Silicalite-poly(furfuryl alcohol) [PFA] composite membranes were prepared by solution casting of silicalite-furfuryl alcohol [FA] suspension on a porous polysulfone substrate and subsequent in situ polymerization of FA. X-ray diffraction, nitrogen sorption, thermogravimetric analysis, scanning electron microscopy, and energy-dispersive X-ray spectroscopy were used to characterize silicalite nanocrystals and silicalite-PFA composite membranes. The silicalite-PFA composite membrane with 20 wt.% silicalite loading exhibits good oxygen/nitrogen selectivity (4.15) and high oxygen permeability (1,132.6 Barrers) at 50°C. Silicalite-PFA composite membranes are promising for the production of oxygen-enriched air for various applications.
poly(furfuryl alcohol); silicalite; composite membrane; air separation
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.
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.
rabbit muscle aldolase; improvement of crystal quality; low-complexity domain; sorting nexin 9
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.
imperfect pseudo-merohedral twinning; fungal fatty acid synthase
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.
aspartate transcarbamoylase; catalytic subunit; Methanococcus jannaschii
A crystallographic investigation of the title compound, C22H28Cl2N4O4, using crystals obtained under different crystallization conditions, revealed the presence of two distinct polymorphic forms. The molecular conformation in the two polymorphs is very different: one adopts a ‘C’ shape, whereas the other adopts an ‘S’ shape. In the latter, the molecule lies across a crystallographic twofold axis. The ‘S’-shaped polymorph undergoes a reversible orthorhombic-to-monoclinic phase transition on cooling, whereas the structure of the ‘C’-shaped polymorph is temperature insensitive.
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
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.
pseudosymmetry; structure determination; cysteine proteases; Mac-1
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.
inosine triphosphate pyrophosphohydrolase
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.
At room temperature, the m-Nitrophenol (m-NPH) appears in two polymorphic structures: orthorhombic and monoclinic forms. In the present work, we shall focus on the monoclinic form of this compound which has a centrosymmetric structure with the space group P21/n. The molecular dipole moment has been estimated experimentally. High resolution single crystal diffraction experiment was performed at low temperature with MoKα radiation. The crystal structure was refined using the multipolar model of Hansen and Coppens (1978). The molecular electron charge density distribution is described accurately. The study reveals the nature of inter-molecular interactions including charge transfer and hydrogen bonds. In this crystal, hydrogen bonds of moderate strength occur between the hydroxyl group and the O atom in the nitro one.
Electron charge density; M-Nitrophenol; XD program; nonlinear optical compound (NLO)
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.
dihydroorotase; conformational change; loop movement; catalytic state; crystal contacts; crystal instability
The design, expression and purification of receptor protein tyrosine phosphatase γ and two mutants and their crystallization in three different crystal forms are described.
Protein tyrosine phosphatase γ is a membrane-bound receptor and is designated RPTPγ. RPTPγ and two mutants, RPTPγ(V948I, S970T) and RPTPγ(C858S, S970T), were recombinantly expressed and purified for X-ray crystallographic studies. The purified enzymes were crystallized using the hanging-drop vapor-diffusion method. Crystallographic data were obtained from several different crystal forms in the absence and the presence of inhibitor. In this paper, a description is given of how three different crystal forms were obtained that were used with various ligands. An orthorhombic crystal form and a trigonal crystal form were obtained both with and without ligand, and a monoclinic crystal form was only obtained in the presence of a particularly elaborated inhibitor.
protein tyrosine phosphatases; hydrolases; inhibitor complexes
The title compound, C13H10ClNO, (I), is a polymorph of the structure, (II), first reported by Gowda et al. [Acta Cryst. (2008), E64, o462]. In the original report, the compound crystallized in the orthorhombic space group Pbca (Z = 8), whereas the structure reported here is monoclinic P21/c (Z = 4). The principal difference between the two forms lies in the relative orientations of the phenyl and benzene rings [dihedral angle = 8.90 (13)° for (I) and 61.0 (1)° for (II)]. The inclination of the amide –CONH– units to the benzoyl ring is more similar [15.8 (7)° for (I) and 18.2 (2)° for (II)]. In both forms, the N—H bonds are anti to the 3-chloro substituents of the aniline rings. In the crystal, intermolecular N—H⋯O hydrogen bonds form C(4) chains along c. These chains are bolstered by weak C—H⋯O interactions that generate R
1(6) and R
1(7) ring motifs.
