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Two crystal structures of rhodopsin that were originally described using trigonal symmetry can be interpreted in a hexagonal unit cell with a smaller asymmetric unit.

The space-group symmetry of two crystal forms of rhodopsin (PDB codes 1gzm and 2j4y; space group P31) can be re-interpreted as hexagonal (space group P64). Two molecules of the G protein-coupled receptor are present in the asymmetric unit in the trigonal models. However, the noncrystallographic twofold axes parallel to the c axis can be treated as crystallographic symmetry operations in the hexagonal space group. This halves the asymmetric unit and makes all of the protein molecules equivalent in these structures. Corrections for merohedral twinning were also applied in the refinement in the higher symmetry space group for one of the structures (2j4y).

The presence of pseudosymmetry can cause problems in structure determination and refinement. The relevant background and representative examples are presented.

It is not uncommon for protein crystals to crystallize with more than a single molecule per asymmetric unit. When more than a single molecule is present in the asymmetric unit, various pathological situations such as twinning, modulated crystals and pseudo translational or rotational symmetry can arise. The presence of pseudosymmetry can lead to uncertainties about the correct space group, especially in the presence of twinning. The background to certain common pathologies is presented and a new notation for space groups in unusual settings is introduced. The main concepts are illustrated with several examples from the literature and the Protein Data Bank.

The title compound, C16H6N6, is a polymorph of the previously reported structure [Kozlov & Goldberg (2008 ▶). Acta Cryst. C64, o498–o501]. Unlike the previously reported monoclinic polymorph (space group P21/c, Z = 8), the title compound reveals ortho­rhom­bic symmetry (space group Pnma, Z = 4). The mol­ecule shows crystallographic mirror symmetry, while the previously reported structure exhibits two independent mol­ecules per asymmetric unit. In the title compound, adjacent mol­ecules are essentially parallel along the c axis and tend to be vertical along the b axis with dihedral angles of 72.02 (6)°. However, in the reported polymorph, the entire crystal structure shows an anti­parallel arrangement of adjacent columns related by inversion centers and the two independent mol­ecules are nearly parallel with a dihedral angle of 2.48 (6)°.

Ferritin from P. furiosus crystallizes in space group C2221, with unit-cell parameters a = 258.1, b = 340.1, c = 266.5 Å and 36 monomers in the asymmetric unit, corresponding to one and a half 24-mers.

Crystals of the title protein have been produced and preliminary structural analysis has been carried out. The crystals belong to the orthorhombic space group C2221, with unit-cell parameters a = 258.1, b = 340.1, c = 266.5 Å. The protein forms a 24-mer of 20 kDa subunits, which assemble with 432 non-crystallographic symmetry. A total of 36 monomers are found in the asymmetric unit, corresponding to one and a half 24-mers.

A new data model for PDB entries of viruses and other biological assemblies with regular noncrystallographic symmetry is described.

A new scheme has been devised to represent viruses and other biological assemblies with regular noncrystallographic symmetry in the Protein Data Bank (PDB). The scheme describes existing and anticipated PDB entries of this type using generalized descriptions of deposited and experimental coordinate frames, symmetry and frame transformations. A simplified notation has been adopted to express the symmetry generation of assemblies from deposited coordinates and matrix operations describing the required point, helical or crystallographic symmetry. Complete correct information for building full assemblies, subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive.

The asymmetric unit of the title compound, C6H16B10, contains one mol­ecule that is close to possessing a non-crystallographic plane of mirror symmetry in the space group Pna21. The orientation of the mol­ecules in the ortho­rhom­bic cell shows that the structure can not be described in the space group Pnma, which has the same systematic absence conditions. The long inner-cluster C—C distance of 1.510 (5) Å is typical for {1,2-Me2-closo-1,2-C2B10} derivatives.

The type II dehydroquinase enzyme is a symmetrical dodecameric protein which crystallizes in either high-symmetry cubic space groups or low-symmetry crystal systems with multiple copies in the asymmetric unit. Both systems have provided challenging examples for molecular replacement; for example, a triclinic crystal form has 16 dodecamers (192 monomers) in the unit cell. Three difficult examples are discussed and two are used as test cases to compare the performance of four commonly used molecular-replacement packages.

