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1.  Adsorption structure of dimethyl ether on silicalite-1 zeolite determined using single-crystal X-ray diffraction 
The most stable sorption site of dimethyl ether on silicalite-1 is the sinusoidal channel. The configuration of guest molecules (linear or bent) plays an important role in determining where the stable sorption site is situated.
The adsorption structures of dimethyl ether (DME) on silicalite-1 zeolite (MFI-type) are determined using single-crystal X-ray diffraction. The structure of low-loaded DME-silicalite-1 indicates that all DME molecules are located in the sinusoidal channel, which is the most stable sorption site based on the van der Waals interaction between DME and the framework. The configuration of guest molecules (linear or bent) plays an important role in determining where the stable sorption site is in the pore system of MFI-type zeolites. Bent molecules favor the sinusoidal channel, while linear molecules favor the straight channel. The contribution of DME–DME interactions is considerable in the high-loaded DME-silicalite-1 structure.
PMCID: PMC4184374  PMID: 25274519
adsorption structure; MFI-type zeolite; silicalite-1; dimethyl ether; single-crystal structure analysis
2.  Three-dimensional rotation electron diffraction: software RED for automated data collection and data processing 
Journal of Applied Crystallography  2013;46(Pt 6):1863-1873.
Implementation of the RED software package for automated collection and processing of rotation electron diffraction data is described.
Implementation of a computer program package for automated collection and processing of rotation electron diffraction (RED) data is described. The software package contains two computer programs: RED data collection and RED data processing. The RED data collection program controls the transmission electron microscope and the camera. Electron beam tilts at a fine step (0.05–0.20°) are combined with goniometer tilts at a coarse step (2.0–3.0°) around a common tilt axis, which allows a fine relative tilt to be achieved between the electron beam and the crystal in a large tilt range. An electron diffraction (ED) frame is collected at each combination of beam tilt and goniometer tilt. The RED data processing program processes three-dimensional ED data generated by the RED data collection program or by other approaches. It includes shift correction of the ED frames, peak hunting for diffraction spots in individual ED frames and identification of these diffraction spots as reflections in three dimensions. Unit-cell parameters are determined from the positions of reflections in three-dimensional reciprocal space. All reflections are indexed, and finally a list with hkl indices and intensities is output. The data processing program also includes a visualizer to view and analyse three-dimensional reciprocal lattices reconstructed from the ED frames. Details of the implementation are described. Data collection and data processing with the software RED are demonstrated using a calcined zeolite sample, silicalite-1. The structure of the calcined silicalite-1, with 72 unique atoms, could be solved from the RED data by routine direct methods.
PMCID: PMC3831301  PMID: 24282334
rotation electron diffraction; electron diffraction tomography; three-dimensional electron diffraction; structure analysis; electron diffraction; computer programs
3.  Creatinine Deiminase Adsorption onto Silicalite-Modified pH-FET for Creation of New Creatinine-Sensitive Biosensor 
In the work, silicalite particles were used for the surface modification of pH-sensitive field-effect transistors (pH-FETs) with the purpose of developing new creatinine-sensitive biosensor. Creatinine deiminase (CD) adsorbed on the surface of silicalite-coated pH-FET served as a bioselective membrane. The biosensor based on CD immobilized in glutaraldehyde vapor (GA) was taken as control. The creatinine-sensitive biosensor obtained by adsorption on silicalite was shown to have better analytical characteristics (two- to threefold increased sensitivity to creatinine, three- to fourfold lesser response and recovery times, a decrease of the detection limit of creatinine determination to 5 μM, etc.).
Additionally, the biosensor based on CD adsorbed on silicalite (Sil/CD) was characterized by high signal reproducibility (relative standard deviation (RSD) for creatinine measurement = 2.6 %) and stability during storage (over 13 months). It was experimentally confirmed that the proposed biosensor was not sensitive either to high concentrations of sodium chloride or to the macromolecular protein fractions and can be used for direct quantitative analysis of creatinine in the blood serum.
It was concluded that the method of CD adsorption on silicalite is well-suited for the creation of creatinine-sensitive biosensor with improved working characteristics.