The crystallization and preliminary X-ray diffraction analysis of sarcosine dimethylglycine methyltransferase from H. halochoris is reported.
Sarcosine dimethylglycine methyltransferase (EC 220.127.116.11) is an enzyme from the extremely halophilic anaerobic bacterium Halorhodospira halochoris. This enzyme catalyzes the twofold methylation of sarcosine to betaine, with S-adenosylmethionine (AdoMet) as the methyl-group donor. This study presents the crystallization and preliminary X-ray analysis of recombinant sarcosine dimethylglycine methyltransferase produced in Escherichia coli. Mass spectroscopy was used to determine the purity and homogeneity of the enzyme material. Two different crystal forms, which initially appeared to be hexagonal and tetragonal, were obtained. However, on analyzing the diffraction data it was discovered that both crystal forms were pseudo-merohedrally twinned. The true crystal systems were monoclinic and orthorhombic. The monoclinic crystal diffracted to a maximum of 2.15 Å resolution and the orthorhombic crystal diffracted to 1.8 Å resolution.
sarcosine dimethylglycine methyltransferase; Halorhodospira halochoris; twinning
A new orthorhombic polymorph of terephthalaldehyde, C8H6O2, with a melting point of 372 K, has been obtained by recrystallization from ethanol. At room temperature, the crystals transform into the well known monoclinic form, with a melting point of 389 K. The crystal structure of the monoclinic form involves C—H⋯O hydrogen bonds, but no such bonds are observed in the orthorhombic form. The molecule is planar.
A lectin from C. roseum seeds (CRL) has been purified, characterized and crystallized.
A lectin from Cymbosema roseum seeds (CRL) was purified, characterized and crystallized. The best crystals grew in a month and were obtained by the vapour-diffusion method using a precipitant solution consisting of 0.1 M Tris–HCl pH 7.8, 8%(w/v) PEG 3350 and 0.2 M proline at a constant temperature of 293 K. A data set was collected to 1.77 Å resolution at a synchrotron-radiation source. CRL crystals are orthorhombic, belonging to space group P212121. Crystallographic refinement and full amino-acid sequence determination are in progress.
Cymbosema roseum; Diocleinae; lectins
Preliminary studies were carried out to purify and crystallize the sample from cat (Felis silvestris catus), a low oxygen-affinity haemoglobin in different crystal forms.
Haemoglobin is a metalloprotein which plays a major role in the transportation of oxygen from the lungs to tissues and of carbon dioxide back to the lungs. The present work reports the preliminary crystallographic study of low oxygen-affinity haemoglobin from cat in different crystal forms. Cat blood was collected, purified by anion-exchange chromatography and crystallized in two different conditions by the hanging-drop vapour-diffusion method under unbuffered low-salt and buffered high-salt concentrations using PEG 3350 as a precipitant. Intensity data were collected using MAR345 and MAR345dtb image-plate detector systems. Cat haemoglobin crystallizes in monoclinic and orthorhombic crystal forms with one and two whole biological molecules (α2β2), respectively, in the asymmetric unit.
haemoglobin; low oxygen affinity
The title compound, C11H13NO2Si, is a low-temperature form of the previously reported room-temperature structure [Garcia et al. (1998 ▶). Acta Cryst. C54, 489–491]. At 298 K, the material crystallizes in the space group Pnma and occupies a crystallographic mirror plane, but at 100 K the space group changes to P212121, the volume decreases by 5% and the molecule distorts. The greatest molecular distortions from C
s symmetry are rotations of the trimethylsilyl and nitro groups by 10.56 (8) and 11.47 (9)°, respectively, to the benzene mean plane. At low temperature, the crystal also becomes an inversion twin, the refined ratio of the twin components being 0.35 (15):0.65 (15).
Two new crystal structures of A. niger α-amylase are reported, one of which reveals two hitherto unobserved maltose-binding sites.
Aspergillus niger α-amylase catalyses the hydrolysis of α-1,4-glucosidic bonds in starch. It shows 100% sequence identity to the A. oryzae homologue (also called TAKA-amylase), three crystal structures of which have been published to date. Two of them belong to the orthorhombic space group P212121 with one molecule per asymmetric unit and one belongs to the monoclinic space group P21 with three molecules per asymmetric unit. Here, the purification, crystallization and structure determination of A. niger α-amylase crystallized in the monoclinic space group P21 with two molecules per asymmetric unit in complex with maltose at 1.8 Å resolution is reported. Furthermore, a novel 1.6 Å resolution orthorhombic crystal form (space group P21212) of the native enzyme is presented. Four maltose molecules are observed in the maltose–α-amylase complex. Three of these occupy active-site subsites −2 and −1, +1 and +2 and the hitherto unobserved subsites +4 (Asp233, Gly234) and +5 (Asp235). The fourth maltose molecule binds at the distant binding sites d1 (Tyr382) and d2 (Trp385), also previously unobserved. Furthermore, it is shown that the active-site groove permits different binding modes of sugar units at subsites +1 and +2. This flexibility of the active-site cleft close to the catalytic centre might be needed for a productive binding of substrate chains and/or release of products.