Type II dehydroquinase is a small (150-amino-acid) protein which in solution packs together to form a dodecamer with 23 cubic symmetry. In crystals of this protein the symmetry of the biological unit can be coincident with the crystallographic symmetry, giving rise to cubic crystal forms with a single monomer in the asymmetric unit. In crystals where this is not the case, multiple copies of the monomer are present, giving rise to significant and often confusing noncrystallographic symmetry in low-symmetry crystal systems. These different crystal forms pose a variety of challenges for solution by molecular replacement. Three examples of structure solutions, including a highly unusual triclinic crystal form with 16 dodecamers (192 monomers) in the unit cell, are described. Four commonly used molecular-replacement packages are assessed against two of these examples, one of high symmetry and the other of low symmetry; this study highlights how program performance can vary significantly depending on the given problem. In addition, the final refined structure of the 16-dodecamer triclinic crystal form is analysed and shown not to be a superlattice structure, but rather an F-centred cubic crystal with frustrated crystallographic symmetry.

M. tuberculosis tetrahydrodipicolinate-N-succinyltransferase, the enzyme that catalyses the fifth reaction step of the lysine-biosynthesis pathway, has been cloned, expressed, purified and crystallized.

Tetrahydrodipicolinate-N-succinyltransferase from Mycobacterium tuberculosis (DapD, Rv1201c) has been cloned, heterologously expressed in Escherichia coli, purified using standard chromatographic techniques and crystallized in the cubic space group I23 or I213. Preliminary diffraction data analysis indicates the presence of five molecules per asymmetric unit. Furthermore, the data exhibit icosahedral point-group symmetry. One possible explanation for this is that the enzyme assembles into a 60-mer exhibiting 235 point-group symmetry and crystallizes as such in space group I23. In this case, the combination of crystallographic and noncrystallographic symmetry elements results in an arrangement of the icosahedrons in the cubic crystal with one pentamer in the asymmetric unit. Another explanation is that the packing of the molecules itself mimics icosahedral symmetry. In this case both space groups I23 and I213 would be possible.

X-ray crystallographic studies on 3'-5' oligomers have provided a great deal of information on the stereochemistry and conformational flexibility of nucleic acids and polynucleotides. In contrast, there is very little information available on 2'-5' polynucleotides. We have now obtained the crystal structure of Cytidylyl-2',5'-Adenosine (C2'p5'A) at atomic resolution to establish the conformational differences between these two classes of polymers. The dinucleoside phosphate crystallises in the monoclinic space group C2, with a = 33.912(4)A, b = 16.824(4)A, c = 12.898(2)A and beta = 112.35(1) with two molecules in the asymmetric unit. Spectacularly, the two independent C2'p5'A molecules in the asymmetric unit form right handed miniature parallel stranded double helices with their respective crystallographic two fold (b axis) symmetry mates. Remarkably, the two mini duplexes are almost indistinguishable. The cytosines and adenines form self-pairs with three and two hydrogen bonds respectively. The conformation of the C and A residues about the glycosyl bond is anti same as in the 3'-5' analog but contrasts the anti and syn geometry of C and A residues in A2'p5'C. The furanose ring conformation is C3' endo, C2' endo mixed puckering as in the C3'p5'A-proflavine complex. A comparison of the backbone torsion angles with other 2'-5' dinucleoside structures reveals that the major deviations occur in the torsion angles about the C3'-C2' and C4'-C3' bonds. A right-handed 2'-5' parallel stranded double helix having eight base pairs per turn and 45 degrees turn angle between them has been constructed using this dinucleoside phosphate as repeat unit. A discussion on 2'-5' parallel stranded double helix and its relevance to biological systems is presented.

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The structure of human carbonic anhydrase II in the monoclinic P21 space group with a doubled a axis from that of the usually observed unit cell has been re-determined and shown that the choice for how the four molecules in the unit cell are grouped (based on their coordinates) into pairs that represent a single asymmetric unit determines whether or not rotational disorder is observed/created during refinement.