PMCID: PMC4816956  PMID: 27033849
Biosensor; Creatinine; Silicalite; pH-sensitive field-effect transistor
4.  Nanosized zeolites as a perspective material for conductometric biosensors creation 
In this work, the method of enzyme adsorption on different zeolites and mesoporous silica spheres (MSS) was investigated for the creation of conductometric biosensors. The conductometric transducers consisted of gold interdigitated electrodes were placed on the ceramic support. The transducers were modified with zeolites and MSS, and then the enzymes were adsorbed on the transducer surface. Different methods of zeolite attachment to the transducer surface were used; drop coating with heating to 200°C turned out to be the best one. Nanozeolites beta and L, zeolite L, MSS, and silicalite-1 (80 to 450 nm) were tested as the adsorbents for enzyme urease. The biosensors with all tested particles except zeolite L had good analytical characteristics. Silicalite-1 (450 nm) was also used for adsorption of glucose oxidase, acetylcholinesterase, and butyrylcholinesterase. The glucose and acetylcholine biosensors were successfully created, whereas butyrylcholinesterase was not adsorbed on silicalite-1. The enzyme adsorption on zeolites and MSS is simple, quick, well reproducible, does not require use of toxic compounds, and therefore can be recommended for the development of biosensors when these advantages are especially important.
PMCID: PMC4429111  PMID: 25991913
Zeolite; Silicalite-1; Mesoporous silica spheres; Enzyme adsorption; Urease; Acetylcholinesterase; Conductometric transducer; Biosensor
5.  A case of structure determination using pseudosymmetry 
When properly applied, pseudosymmetry can be used to improve crystallographic phases through averaging and to facilitate crystal structure determination.
Here, a case is presented of an unusual structure determination which was facilitated by the use of pseudosymmetry. Group A streptococcus uses cysteine protease Mac-1 (also known as IdeS) to evade the host immune system. Native Mac-1 was crystallized in the orthorhombic space group P21212. Surprisingly, crystals of the inactive C94A mutant of Mac-1 displayed monoclinic symmetry with space group P21, despite the use of native orthorhombic Mac-1 microcrystals for seeding. Attempts to solve the structure of the C94A mutant by MAD phasing in the monoclinic space group did not produce an interpretable map. The native Patterson map of the C94A mutant showed two strong peaks along the (1 0 1) diagonal, indicating possible translational pseudosymmetry in space group P21. Interestingly, one-third of the monoclinic reflections obeyed pseudo-orthorhombic P21212 symmetry similar to that of the wild-type crystals and could be indexed and processed in this space group. The pseudo-orthorhombic and monoclinic unit cells were related by the following vector operations: a m = b o − c o, b m = a o and c m = −2c o − b o. The pseudo-orthorhombic subset of data produced good SAD phases, leading to structure determination with one monomer in the asymmetric unit. Subsequently, the structure of the Mac-1 mutant in the monoclinic form was determined by molecular replacement, which showed six molecules forming three translationally related dimers aligned along the (1 0 1) diagonal. Knowing the geometric relationship between the pseudo-orthorhombic and the monoclinic unit cells, all six molecules can be generated in the monoclinic unit cell directly without the use of molecular replacement. The current case provides a successful example of the use of pseudosymmetry as a powerful phase-averaging method for structure determination by anomalous diffraction techniques. In particular, a structure can be solved in a higher pseudosymmetry subcell in which an NCS operator becomes a crystallographic operator. The geometrical relationships between the subcell and parental cell can be used to generate a complete molecular representation of the parental asymmetric unit for refinement.
PMCID: PMC2789005  PMID: 19966420
pseudosymmetry; structure determination; cysteine proteases; Mac-1
6.  Development of Silicalite/Glucose Oxidase-Based Biosensor and Its Application for Glucose Determination in Juices and Nectars 
The application of silicalite for improvement of enzyme adsorption on new stainless steel electrodes is reported. Glucose oxidase (GOx) was immobilized by two methods: cross-linking by glutaraldehyde (GOx-GA) and cross-linking by glutaraldehyde along with GOx adsorption on silicalite-modified electrode (SME) (GOx-SME-GA). The GOx-SME-GA biosensors were characterized by a four- to fivefold higher sensitivity than GOx-GA biosensor. It was concluded that silicalite together with GA sufficiently enhances enzyme adhesion on stainless steel electrodes. The developed GOx-SME-GA biosensors were characterized by good reproducibility of biosensor preparation (relative standard deviation (RSD)—18 %), improved signal reproducibility (RSD of glucose determination was 7 %), and good storage stability (29 % loss of activity after 18-day storage). A series of fruit juices and nectars was analyzed using GOx-SME-GA biosensor for determination of glucose concentration. The obtained results showed good correlation with the data of high-performance liquid chromatography (HPLC) (R = 0.99).
PMCID: PMC4740475  PMID: 26842792
Enzyme immobilization; Silicalite; Glucose oxidase; Conductometric transducer; Biosensor
7.  Study of zeolite influence on analytical characteristics of urea biosensor based on ion-selective field-effect transistors 
Nanoscale Research Letters  2014;9(1):124.
