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PubMed2004

Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): a novel fold with a conserved sequence motif.

UPF0040 is a family of proteins implicated in a cellular function of bacteria cell division. There is no structure information available on protein of this family. We have determined the crystal structure of a protein from Mycoplasma pneumoniae that belongs to this family using X-ray crystallography. Structural homology search reveals that this protein has a novel fold with no significant similarity to any proteins of known three-dimensional structure. The crystal structures of the protein in three different crystal forms reveal that the protein exists as a ring of octamer. The conserved protein residues, including a highly conserved DXXXR motif, are examined on the basis of crystal structure.

Amino Acid Motifs↗

PubMed2004

The surprisingly elusive crystal structure of sodium metabisulfite.

The crystal structure of Na2S2O5, a simple and common ionic compound, is reported here for the first time. The crystals form non-merohedral twins, with the twin domains related by a twofold axis which bisects the angle between the a and c axes of each unit cell. The structure was determined from a single-crystal fragment of a twinned crystal that had undergone cleavage along the twin boundary. In addition to the problems associated with twinning, space-group determination proved difficult as well, with the structure initially determined in the P2(1) space group appearing to be disordered with two rotational conformers of the metabisulfite ion occupying equivalent sites in the lattice. An analysis at low temperature provided new weak reflections which were inconsistent with the original unit cell, but indexed to the correct unit cell, allowing for space group and crystal structure determination. The apparent structure, which appeared disordered in P2(1), seems to have resulted from an apparently fortuitous superposition of two conformationally inequivalent S2O5(2-) anions in the asymmetric unit of the correct structure in the P2(1)/n space group. The metabisulfite ions in this structure do not adopt the C(s) geometry observed in previously determined crystal structures containing S2O5(2-). The structures of both ions in the asymmetric unit are effectively conformational mirror images of one another with two of the O atoms on each S atom in the ion approaching an eclipsed geometry. This observation provides further evidence that the structures of sulfur-oxy anions in the solid state are dictated mainly by interionic coulombic forces rather than by intraionic bonding interactions

Journal Article↗

PubMed2006

Structural basis of the sulphate starvation response in E. coli: crystal structure and mutational analysis of the cofactor-binding domain of the Cbl transcriptional regulator.

Cbl is a member of the large family of LysR-type transcriptional regulators (LTTRs) common in bacteria and found also in Archaea and algal chloroplasts. The function of Cbl is required in Escherichia coli for expression of sulphate starvation-inducible (ssi) genes, associated with the biosynthesis of cysteine from organic sulphur sources (sulphonates). Here, we report the crystal structure of the cofactor-binding domain of Cbl (c-Cbl) from E. coli. The overall fold of c-Cbl is very similar to the regulatory domain (RD) of another LysR family member, CysB. The RD is composed of two subdomains enclosing a cavity, which is expected to bind effector molecules. We have constructed and analysed several full-length Cbl variants bearing single residue substitutions in the RD that affect cofactor responses. Using in vivo and in vitro transcription assays, we demonstrate that pssuE, a Cbl responsive promoter, is down-regulated not only by the cofactor, adenosine phosphosulphate (APS), but also by thiosulphate, and, that the same RD determinants are important for the response to both cofactors. We also demonstrate the effects of selected site-directed mutations on Cbl oligomerization and discuss these in the context of the structure. Based on the crystal structure and molecular modelling, we propose a model for the interaction of Cbl with adenosine phosphosulphate.

Adenosine Phosphosulfate↗

PubMed1989

Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex.