The crystal structure of human carbonic anhydrase II in the monoclinic P21 space group with a doubled a axis from that of the usually observed unit cell has recently been reported, with one of the two molecules in the asymmetric unit demonstrating rotational disorder [Robbins et al. (2010 ▶), Acta Cryst. D66, 628–634]. The structure has been redetermined, with the coordinates of both pseudo-symmetrically related molecules in the crystallographic asymmetric unit translated by x′ = x ± 1/4, and no rotational disorder is observed. This corresponds to a different choice of how the four molecules in the unit cell should be grouped into pairs that represent a single asymmetric unit.

Search spaces in the method of molecular replacement are shown to be coset spaces of the Lie group of rigid-body motions by the chiral space group of a crystal. The resulting ‘motion space’ can be endowed with a quasigroup operation that has interesting properties which are explored here.

Molecular replacement (MR) is a well established method for phasing of X-ray diffraction patterns for crystals composed of biological macromolecules of known chemical structure but unknown conformation. In MR, the starting point is known structural domains that are presumed to be similar in shape to those in the macromolecular structure which is to be determined. A search is then performed over positions and orientations of the known domains within a model of the crystallographic asymmetric unit so as to best match a computed diffraction pattern with experimental data. Unlike continuous rigid-body motions in Euclidean space and the discrete crystallographic space groups, the set of motions over which molecular replacement searches are performed does not form a group under the operation of composition, which is shown here to lack the associative property. However, the set of rigid-body motions in the asymmetric unit forms another mathematical structure called a quasigroup, which can be identified with right-coset spaces of the full group of rigid-body motions with respect to the chiral space group of the macromolecular crystal. The algebraic properties of this space of motions are articulated here.

Crystals of the C-terminal 10 kDa lid subdomain from the C. elegans chaperone Hsp70 have been obtained that diffract X-rays to ∼3.5 Å and belong to space group I212121. Analysis of X-ray data and initial heavy-atom phasing reveals 24 monomers in the asymmetric unit related by 432 non-crystallographic symmetry.

Hsp70 is an important molecular chaperone involved in the regulation of protein folding. Crystals of the C-terminal 10 kDa helical lid domain (residues 542–640) from a Caenorhabditis elegans Hsp70 homologue have been produced that diffract X-rays to ∼3.4 Å. Crystals belong to space group I212121, with unit-cell parameters a = b = 197, c = 200 Å. The Matthews coefficient, self-rotation function and Patterson map indicate 24 monomers in the asymmetric unit, showing non-crystallographic 432 symmetry. Molecular-replacement studies using the corresponding domain from rat, the only eukaryotic homologue with a known structure, failed and a mercury derivative was obtained. Preliminary MAD phasing using SHELXD and SHARP for location and refinement of the heavy-atom substructure and SOLOMON for density modification produced interpretable maps with a clear protein–solvent boundary. Further density-modification, model-building and refinement are currently under way.

Here, the expression, purification, crystallization and preliminary crystallographic analysis of SP0987 from Streptococcus pneumoniae TIGR4 are reported.

Streptococcus pneumoniae SP0987, which was identified as a hypothetical protein, has a very low sequence identity to other well characterized lysozyme structures. Since determination of three-dimensional structure is a powerful means of functional characterization, X-ray crystallography has been used to accomplish this task. Here, the expression, purification, crystallization and preliminary crystallographic analysis of SP0987 from Streptococcus pneumoniae TIGR4 are reported. The crystal belonged to space group P212121 (with unit-cell parameters a = 36.46, b = 40.89, c = 147.44 Å) and diffracted to a resolution of 1.85 Å. The crystals are most likely to contain one molecule in the asymmetric unit, with a V M value of 2.02 Å3 Da−1.

An X-ray structural model can be reassigned to a higher symmetry space group using the presented framework if its noncrystallographic symmetry operators are close to being exact crystallographic relationships. About 2% of structures in the Protein Data Bank can be reclassified in this way.