A possibility of the creation of potentiometric biosensor by adsorption of enzyme urease on zeolite was investigated. Several variants of zeolites (nano beta, calcinated nano beta, silicalite, and nano L) were chosen for experiments. The surface of pH-sensitive field-effect transistors was modified with particles of zeolites, and then the enzyme was adsorbed. As a control, we used the method of enzyme immobilization in glutaraldehyde vapour (without zeolites). It was shown that all used zeolites can serve as adsorbents (with different effectiveness). The biosensors obtained by urease adsorption on zeolites were characterized by good analytical parameters (signal reproducibility, linear range, detection limit and the minimal drift factor of a baseline). In this work, it was shown that modification of the surface of pH-sensitive field-effect transistors with zeolites can improve some characteristics of biosensors.
PMCID: PMC3995320  PMID: 24636423
Biosensor; Urease; Silicalite; Zeolite; Nano beta; Nano L; pH-sensitive field-effect transistor
8.  Application of silicalite-modified electrode for the development of sucrose biosensor with improved characteristics 
The application of silicalite for improvement of working characteristics of conductometric enzyme biosensors for determination of sucrose was studied in this research. Biosensors based on different types of silicalite-modified electrodes were studied and compared according to their analytical characteristics. Polyethylenimine/glutaraldehyde/silicalite-modified biosensors showed higher sensitivity compared with others type of biosensors. Moreover, the polyethylenimine/glutaraldehyde/silicalite sucrose biosensors were characterized by high selectivity and signal reproducibility (relative standard deviation (RSD) = 2.78% for glucose measurements and RSD = 3.2% for sucrose measurements). Proposed biosensors were used for determination of sucrose in different samples of beverages. The obtained results had good correlation with results obtained by HPLC. Thus, polyethylenimine/glutaraldehyde/silicalite-modified biosensors have shown perspective characteristics for the development of effective conductometric enzyme biosensors.
PMCID: PMC4388068  PMID: 25873843
Sucrose biosensor; Silicalite; Conductometric transducer
9.  Rate-dependent phase transitions in Li2FeSiO4 cathode nanocrystals 
Scientific Reports  2015;5:8599.
Nanostructured lithium metal orthosilicate materials hold a lot of promise as next generation cathodes but their full potential realization is hampered by complex crystal and electrochemical behavior. In this work Li2FeSiO4 crystals are synthesized using organic-assisted precipitation method. By varying the annealing temperature different structures are obtained, namely the monoclinic phase at 400°C, the orthorhombic phase at 900°C, and a mixed phase at 700°C. The three Li2FeSiO4 crystal phases exhibit totally different charge/discharge profiles upon delithiation/lithiation. Thus the 400°C monoclinic nanocrystals exhibit initially one Li extraction via typical solid solution reaction, while the 900°C orthorhombic crystals are characterized by unacceptably high cell polarization. In the meantime the mixed phase Li2FeSiO4 crystals reveal a mixed cycling profile. We have found that the monoclinic nanocrystals undergo phase transition to orthorhombic structure resulting in significant progressive deterioration of the material's Li storage capability. By contrast, we discovered when the monoclinic nanocrystals are cycled initially at higher rate (C/20) and subsequently subjected to low rate (C/50) cycling the material's intercalation performance is stabilized. The discovered rate-dependent electrochemically-induced phase transition and stabilization of lithium metal silicate structure provides a novel and potentially rewarding avenue towards the development of high capacity Li-ion cathodes.
PMCID: PMC4341213  PMID: 25715655
10.  Structure of the orthorhombic form of human inosine triphosphate pyrophosphatase 
X-ray crystallographic analysis of human inosine triphosphate pyrophosphohydrolase provided the secondary structure and active-site structure at 1.6 Å resolution in an orthorhombic crystal form. The structure gives a framework for future structure–function studies employing site-directed mutagenesis and for the identification of substrate/product-binding sites.
The structure of human inosine triphosphate pyrophosphohydrolase (ITPA) has been determined using diffraction data to 1.6 Å resolution. ITPA contributes to the accurate replication of DNA by cleansing cellular dNTP pools of mutagenic nucleotide purine analogs such as dITP or dXTP. A similar high-resolution unpublished structure has been deposited in the Protein Data Bank from a monoclinic and pseudo-merohedrally twinned crystal. Here, cocrystallization of ITPA with a molar ratio of XTP appears to have improved the crystals by eliminating twinning and resulted in an orthorhombic space group. However, there was no evidence for bound XTP in the structure. Comparison with substrate-bound NTPase from a thermophilic organism predicts the movement of residues within helix α1, the loop before α6 and helix α7 to cap off the active site when substrate is bound.
