34 kDa; 701 amino-acid residues). The co-overproduction of the two chaperones with 12R-­LOX resulted in increased solubility of 12R-­LOX and allowed the purification of milligram amounts of active enzyme for structural studies by X-ray diffraction. The lipoxygenase protein was purified on an affinity column and a gel-filtration column with chaperone protein (MW 57.16 kDa). The LOXR–chaperone complex was crystallized with ligand by the hanging-drop vapor-diffusion method using 1.5 M ammonium hydrogen phosphate as precipitant. The crystals belonged to the monoclinic system, space group P21, with unit-cell parameters a = 138.97, b = 266.11, c = 152.26 Å, β = 101.07°. Based on the calculated Matthews coefficient (3.1 Å3 Da−1), it is estimated that one molecule of LOXR complexed with two molecules of chaperone is present in the asymmetric unit of the crystal lattice. X-ray diffraction data were collected to 4 Å resolution using synchrotron radiation.
doi:10.1107/S1744309111021361
PMCID: PMC3151124  PMID: 21821891
12R-LOX; lipoxygenases; chaperones

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