The crystal structure of the complex of the anti-lysozyme HyHEL-10 Fab and hen egg white lysozyme has been determined to a nominal resolution of 3.0 A. The antigenic determinant (epitope) on the lysozyme is discontinuous, consisting of residues from four different regions of the linear sequence. It consists of the exposed residues of an alpha-helix together with surrounding amino acids. The epitope crosses the active-site cleft and includes a tryptophan located within this cleft. The combining site of the antibody is mostly flat with a protuberance made up of two tyrosines that penetrate the cleft. All six complementarity-determining regions of the Fab contribute at least one residue to the binding; one residue from the framework is also in contact with the lysozyme. The contacting residues on the antibody contain a disproportionate number of aromatic side chains. The antibody-antigen contact mainly involves hydrogen bonds and van der Waals interactions; there is one ion-pair interaction but it is weak.

Antibodies, Monoclonal↗

PubMed2006

Bi3+/M2+ oxyphosphate: a continuous series of polycationic species from the 1D single chain to the 2D planes. Part 1: From HREM images to crystal-structure deduction.

This work deals with the crystal-structure deduction of new structural types of Bi3+-M2+ oxyphosphates (M is a transition element) from HREM images. Previous studies showed the unequivocal attribution of particular HREM contrasts to the corresponding Bi/M/O-based polycationic species in similar materials. On this basis, the examination of isolated crystallites of polyphased samples led to new HREM contrasts assigned to new polycationic species in three new structural types. This helped us to solve one crystal structure, and the two other forms have been deduced through HREM image decoding. It helped to model the investigated materials from the structural point of view as well as the chemical one. The three assumed crystal structures are formed by polycationic ribbons, n tetrahedra wide, surrounded by PO4 groups, as already encountered in these series of oxyphosphates. However, here we deal with the original n= 4-6 cases, whereas, up to this work, only the n= 1-3 ribbons have been reported. The greater size of ribbons is associated with particular structural modifications responsible for complex HREM contrasts. The validity of the proposed models is verified in Part 2 of this work.

Journal Article↗

PubMed2003

Correspondence between molecular functionality and crystal structures. Supramolecular chemistry of a family of homologated aminophenols.

The crystal structures and packing features of a family of 13 aminophenols, or supraminols, are analyzed and correlated. These compounds are divided into three groups: (a) compounds 1-5 with methylene spacers of the general type HO-C6H4-(CH2)n-C6H4-NH2 (n = 1 to 5) and both OH and NH2 in a para position; (b) compounds 1a, 2a, 2b, 2c, and 3a in which one or more of the methylene linkers in 1 to 3 are exchanged with an S-atom; and (c) compounds 2d, 1b, and 6a prepared with considerations of crystal engineering and where the crystal structures may be anticipated on the basis of structures 1-5,1a, 2a, 2b, 2c, and 3a. These 13 aminols can be described in terms of three major supramolecular synthons based on hydrogen bonding between OH and NH2 groups: the tetrameric loop or square motif, the infinite N(H)O chain, and the beta-As sheet. These three synthons are not completely independent of each other but interrelate, with the structures tending toward the more stable beta-As sheet in some cases. Compounds 1-5 show an alternation in melting points, and compounds with n = even exhibit systematically higher melting points compared to those with n = odd. The alternating melting points are reflected in, and explained by, the alternation in the crystal structures. The n = odd structures tend toward the beta-As sheet as n increases and can be considered as a variable series whereas for n = even, the beta-As sheet is invariably formed constituting a fixed series. Substitution of a methylene group by an isosteric S-atom may causes a change in the crystal structure. These observations are rationalized in terms of geometrical and chemical effects of the functional groups. This study shows that even for compounds with complex crystal structures the packing may be reasonably anticipated provided a sufficient number of examples are available.

Journal Article↗

PubMed1995

Towards structure-based drug design: crystal structure of a multisubstrate adduct complex of glycinamide ribonucleotide transformylase at 1.96 A resolution.