PMCID: PMC2225220  PMID: 17077483
inosine triphosphate pyrophosphohydrolase
11.  Enhancement of CO2 Adsorption and Catalytic Properties by Fe-Doping of [Ga2(OH)2(L)] (H4L = Biphenyl-3,3′,5,5′-tetracarboxylic Acid), MFM-300(Ga2) 
Inorganic Chemistry  2016;55(3):1076-1088.
Metal–organic frameworks (MOFs) are usually synthesized using a single type of metal ion, and MOFs containing mixtures of different metal ions are of great interest and represent a methodology to enhance and tune materials properties. We report the synthesis of [Ga2(OH)2(L)] (H4L = biphenyl-3,3′,5,5′-tetracarboxylic acid), designated as MFM-300(Ga2), (MFM = Manchester Framework Material replacing NOTT designation), by solvothermal reaction of Ga(NO3)3 and H4L in a mixture of DMF, THF, and water containing HCl for 3 days. MFM-300(Ga2) crystallizes in the tetragonal space group I4122, a = b = 15.0174(7) Å and c = 11.9111(11) Å and is isostructural with the Al(III) analogue MFM-300(Al2) with pores decorated with −OH groups bridging Ga(III) centers. The isostructural Fe-doped material [Ga1.87Fe0.13(OH)2(L)], MFM-300(Ga1.87Fe0.13), can be prepared under similar conditions to MFM-300(Ga2) via reaction of a homogeneous mixture of Fe(NO3)3 and Ga(NO3)3 with biphenyl-3,3′,5,5′-tetracarboxylic acid. An Fe(III)-based material [Fe3O1.5(OH)(HL)(L)0.5(H2O)3.5], MFM-310(Fe), was synthesized with Fe(NO3)3 and the same ligand via hydrothermal methods. [MFM-310(Fe)] crystallizes in the orthorhombic space group Pmn21 with a = 10.560(4) Å, b = 19.451(8) Å, and c = 11.773(5) Å and incorporates μ3-oxo-centered trinuclear iron cluster nodes connected by ligands to give a 3D nonporous framework that has a different structure to the MFM-300 series. Thus, Fe-doping can be used to monitor the effects of the heteroatom center within a parent Ga(III) framework without the requirement of synthesizing the isostructural Fe(III) analogue [Fe2(OH)2(L)], MFM-300(Fe2), which we have thus far been unable to prepare. Fe-doping of MFM-300(Ga2) affords positive effects on gas adsorption capacities, particularly for CO2 adsorption, whereby MFM-300(Ga1.87Fe0.13) shows a 49% enhancement of CO2 adsorption capacity in comparison to the homometallic parent material. We thus report herein the highest CO2 uptake (2.86 mmol g–1 at 273 K at 1 bar) for a Ga-based MOF. The single-crystal X-ray structures of MFM-300(Ga2)-solv, MFM-300(Ga2), MFM-300(Ga2)·2.35CO2, MFM-300(Ga1.87Fe0.13)-solv, MFM-300(Ga1.87Fe0.13), and MFM-300(Ga1.87Fe0.13)·2.0CO2 have been determined. Most notably, in situ single-crystal diffraction studies of gas-loaded materials have revealed that Fe-doping has a significant impact on the molecular details for CO2 binding in the pore, with the bridging M–OH hydroxyl groups being preferred binding sites for CO2 within these framework materials. In situ synchrotron IR spectroscopic measurements on CO2 binding with respect to the −OH groups in the pore are consistent with the above structural analyses. In addition, we found that, compared to MFM-300(Ga2), Fe-doped MFM-300(Ga1.87Fe0.13) shows improved catalytic properties for the ring-opening reaction of styrene oxide, but similar activity for the room-temperature acetylation of benzaldehyde by methanol. The role of Fe-doping in these systems is discussed as a mechanism for enhancing porosity and the structural integrity of the parent material.
Key structural insights were obtained for CO2-loaded MFM-300(Ga2) and mixed GaFe analogues by combining in situ single-crystal X-ray diffraction and in situ polarized IR spectroscopic studies. These static and dynamic experiments revealed that the adsorbed CO2 molecules in MFM-300(Ga2) form hydrogen bonds with the free −OH groups on the surface of the pores, and a previously unobserved pattern of intermolecular dipole interactions was found to stabilize two CO2 molecules within the pores.
PMCID: PMC4805307  PMID: 26757137
12.  Dramatic improvement of crystal quality for low-­temperature-grown rabbit muscle aldolase 
Rabbit muscle aldolase (RMA) was crystallized in complex with the low-complexity domain (LC4) of sorting nexin 9. Monoclinic crystals were obtained at room temperature that displayed large mosaicity and poor X-ray diffraction. However, orthorhombic RMA–LC4 crystals grown at 277 K under similar conditions exhibited low mosaicity, allowing data collection to 2.2 Å Bragg spacing and structure determination.