Up to 2% of X-ray structures in the Protein Data Bank (PDB) potentially fit into a higher symmetry space group. Redundant protein chains in these structures can be made compatible with exact crystallographic symmetry with minimal atomic movements that are smaller than the expected range of coordinate uncertainty. The incidence of problem cases is somewhat difficult to define precisely, as there is no clear line between underassigned symmetry, in which the subunit differences are unsupported by the data, and pseudosymmetry, in which the subunit differences rest on small but significant intensity differences in the diffraction pattern. To help catch symmetry-assignment problems in the future, it is useful to add a validation step that operates on the refined coordinates just prior to structure deposition. If redundant symmetry-related chains can be removed at this stage, the resulting model (in a higher symmetry space group) can readily serve as an isomorphous replacement starting point for re-refinement using re-indexed and re-integrated raw data. These ideas are implemented in new software tools available at http://cci.lbl.gov/labelit.

We report here the crystal structure of the DNA hexamer duplex d(CGCGCA).d(TGCGCG) at 1.71 Å resolution. The crystals, in orthorhombic space group, were grown in the presence of cobalt hexammine, a known inducer of the left-handed Z form of DNA. The interaction of this ion with the DNA helix results in a change of the adenine base from the common amino tautomeric form to the imino tautomer. Consequently the A:T base pair is disrupted from the normal Watson–Crick base pairing to a ‘wobble’ like base pairing. This change is accommodated easily within the helix, and the helical parameters are those expected for Z-DNA. When the cobalt hexammine concentration is decreased slightly in the crystallization conditions, the duplex crystallizes in a different, hexagonal space group, with two hexamer duplexes in the asymmetric unit. One of these is situated on a crystallographic 6-fold screw axis, leading to disorder. The tautomeric shift is not observed in this space group. We show that the change in inter-helix interactions that lead to the two different space groups probably arise from the small decrease in ion concentration, and consequently disordered positions for the ion.

We have determined the X-ray structure of the complex between the DNA quadruplex d(5′-GGGG-3′)4 and daunomycin, as a potential model for studying drug–telomere interactions. The structure was solved at 1.08 Å by direct methods in space group I4. The asymmetric unit comprises a linear arrangement of one d(GGGG) strand, four daunomycin molecules, a second d(GGGG) strand facing in the opposite direction to the first, and Na and Mg cations. The crystallographic 4-fold axis generates the biological unit, which is a 12-layered structure comprising two sets of four guanine layers, with four layers each of four daunomycins stacked between the 5′ faces of the two quadruplexes. The daunomycin layers fall into two groups which are novel in their mode of self assembly. The only contacts between daunomycin molecules within any one of these layers are van der Waals interactions, however there is substantial π–π stacking between successive daunomycin layers and also with adjacent guanine layers. The structure differs significantly from all other parallel d(TGGGGT)4 quadruplexes in that the 5′ guanine adopts the unusual syn glycosyl linkage, refuting the widespread belief that such conformations should all be anti. In contrast to the related d(TGGGGT)/daunomycin complex, there are no ligand–quadruplex groove insertion interactions.

The mutagenesis, crystallization and preliminary crystallographic analysis of M. arthritidis-derived mitogen is described.

Mycoplasma arthritidis-derived mitogen (MAM) functions as a conventional superantigen (SAg). Although recombinant MAM has been crystallized by the hanging-drop vapour-diffusion method, the crystals diffracted poorly to only 5.0 Å resolution, with large unit-cell parameters a = 163.8, b = 93.0, c = 210.9 Å, β = 93.7° in the monoclinic space group P21. Unit-cell content analysis revealed that as many as 24 molecules could be present in the asymmetric unit. Systematic alanine mutagenesis was applied in order to search for mutants that give crystals of better quality. Two mutants, L50A and K201A, were crystallized under the same conditions as wild-type MAM (MAMwt). Crystals of the L50A mutant are isomorphous with those of MAMwt, while a new crystal form was obtained for the K201 mutant, belonging to the cubic space group P4132 with unit-cell parameters a = b = c = 181.9 Å. Diffraction data were collected to 3.6 and 2.8 Å resolution from crystals of the MAM L50A and K201A mutants, respectively. Molecular-replacement calculations suggest the presence of two molecules in the asymmetric unit for the MAM K201A mutant crystal, resulting in a V M of 5.0 Å Da−1 and a solvent content of 75%. An interpretable electron-density map for the MAM K201A mutant crystal was produced using the molecular-replacement method.