An inhibitor complex structure of glycinamide ribonucleotide transformylase (GAR-Tfase; EC 2.1.2.2) from Escherichia coli has been determined with a multisubstrate adduct BW1476U89 to an R-value of 19.1% at 1.96 A resolution. The structure was determined by a combination of molecular and single isomorphous replacement using data from two different monoclinic crystal lattices and collecting data from crystals soaked in 20% (w/v) methyl-pentanediol as cryoprotectant for shock-freezing at -150 degrees C. The multisubstrate adduct is bound in an extended crevice at the interface between the two functional domains of the enzyme. This inhibitor is positioned in the binding site by three sets of tight interactions with its phosphate, glutamate and pyrimidone ring moieties, while its interventing linker atoms are more flexible and adopt two distinct sets of conformations. The highly conserved Arg103, His108 and Gln170 residues that are key in ligand binding and catalysis (His108), have compensatory conformational variation that gives some clues as to their role in substrate specificity and in the formyl transfer. The molecular design of 1476U89 as a multisubstrate adduct inhibitor (Ki approximately 100 pM at pH 8.5), is confirmed as it closely mimics the shape, molecular interaction and combined binding constants of the natural 10-formyltetrahydrofolate (10-CHO-H4F; Km approximately 77.4 microM at pH 8.5) and glycinamide-ribonucleotide (GAR; Km approximately 8.1 microM at pH 8.5) substrates. The stereochemistry of this ligand complex suggests that His108 may act as an electrophile stabilizing the oxyanion of the tetrahedral intermediate that is formed as a result of the direct attack on the 10-CHO-H4F by the amino group of GAR. Structural comparison of the folate binding modes among GAR-Tfase, dihydrofolate reductase and thymidylate synthase reveals that folate derivates bound to GAR-Tfase differentially adopt the trans conformation for the dihedral angle between atoms C-6 and C-9 providing a handle for targeting specific folate-dependent enzymes. The structural information derived from two different discrete conformations of the ligand in the binding site also suggests several leads for the de novo design of inhibitors of GAR-Tfase that may develop into useful chemotherapeutic agents.

Acyltransferases↗

PubMed2006

Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis.

The developing science called structural genomics has focused to date mainly on high-throughput expression of individual proteins, followed by their purification and structure determination. In contrast, the term structural biology is used to denote the determination of structures, often complexes of several macromolecules, that illuminate aspects of biological function. Here we bridge structural genomics to structural biology with a procedure for determining protein complexes of previously unknown function from any organism with a sequenced genome. From computational genomic analysis, we identify functionally linked proteins and verify their interaction in vitro by coexpression/copurification. We illustrate this procedure by the structural determination of a previously unknown complex between a PE and PPE protein from the Mycobacterium tuberculosis genome, members of protein families that constitute approximately 10% of the coding capacity of this genome. The predicted complex was readily expressed, purified, and crystallized, although we had previously failed in expressing individual PE and PPE proteins on their own. The reason for the failure is clear from the structure, which shows that the PE and PPE proteins mate along an extended apolar interface to form a four-alpha-helical bundle, where two of the alpha-helices are contributed by the PE protein and two by the PPE protein. Our entire procedure for the identification, characterization, and structural determination of protein complexes can be scaled to a genome-wide level.

Bacterial Proteins↗

PubMed2005

Comparing hypothetical structures generated in the third Cambridge blind test of crystal structure prediction.

In the third Cambridge blind test of crystal structure prediction, participants submitted extended lists of up to 100 hypothetical structures. In this paper these lists are analyzed for the two small semi-rigid molecules, hydantoin and azetidine, by performing a new energy minimization using an accurate force field, and grouping these newly minimized structures into clusters of equivalent structures. Many participants found the same low-energy structures, but no list appeared to be complete even for the structures with one independent molecule in the asymmetric unit. This may well be due to the fact that a cutoff at even 100 structures cannot ensure the presence of a structure that has a relatively high ranking in another force field. Moreover, some structures should have possibly been discarded because they correspond to transition states rather than true energy minima. The r.m.s. deviation between energies in corresponding clusters was calculated to compare the reported relative crystal energies for each pair of participants. Some groups of force fields show a reasonably good correspondence, yet the order of magnitude of their discrepancies is comparable to the energy differences between, say, the first ten structures of lowest energy. Therefore, even if we assume that energy is a sufficient criterion, it is not surprising that crystal structure predictions are still inconsistent and unreliable.