Rabbit muscle aldolase (RMA) was crystallized in complex with the low-complexity domain (LC4) of sorting nexin 9. Monoclinic crystals were obtained at room temperature that displayed large mosaicity and poor X-ray diffraction. However, orthorhombic RMA–LC4 crystals grown at 277 K under similar conditions exhibited low mosaicity, allowing data collection to 2.2 Å Bragg spacing and structure determination. It was concluded that the improvement of crystal quality as indicated by the higher resolution of the new RMA–LC4 complex crystals was a consequence of the introduction of new lattice contacts at lower temperature. The lattice contacts corresponded to an increased number of interactions between high-entropy side chains that mitigate the lattice strain incurred upon cryocooling and accompanying mosaic spread increases. The thermodynamically unfavorable immobilization of high-entropy side chains used in lattice formation was compensated by an entropic increase in the bulk-solvent content owing to the greater solvent content of the crystal lattice.
PMCID: PMC2864701  PMID: 20445268
rabbit muscle aldolase; improvement of crystal quality; low-complexity domain; sorting nexin 9
13.  Crystal structure of benzene-1,3,5-tri­carb­oxy­lic acid–4-pyridone (1/3) 
A 5:1 mixture of 4-hy­droxy­pyridine with benzene 1,3,5-tri­carb­oxy­lic acid in methanol yields the title hydrogen-bonded framework compound. This compound crystallizes in the ortho­rhom­bic space group Pna21 and is a polymorph of the same stoichiometric species, reported in Cc.
Slow co-crystallization of a solution of benzene-1,3,5-tri­carb­oxy­lic acid with a large excess of 4-hy­droxy­pyridine produces an inter­penetrating, three-dimensional, hydrogen-bonded framework consisting of three 4-pyridone and one benzene-1,3,5-tri­carb­oxy­lic acid mol­ecules, C9H6O6·3C5H5NO. This structure represents an ortho­rhom­bic polymorph of the previously reported C-centered, monoclinic structure [Campos-Gaxiola et al. (2014 ▸). Acta Cryst. E70, o453–o454].
PMCID: PMC4644998  PMID: 26594492
crystal structure; hydrogen-bond framework; polymorph
14.  Expression, purification, crystallization and structure determination of two glutathione S-transferase-like proteins from Shewanella oneidensis  
The production and purification of recombinant SoGST3 and SoGST6, two GST-like proteins from S. oneidensis, are reported and preliminary crystallographic studies of crystals of the recombinant enzymes are presented.
Genome analysis of Shewanella oneidensis, a Gram-negative bacterium with an unusual repertoire of respiratory and redox capabilities, revealed the presence of six glutathione S-transferase-like genes (sogst1–sogst6). Glutathione S-­transferases (GSTs; EC are found in all kingdoms of life and are involved in phase II detoxification processes by catalyzing the nucleophilic attack of reduced glutathione on diverse electrophilic substrates, thereby decreasing their reactivity. Structure–function studies of prokaryotic GST-like proteins are surprisingly underrepresented in the scientific literature when compared with eukaryotic GSTs. Here, the production and purification of recombinant SoGST3 (SO_1576) and SoGST6 (SO_4697), two of the six GST-like proteins in S. oneidensis, are reported and preliminary crystallographic studies of crystals of the recombinant enzymes are presented. SoGST3 was crystallized in two different crystal forms in the presence of GSH and DTT that diffracted to high resolution: a primitive trigonal form in space group P31 that exhibited merohedral twinning with a high twin fraction and a primitive monoclinic form in space group P21. SoGST6 yielded primitive orthorhombic crystals in space group P212121 from which diffraction data could be collected to medium resolution after application of cryo-annealing protocols. Crystal structures of both SoGST3 and SoGST6 have been determined based on marginal search models by maximum-likelihood molecular replacement as implemented in the program Phaser.
PMCID: PMC2496851  PMID: 18540073
glutathione S-transferases; Shewanella oneidensis
15.  Structure, hydrogen bonding and thermal expansion of ammonium carbonate monohydrate 
Single-crystal neutron diffraction, ab initio calculations and Raman spectroscopy are applied to understand the structure and hydrogen bonding of ammonium carbonate monohydrate, a hitherto poorly characterized substance, particularly in relation to other ammonium-bearing compounds.