β-UPSe was synthesized from the reaction of U2Se3, P and Se in a CsCl flux in a fused-silica tube. It crystallizes with four formula units in the tetra­gonal space group I4/mmm in the UGeTe structure type. The asymmetric unit comprises one U (site symmetry 4mm), one Se (4mm), and one P (mmm.) atom. The U atom is coordinated in a monocapped square-anti­prismatic arrangement, where the square face is formed by P atoms and the other five vertices are Se atoms. The P site is disordered about a mirror plane, showing half-ocupancy for each of the two resulting P atoms. The title structure is related to that of α-UPSe, which crystallizes with two formula units in the tetra­gonal space group P4/nmm in the PbFCl structure type.

The title compound, C27H45Cl, is a second monoclinic polymorph which crystallizes in the space group P21 with four crystallographically independent mol­ecules in the asymmetric unit. The structure was previously reported [Bernal et al. (1940 ▶). Philos. Trans. R. Soc. London Ser. B, 239, 135–182; Vani & Vijayan (1979 ▶). Mol. Cryst. Liq. Cryst. 51, 253–264], also in the space group P21, but with two unique mol­ecules in the asymmetric unit. As in the previously reported structures, rings A and C in the mol­ecule adopt chair conformations with half-chair conformations for rings B and D. The ring junctions B–C and C–D are trans, whereas the junction A–B is quasi-trans. In the crystal structure, mol­ecules are arranged in a head-to-tail fashion along a and are stacked along the b axis.

The asymmetric unit of the title compound, C8H8O2, contains two crystallographically independent mol­ecules, which form dimers linked by O⋯H—O hydrogen bonds. The benzene rings in the dimers are inclined at a dihedral angle of 7.30 (8)° and both methyl groups display rotational disorder. This redetermination results in a crystal structure with significantly higher precision than the original determination [Ellas & García-Blanco (1963 ▶). Acta Cryst. 16, 434], in which the authors reported only the unit-cell parameters and space group, without any detailed information on the atomic arrangement. In the crystal, dimers are connected by weak C—H⋯O inter­actions, forming R 2 2(10) and R 4 4(18) rings along [110] and an infinite zigzag chain of dimers along the [001] direction also occurs.

The crystal structure of a probable pyridoxine 5′-phosphate oxidase, Rv2074 from M. tuberculosis, has been solved by the two-wavelength anomalous dispersion method and has been refined at 1.6 Å resolution. Two citric acid molecules are bound fortuitously to the possible active site of Rv2074.

The crystal structure of a conserved hypothetical protein corresponding to open reading frame Rv2074 from Mycobacterium tuberculosis (Mtb) has been solved by the two-wavelength anomalous dispersion method. Refinement of the molecular structure at 1.6 Å resolution resulted in an R work of 0.178 and an R free of 0.204. The crystal asymmetric unit contains an Rv2074 monomer; however, the crystallographic twofold symmetry operation of space group P43212 generates dimeric Rv2074. Each monomer folds into a six-stranded antiparallel β-barrel flanked by two α-helices. The three-dimensional structure of Rv2074 is very similar to that of Mtb Rv1155, a probable pyridoxine 5′-­phosphate oxidase (PNPOx), which corroborates well with the relatively high sequence similarity (52%) between the two. A structural comparison between Rv2074 and Rv1155 revealed that the core structure (a six-stranded β-barrel) is also well conserved; the major differences between the two lie in the N- and C-­termini and in the small helical domain. Two citric acid molecules were observed in the active site of Rv2074, the crystals of which were grown in 0.2 M sodium citrate buffer pH 5.0. The citric acid molecules are bound to Rv2074 by hydrogen-bonding interactions with Thr55, Gln60 and Lys61. One of the two citric acid molecules occupies the same spatial position that corresponds to the position of the phosphate and ribose sugar moieties of the flavin mononucleotide (FMN) in the Mtb Rv1155–FMN, Escherichia coli PNPOx–FMN and human PNPOx–FMN complex structures. Owing to its extensive structural similarity with Mtb Rv1155 and to the E. coli and human PNPOx enzymes, Rv2074 may be involved in the final step in the biosynthesis of pyridoxal 5′-phosphate (PLP; a vitamin B6).