Algorithms↗

PubMed2005

A third blind test of crystal structure prediction.

Following the interest generated by two previous blind tests of crystal structure prediction (CSP1999 and CSP2001), a third such collaborative project (CSP2004) was hosted by the Cambridge Crystallographic Data Centre. A range of methodologies used in searching for and ranking the likelihood of predicted crystal structures is represented amongst the 18 participating research groups, although most are based on the global minimization of the lattice energy. Initially the participants were given molecular diagrams of three molecules and asked to submit three predictions for the most likely crystal structure of each. Unlike earlier blind tests, no restriction was placed on the possible space group of the target crystal structures. Furthermore, Z' = 2 structures were allowed. Part-way through the test, a partial structure report was discovered for one of the molecules, which could no longer be considered a blind test. Hence, a second molecule from the same category (small, rigid with common atom types) was offered to the participants as a replacement. Success rates within the three submitted predictions were lower than in the previous tests - there was only one successful prediction for any of the three ;blind' molecules. For the ;simplest' rigid molecule, this lack of success is partly due to the observed structure crystallizing with two molecules in the asymmetric unit. As in the 2001 blind test, there was no success in predicting the structure of the flexible molecule. The results highlight the necessity for better energy models, capable of simultaneously describing conformational and packing energies with high accuracy. There is also a need for improvements in search procedures for crystals with more than one independent molecule, as well as for molecules with conformational flexibility. These are necessary requirements for the prediction of possible thermodynamically favoured polymorphs. Which of these are actually realised is also influenced by as yet insufficiently understood processes of nucleation and crystal growth.

Algorithms↗

PubMed2002

Crystal structure of neotame anhydrate polymorph G.

PURPOSE: To determine the crystal structure of the neotame anhydrate polymorph G and to evaluate X-ray powder diffractometry (XRPD) with molecular modeling as an alternative method for determining the crystal structure of this conformationally flexible dipeptide. METHODS: The crystal structure of polymorph G was determined by single crystal X-ray crystallography (SCXRD) and also from the X-ray powder diffraction (XRPD) pattern using molecular modeling (Cerius2, Powder Solve module). RESULTS: From SCXRD, polymorph G crystals are orthorhombic with space group of P2(1)2(1)2(1) with Z = 4, unit cell constants: a = 5.5999(4), b = 11.8921(8), c = 30.917(2) A, and one neotame molecule per asymmetric unit. The XRPD pattern of polymorph G, analyzed by Cerius2 software, led to the same P2(1)2(1)2(1) space group and almost identical unit cell dimensions. However, with 13 rigid bodies defined, Cerius2 gives a conformation of the neotame molecule, which is different from that determined by SCXRD. CONCLUSIONS: For neotame anhydrate polymorph G, the unit cell dimensions calculated from XRPD were almost identical to those determined by SCXRD. However, the crystal structure determined by XRPD closely resembled that determined by SCXRD, only when the correct conformation of the neotame molecule had been chosen before detailed analysis of the XRPD pattern.

Crystallization↗

PubMed1984

Conformational changes of cholesteryl palmitoleate in the crystal structure at low temperature.