We have determined the crystal structure of ammonium carbonate monohydrate, (NH4)2CO3·H2O, using Laue single-crystal diffraction methods with pulsed neutron radiation. The crystal is orthorhombic, space group Pnma (Z = 4), with unit-cell dimensions a = 12.047 (3), b = 4.453 (1), c = 11.023 (3) Å and V = 591.3 (3) Å3 [ρcalc = 1281.8 (7) kg m−3] at 10 K. The single-crystal data collected at 10 and 100 K are complemented by X-ray powder diffraction data measured from 245 to 273 K, Raman spectra measured from 80 to 263 K and an athermal zero-pressure calculation of the electronic structure and phonon spectrum carried out using density functional theory (DFT). We find no evidence of a phase transition between 10 and 273 K; above 273 K, however, the title compound transforms first to ammonium sesquicarbonate monohydrate and subsequently to ammonium bicarbonate. The crystallographic and spectroscopic data and the calculations reveal a quite strongly hydrogen-bonded structure (E HB ≃ 30–40 kJ mol−1), on the basis of H⋯O bond lengths and the topology of the electron density at the bond critical points, in which there is no free rotation of the ammonium cation at any temperature. The barrier to free rotation of the ammonium ions is estimated from the observed librational frequency to be ∼ 36 kJ mol−1. The c-axis exhibits negative thermal expansion, but the thermal expansion behaviour of the a and b axes is ormal.
PMCID: PMC4468514  PMID: 25449618
ammonium carbonate; neutron diffraction; Raman spectroscopy; density functional theory
16.  A co-crystal between benzene and ethane: a potential evaporite material for Saturn’s moon Titan 
IUCrJ  2016;3(Pt 3):192-199.
A 3:1 stoichiometric co-crystal of benzene and ethane has been structurally characterized at 90 K using synchrotron powder X-ray diffraction following in situ crystal growth at 130 K. The conditions under which the co-crystal forms identify it as a potential evaporite material on the surface of Saturn’s moon Titan.
Using synchrotron X-ray powder diffraction, the structure of a co-crystal between benzene and ethane formed in situ at cryogenic conditions has been determined, and validated using dispersion-corrected density functional theory calculations. The structure comprises a lattice of benzene molecules hosting ethane molecules within channels. Similarity between the intermolecular interactions found in the co-crystal and in pure benzene indicate that the C—H⋯π network of benzene is maintained in the co-crystal, however, this expands to accommodate the guest ethane molecules. The co-crystal has a 3:1 benzene:ethane stoichiometry and is described in the space group with a = 15.977 (1) Å and c = 5.581 (1) Å at 90 K, with a density of 1.067 g cm−3. The conditions under which this co-crystal forms identify it is a potential that forms from evaporation of Saturn’s moon Titan’s lakes, an evaporite material.
PMCID: PMC4856141  PMID: 27158505
co-crystals; molecular crystallography; synchrotron powder diffraction; Titan; evaporite
17.  Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRζ fragments 
P212121 crystals of SIV Nef core domain bound to a peptide fragment of the T-cell receptor ζ subunit exhibited noncrystallographic symmetry and nearly perfect pseudo-merohedral twinning simulating tetragonal symmetry. For a different peptide fragment, nontwinned tetragonal crystals were observed but diffracted to lower resolution. The structure was determined after assignment of the top molecular-replacement solutions to various twin or NCS domains followed by refinement under the appropriate twin law.
HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling ζ subunit of the T-­cell receptor (TCRζ). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nefcore) in complex with two different TCRζ fragments are described. The structure of SIVmac239 Nefcore bound to the longer TCRζ polypeptide (Leu51–Asp93) was determined to 3.7 Å resolution (R work = 28.7%) in the tetragonal space group P43212. The structure of SIVmac239 Nefcore in complex with the shorter TCRζ polypeptide (Ala63–Arg80) was determined to 2.05 Å resolution (R work = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P212121. The reduction in crystal space-group symmetry induced by the truncated TCRζ polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, −l) and a and b unit-cell parameters that were nearly identical predisposed the P212121 crystal form to pseudo-merohedral twinning.
PMCID: PMC2815668  PMID: 20124696
pseudo-merohedral twinning; noncrystallographic symmetry; pseudosymmetry; human immunodeficiency virus; Nef; T-cell receptor
18.  Crystallization and preliminary X-ray crystallographic analysis of the oxysterol-binding protein Osh3 from Saccharomyces cerevisiae  
The PH domain and ORD of the oxysterol-binding protein Osh3 from S. cerevisae were crystallized and X-ray diffraction data were collected.