α-amylase; Aspergillus niger; maltose; Aspergillus oryzae; TAKA-amylase
The title compound, C13H10Cl2N2S, represents a monoclinic polymorph of the previously reported orthorhombic form [Ramnathan et al. (1996 ▶). Acta Cryst. C52, 134–136]. The molecule is twisted with the dihedral angle between the benzene rings being 55.37 (7)°. The N—H atoms are syn to each other, which contrasts their anti disposition in the orthorhombic form. In the crystal, molecules assemble into zigzag chains along the c axis via N—H⋯S hydrogen bonds. Chains are connected into layers via C—H⋯Cl interactions, and these stack along the a axis.
X-ray diffraction data from the targeting (FAT) domain of focal adhesion kinase (FAK) were collected from a single crystal that diffracted to 1.99 Å resolution.
X-ray diffraction data from the targeting (FAT) domain of focal adhesion kinase (FAK) were collected from a single crystal that diffracted to 1.99 Å resolution and reduced to the primitive orthorhombic lattice. A single molecule was predicted to be present in the asymmetric unit based on the Matthews coefficient. The data were phased using molecular-replacement methods using an existing model of the FAK FAT domain. All structures of human focal adhesion kinase FAT domains solved to date have been solved in a C-centered orthorhombic space group.
focal adhesion kinase; targeting domain
Single crystals of α-Ba2P2O7, dibarium diphosphate, were obtained by solid-state reaction. The orthorhombic structure is isotypic with α-Sr2P2O7 and is the second polymorph obtained for this composition. The structure is built from two different BaO9 polyhedra (both with m symmetry), with Ba—O distances in the ranges 2.7585 (10)–3.0850 (6) and 2.5794 (13)–2.9313 (4) Å. These polyhedra are further linked by sharing corners along  and either edges or triangular faces perpendicularly to  to form the three-dimensional framework. This polyhedral linkage delimits large channels parallel to  where the P2O7 diphosphate anions are located. These groups (symmetry m) are characterized by a P—O—P angle of 131.52 (9)° and an eclipsed conformation. They are connected to the BaO9 polyhedra through edges and corners.
In the title orthorhombic polymorph (space group Iba2), C17H13N, the dihedral angle between the benzene rings is 55.99 (10)° and the azepine ring adopts a boat conformation. In the crystal, molecules are linked by C—H⋯π contacts. The previously-reported polymorph [Yousuf et al. (2012 ▶). Acta Cryst. E68, o1101] crystallizes in the monoclinic system (space group P21/c) with two molecules in the asymmetric unit.
Three different crystal forms were obtained of human saposin C. The structures could not be determined by molecular replacement using known solution structures of the protein as search models, supporting the notion of a highly flexible protein.
The amphiphilic saposin proteins (A, B, C and D) act at the lipid–water interface in lysosomes, mediating the hydrolysis of membrane building blocks by water-soluble exohydrolases. Human saposin C activates glucocerebrosidase and β-galactosylceramidase. The protein has been expressed in Pichia pastoris, purified and crystallized in three different crystal forms, diffracting to a maximum resolution of 2.5 Å. Hexagonal crystals grew from 2-propanol-containing solution and contain a single molecule in the asymmetric unit according to the Matthews coefficient. Orthorhombic and tetragonal crystals were both obtained with pentaerythritol ethoxylate and are predicted to contain two molecules in the asymmetric unit. Attempts to determine the respective crystal structures by molecular replacement using either the known NMR structure of human saposin C or a related crystal structure as search models have so far failed. The failure of the molecular-replacement method is attributed to conformational changes of the protein, which are known to be required for its biological activity. Crystal structures of human saposin C therefore might be the key to mapping out the conformational trajectory of saposin-like proteins.
sphingolipid-activator proteins; saposin-like proteins; saposin C; protein flexibility
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.
prefoldin; β subunit; Gim complex; Yke2