At 123 K, crystals of cholesteryl cis-9-hexadecenoate (cholesteryl palmitoleate, C45H74O2) are monoclinic, space group P2(1) with cell dimensions a = 12.917(7), b = 8.910(5), c = 34.04(1) A, beta = 94.95(7) degrees [lambda(CuK alpha) = 1.5424 A] having two independent molecules (A and B) per unit cell. The crystal structure has been determined from 6178 reflections with sin theta/lambda less than or equal to 0.56 A-1, of which 3406 gave [F] greater than 3 sigma. Structure refinement by alternating cycles of Fourier syntheses and block diagonal least squares gave R = 0.24 for all reflections, R = 0.13 for reflections [F] greater than 3 sigma. At 123 K, the crystal structure consists of closely packed layers very similar to those at 295 K. However, there are major conformational differences in the layer interface region, which affect the ester chain of molecule B and the C(17) tail of molecule A. Although the electron density is diffuse in this region, the B-chain, which is bent, appears to be ordered at 123 K and has a different conformation from the disordered B-chains at 295 K. The change in the A-tail, which is twisted at 123 K and extended at 295 K, is very similar to that which occurs in two of the molecules when anhydrous cholesterol undergoes phase transition. Measurements of the unit cell dimensions at twelve temperatures (295 K to 123 K) indicate that the major changes in the crystal structure of cholesteryl palmitoleate occur in a 10 K range near 173 K.

Cholesterol Esters↗

PubMed2004

Crystal structure and surface properties of an investigational drug--a case study.

In this study we investigate the correlations between the single crystal structure, the crystal habitat and morphology, and surface energetics of an investigational pharmaceutical compound. Crystal structure of this investigational pharmaceutical solid has been solved from single crystal X-ray analysis. Crystallographic data are as follows: triclinic, P1 (no. 1), a = 6.1511 (8) A, b = 13.5004 (18) A, c = 17.417 (2) A, alpha = 68.259 (2) degrees, beta = 80.188 (2) degrees, gamma = 82.472 (2) degrees, V = 1320.2 (3) A(3), Z = 2. The external morphology of this crystalline solid was predicted by molecular modelling using attachment energies to be thin-plate like with a dominant face (001). The predicted morphology was confirmed by scanning electron micrographs (SEM) and the Miller Index of the dominant face was complemented by X-ray powder diffraction (XRPD) method. The microscopic layering structures of crystals and surface stability of the dominant faces were investigated using atomic force microscopy (AFM). Contact angle measurement showed that the surface of the dominant face is hydrophilic as predicted from crystal structure.

Crystallization↗

PubMed1998

Crystal structures of native and recombinant yeast fumarase.

Crystal structures for both native and recombinant forms of yeast fumarase from Saccharomyces cerevisiae have been completed to moderate resolution by two separate laboratories. The recombinant form was obtained by the construction of an expression plasmid for Escherichia coli. Despite a high level of amino acid sequence similarity, purification of the eukaryotic enzyme from the wild-type prokaryotic enzyme was feasible. The crystal structure of the native form, NY-fumarase, encompasses residues R22 through M484, while the recombinant form, RY-fumarase, consists of residues S27 through L485. Both crystal structures lack the N-terminal translocation segment. Each subunit of the homo-tetrameric protein has three domains. The active site is formed by segments from each of three polypeptide chains. The results of these studies on the eukaryotic proteins are unique, since the recombinant form was done in the absence of dicarboxylic acid and has an unoccupied active site. As a comparison, native fumarase was crystallized in the presence of the competitive inhibitor, meso-tartrate. Meso-tartrate occupies a position close to that of the bound citrate molecule found in the active site of the E. coli enzyme. This inhibitor participates in hydrogen bonding to an active-site water molecule. The independent determination of the two structures provides further evidence that an active-site water molecule may play an active role in the fumarase-catalyzed reaction.

Binding Sites↗

PubMed2005

Crystal structure of wild-type chaperonin GroEL.

The 2.9A resolution crystal structure of apo wild-type GroEL was determined for the first time and represents the reference structure, facilitating the study of structural and functional differences observed in GroEL variants. Until now the crystal structure of the mutant Arg13Gly, Ala126Val GroEL was used for this purpose. We show that, due to the mutations as well as to the presence of a crystallographic symmetry, the ring-ring interface was inaccurately described. Analysis of the present structure allowed the definition of structural elements at this interface, essential for understanding the inter-ring allosteric signal transmission. We also show unambiguously that there is no ATP-induced 102 degrees rotation of the apical domain helix I around its helical axis, as previously assumed in the crystal structure of the (GroEL-KMgATP)(14) complex, and analyze the apical domain movements. These results enabled us to compare our structure with other GroEL crystal structures already published, allowing us to suggest a new route through which the allosteric signal for negative cooperativity propagates within the molecule. The proposed mechanism, supported by known mutagenesis data, underlines the importance of the switching of salt bridges.