Oxysterol-binding protein (OSBP) related proteins (ORPs) are conserved from yeast to humans and are implicated in regulation of sterol homeostasis and in signal transduction pathways. Osh3 of Saccharomyces cerevisiae is a pleckstrin-homology (PH) domain-containing ORP member that regulates phosphoinositide metabolism at endoplasmic reticulum–plasma membrane contact sites. The N-terminal PH domain of Osh3 was purified and crystallized as a lysozyme fusion and the resulting crystal diffracted to 2.3 Å resolution. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 98.03, b = 91.31, c = 84.13 Å, β = 81.41°. With two molecules in the asymmetric unit, the Matthews coefficient was 3.13 Å3 Da−1. Initial attempts to solve the structure by molecular-replacement techniques using T4 lysozyme as a search model were successful. The C-terminal OSBP-related domain (OBD) of Osh3 was crystallized by the vapour-diffusion method and the resulting crystal diffracted to 1.5 Å resolution. The crystal was orthorhombic, belonging to space group P212121, with unit-cell parameters a = 41.57, b = 87.52, c = 100.58 Å. With one molecule in the asymmetric unit, the Matthews coefficient was 2.01 Å3 Da−1. Initial attempts to solve the structure by the single-wavelength anomalous dispersion technique using bromine were successful.
PMCID: PMC3509973  PMID: 23192032
oxysterol-binding protein; Osh3; Saccharomyces cerevisiae
19.  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.
PMCID: PMC2631638  PMID: 19171964
imperfect pseudo-merohedral twinning; fungal fatty acid synthase
20.  Crystallization and initial X-ray diffraction studies of the flavoenzyme NAD(P)H:(acceptor) oxidoreductase (FerB) from the soil bacterium Paracoccus denitrificans  
The flavin-dependent enzyme FerB from P. denitrificans has been purified and both native and SeMet-substituted FerB have been crystallized. The two variants crystallized in two different crystallographic forms belonging to the monoclinic space group P21 and the orthorhombic space group P21212, respectively. X-ray diffraction data were collected to 1.75 Å resolution for both forms.
The flavin-dependent enzyme FerB from Paracoccus denitrificans reduces a broad range of compounds, including ferric complexes, chromate and most notably quinones, at the expense of the reduced nicotinamide adenine dinucleotide cofactors NADH or NADPH. Recombinant unmodified and SeMet-substituted FerB were crystallized under similar conditions by the hanging-drop vapour-diffusion method with microseeding using PEG 4000 as the precipitant. FerB crystallized in several different crystal forms, some of which diffracted to approximately 1.8 Å resolution. The crystals of native FerB belonged to space group P21, with unit-cell parameters a = 61.6, b = 110.1, c = 65.2 Å, β = 118.2° and four protein molecules in the asymmetric unit, whilst the SeMet-substituted form crystallized in space group P21212, with unit-cell parameters a = 61.2, b = 89.2, c = 71.5 Å and two protein molecules in the asymmetric unit. Structure determination by the three-wavelength MAD/MRSAD method is now in progress.
PMCID: PMC2852337  PMID: 20383015
flavoenzymes; quinone reductases; Paracoccus denitrificans
21.  Pseudomerohedrally twinned monoclinic structure of unfolded ‘free’ nona­ctin: comparative analysis of its large conformational change upon encapsulation of alkali metal ions 
The title compound, C40H64O12, crystallizes in a pseudo­merohedrally twinned primitive monoclinic cell with similar contributions of the two twin components. There are two symmetry-independent half-mol­ecules of nona­ctin in the asymmetric unit. Each mol­ecule has a pseudo-S 4 symmetry and resides on a crystallographic twofold axis; the axes pass through the mol­ecular center of mass and are perpendicular to the plane of the macrocycle. The literature description of the room-temperature structure of nona­ctin as an order–disorder structure in an ortho­rhom­bic unit cell is corrected. We report a low-temperature high-precision ordered structure of ‘free’ nona­ctin that allowed for the first time precise determination of its bond distances and angles. It possesses an unfolded and more planar geometry than its complexes with encapsulated Na+, K+, Cs+, Ca2+ or NH4 + cations that exhibit more isometric overall conformations.
PMCID: PMC2816929  PMID: 19805886
22.  Crystallographic characterization of two novel crystal forms of human insulin induced by chaotropic agents and a shift in pH 
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.
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.
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.
PMCID: PMC2241603  PMID: 18093308
23.  Structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form 
Acta Crystallographica Section F  2008;64(Pt 9):776-780.
The structure of the catalytic subunit of M. jannaschii aspartate transcarbamoylase has been determined in space group P212121 using synchrotron data to a resolution of 3.0 Å and was refined to a final R work and R free of 0.215 and 0.269, respectively.