The problems encountered during the phasing and structure determination of the packaging enzyme P4 from bacteriophage ϕ13 using the anomalous signal from selenium in a single-wavelength anomalous dispersion experiment (SAD) are described. The oligomeric state of P4 in the virus is a hexamer (with sixfold rotational symmetry) and it crystallizes in space group C2, with four hexamers in the crystallographic asymmetric unit. Current state-of-the-art ab initio phasing software yielded solutions consisting of 96 atoms arranged as sixfold symmetric clusters of Se atoms. However, although these solutions showed high correlation coefficients indicative that the substructure had been solved, the resulting phases produced uninterpretable electron-density maps. Only after further analysis were correct solutions found (also of 96 atoms), leading to the eventual identification of the positions of 120 Se atoms. Here, it is demonstrated how the difficulties in finding a correct phase solution arise from an intricate false-minima problem.

The asymmetric unit of the title compound, C12H10N4O2, contains three half-mol­ecules. Each half-mol­ecule is completed by crystallographic inversion symmetry. The title compound, (I), is a polymorph of the structure, (II), reported by Hsu & Chen [Eur. J. Inorg. Chem. (2004), 1488–1493]. In the original report, the compound crystallized in the tetra­gonal space group P 21c (Z = 8), whereas the structure reported here is triclinic (P , Z = 3). In both forms, each oxamide mol­ecule is almost planar (with maximum deviations are 0.266 and 0.166 Å) and the O atoms are trans oriented. The principal difference between the two forms lies in the different hydrogen-bonding patterns. In (I), two N—H⋯O and one N—H⋯N hydrogen bonds link the mol­ecules, forming a two-dimensional network, whereas in (II) there are no classical hydrogen bonds to O atoms and only weak C—H⋯O inter­actions are found along with rings of N—H⋯N bonds.

The crystal structure of the photosynthetic A 4 isoform of glyceraldehyde-3-phosphate dehydrogenase from the model plant A. thaliana has been solved at 2.6 Å resolution. The tetrameric structure includes four molecules of NAD and eight sulfate ions occupying the P sites involved in catalysis.

The crystal structure of the A 4 isoform of photosynthetic glyceraldehyde-3-­phosphate dehydrogenase (GAPDH) from Arabidopsis thaliana, expressed in recombinant form and complexed with NAD, is reported. The crystals, which were grown in 2.4 M ammonium sulfate and 0.1 M sodium citrate, belonged to space group I222. The asymmetric unit includes ten subunits, i.e. two independent tetramers plus a dimer that generates a third tetramer by a crystallographic symmetry operation. The crystal structure was solved by molecular replacement and refined to an R factor of 23.7% and an R free factor of 28.9% at 2.6 Å resolution. In the final model, each subunit binds one NAD+ molecule and two sulfates, which occupy the Ps and the Pi anion-binding sites. Detailed knowledge of this structure is instrumental for structural investigation of supramolecular complexes of A 4-GAPDH, phosphoribulokinase and CP12, which are involved in the regulation of photosynthesis in the model plant A. thaliana.

The X-ray crystallographic structure of cellulose IIIII is characterized by disorder; the unit cell (space group P21; a=4.45Å, b=7.64Å c=10.36Å, α=β=90°, γ=106.96°) is occupied by one chain that is the average of statistically disordered antiparallel chains. 13C CP/MAS NMR studies reveal the presence of three distinct molecular conformations that can be interpreted as a mixture of two different crystal forms, one equivalent to cellulose IIII, and another with two independent glucosyl conformations in the asymmetric unit. Both X-ray crystallographic and 13C NMR spectroscopic results are consistent with an aggregated microdomain structure for cellulose IIIII. This structure can be generated from a new crystal form (space group P21; a=4.45Å, b=14.64Å c=10.36Å, α=β=90°, γ=90.05°; two crystallographically independent and antiparallel chains; gt hydroxymethyl groups) by multiple dislocation defects. These defects produce microdomains of the new crystal form and cellulose IIII that scanning microprobe diffraction studies show are distributed consistently through the cellulose IIIII fiber.