Adenosine Triphosphate↗

PubMed2006

A method for hierarchical comparative analysis of crystal structures.

A geometrical-topological description of crystal structure as a three-dimensional graph with coloured nodes, weighted and coloured edges is used to generate a hierarchical sequence of the structure representations. The solid angles of Voronoi-Dirichlet polyhedra of atoms are used as the edge weights and the nodes and edges are coloured according to chemical reasons. Two operations are defined to derive the representations: contracting an atom to other atoms keeping the local connectivity, and removing an atom together with all its bonds. The atoms of the crystal structure are called origin, removed, contracted or target according to their roles in the operations. Each structure representation is described as a labelled quotient graph and determined by (i) colours of the graph nodes and edges, (ii) some level for edge weights, and (iii) an arrangement of atoms according to their roles. The computer enumeration and topological comparative analysis of all representations for crystal structures of any composition and complexity are implemented into the TOPOS program package. The advantages of the method are shown by the analysis of typical inorganic compounds and a molecular packing.

Journal Article↗

PubMed2005

Validation of a search technique for crystal structure prediction of flexible molecules by application to piracetam.

A new approach to the crystal structure prediction of flexible molecules is presented. It is applied to piracetam, whose conformational polymorphs exhibit a variety of hydrogen-bond motifs but lack the intramolecular hydrogen bond found in the gas-phase ab initio optimized conformer. Stable crystal packing can result when favourable intermolecular interactions are made possible when the molecule distorts from the gas-phase conformation. If the resulting intermolecular lattice energy is sufficiently favourable to compensate for the intramolecular energy penalty associated with the suboptimal gas-phase conformation, then the crystal structure may be experimentally feasible. The new approach involves searching for low-energy crystal structures using a large number of rigid conformers, firstly to systematically explore which regions of conformational space could give rise to low-energy hydrogen-bonded crystal structures, and then to refine the search using crystallographic insight to optimize particular intermolecular interactions. The timely discovery of a new polymorph (form IV) by an independent experimental team allowed this approach to be validated by way of a ;blind test' of crystal structure prediction. Form IV was successfully identified as the most favourable computed crystal structure with a conformation very distinct from that in the previously known polymorphs.

Chemistry↗

PubMed2002

Symmetry-general ab initio computation of physical properties using quantum software integrated with crystal structure databases: results and perspectives.

The timely integration of crystal structure databases, such as CRYSTMET, ICSD etc., with quantum software, like VASP, OresteS, ElectrA etc., allows ab initio cell and structure optimization on existing pure-phase compounds to be performed seamlessly with just a few mouse clicks. Application to the optimization of rough structure models, and possibly new atomic arrangements, is detailed. The ability to reproduce observed cell data can lead to an assessment of the intrinsic plausibility of a structure model, even without a competing model. The accuracy of optimized atom positions is analogous to that from routine powder studies. Recently, the ab initio symmetry-general least-squares extraction of the coefficients of the elastic tensor for pure-phase materials using data from corresponding entries in crystal structure databases was automated. A selection of highly encouraging results is presented, stressing the complementarity of simulation and experiment. Additional physical properties also appear to be computable using existing quantum software under the guidance of an automation scheme designed following the above automation for the elastic tensor. This possibility creates the exciting perspective of mining crystal structure databases for new materials with combinations of physical properties that were never measured before. Crystal structure databases can accordingly be expected to become the cornerstone of materials science research within a very few years, adding immense practical value to the archived structure data.

Journal Article↗