Crystals of the catalytic subunit of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form contain four crystallo­graphically independent trimers which associate in pairs to form stable staggered complexes that are similar to each other and to a previously determined monoclinic C2 form. Each subunit has a sulfate in the central channel. The catalytic subunits in these complexes show flexibility, with the elbow angles of the monomers differing by up to 7.4° between crystal forms. Moreover, there is also flexibility in the relative orientation of the trimers around their threefold axis in the complexes, with a difference of 4° between crystal forms.
PMCID: PMC2531265  PMID: 18765902
aspartate transcarbamoylase; catalytic subunit; Methanococcus jannaschii
24.  Structure of the T109S mutant of Escherichia coli dihydroorotase complexed with the inhibitor 5-­fluoroorotate: catalytic activity is reflected by the crystal form 
A single-point mutant (T109S) of E. coli dihydroorotase initially crystallizes so that the two monomers of the dimer are related by a crystallographic twofold axis. In the presence of substrate, conversion to the previously observed asymmetric dimer with substrate bound in one subunit and product in the other is observed.
Crystals of a single-point mutant (T109S) of Escherichia coli dihydroorotase (DHOase) with diminished activity grown in the presence of l-dihydroorotate (l-DHO) are tetragonal, with a monomer in the asymmetric unit. These crystals are extremely unstable and disintegrate shortly after formation, which is followed by the growth of orthorhombic crystals from the remnants of the tetragonal crystals or at new nucleation sites. Orthorhombic crystals, for which a structure has previously been reported [Thoden et al. (2001 ▶), Biochemistry, 40, 6989–6997; Lee et al. (2005 ▶), J. Mol. Biol. 348, 523–533], contain a dimer of DHOase in the asymmetric unit; the active site of one monomer contains the substrate N-carbamyl-l-aspartate (l-CA-asp) and the active site of the other monomer contains the product of the reaction, l-DHO. In the subunit with l-­DHO in the active site, a surface loop (residues 105–115) is ‘open’. In the other subunit, with l-CA-asp in the active site, the loop folds inwards, forming specific hydrogen bonds from the loop to the l-CA-asp. The tetragonal crystal form can be stabilized by crystallization in the presence of the inhibitor 5-fluoroorotate (FOA), a product (l-DHO) mimic. Crystals of the complex of T109S DHOase with FOA are tetragonal, space group P41212, with unit-cell parameters a = b = 72.6, c = 176.1 Å. The structure has been refined to R and R free values of 0.218 and 0.257, despite severe anisotropy of the diffraction. In this structure, the flexible loops are both in the ‘open’ conformation, which is consistent with FOA, like l-­DHO, binding at both sites. The behaviour of the T109S mutant crystals of DHOase in the presence of l-DHO is explained by initial binding of l-DHO to both subunits, followed by slow conversion to l-CA-asp, with consequent movement of the flexible loop and dissolution of the crystals. Orthorhombic crystals are then able to grow in the presence of l-DHO and l-CA-asp.
PMCID: PMC2330171  PMID: 17329804
dihydroorotase; conformational change; loop movement; catalytic state; crystal contacts; crystal instability
25.  Two forms of (naphthalen-1-yl)boronic acid 
Two polymorphs of the title compound, C10H9BO2, were prepared by recystallization from different solvents at room temperature. Both forms demonstrate nearly identical mol­ecular structures with all naphthalene group atoms located in one plane and all boronic acid atoms in another. In each extended structure, mol­ecules form dimers, connected via two O—H⋯O hydrogen bonds. The dimers are connected by further O—H⋯O hydrogen bonds, forming layered networks. The resulting layers are practically identical in both forms but are shifted along the [010] axis in the two forms, resulting in a slightly more effective packing for the monoclinic structure compared to the ortho­rhom­bic form.
Two polymorphs of the title compound, C10H9BO2, were prepared by recystallization from different solvents at room temperature. Both forms demonstrate nearly identical mol­ecular structures with all naphthalene group atoms located in one plane and all boronic acid atoms in another: the dihedral angles between these planes are 39.88 (5) and 40.15 (5)° for the two asymmetric mol­ecules of the ortho­rhom­bic form and 40.60 (3)° for the single asymmetric mol­ecule in the monoclinic form. In each extended structure, mol­ecules form dimers, connected via two O—H⋯O hydrogen bonds. The dimers are connected by further O—H⋯O hydrogen bonds, forming layered networks in the (001) plane and the (100) plane in the ortho­rhom­bic and monoclinic forms, respectively. The resulting layers are practically identical in both forms. However, these layers are shifted along the [010] axis in the two forms, resulting in a slightly more effective packing for monoclinic structure (packing index = 0.692) compared to the ortho­rhom­bic form (0.688).
PMCID: PMC5120708  PMID: 27920918
crystal structure; aryl­boronic acid; hydrogen-bond network; polymorph

Results 1-25 (1441159)