Non-crystallographic Axis Research Articles

Redetermination of di-ammonium trivanadate, (NH4)2V3O8.

The crystal structure of (NH4)2V3O8 has been reported twice using single-crystal X-ray data [Theobald et al. (1984 ▸). J. Phys. Chem. Solids, 45, 581-587; Range et al. (1988 ▸). Z. Naturforsch. Teil B, 43, 309-317]. In both cases, the orientation of the ammonium cation in the asymmetric unit was poorly defined: in Theobald's study, the shape and dimensions were constrained for NH4 +, while in Range's study, H atoms were not included. In the present study, we collected a highly redundant data set for this ternary oxide, at 0.61 Å resolution, using Ag Kα radiation. These accurate data reveal that the NH4 + cation is disordered by rotation around a non-crystallographic axis. The rotation axis coincides with one N-H bond lying in the mirror m symmetry element of space-group type P4bm, and the remaining H sites were modelled over two disordered positions, with equal occupancy. It therefore follows that the NH4 + cations filling the space available in the (001) layered structure formed by (V3O8)2- ions do not form strong N-H⋯O hydrogen bonds with the mixed-valent oxidovanadate(IV,V) anions. This feature could have consequences for the Li-ion inter-calation properties of this material, which is used as a cathode for supercapacitors.

3D Electron Diffraction: The Nanocrystallography Revolution.

Crystallography of nanocrystalline materials has witnessed a true revolution in the past 10 years, thanks to the introduction of protocols for 3D acquisition and analysis of electron diffraction data. This method provides single-crystal data of structure solution and refinement quality, allowing the atomic structure determination of those materials that remained hitherto unknown because of their limited crystallinity. Several experimental protocols exist, which share the common idea of sampling a sequence of diffraction patterns while the crystal is tilted around a noncrystallographic axis, namely, the goniometer axis of the transmission electron microscope sample stage. This Outlook reviews most important 3D electron diffraction applications for different kinds of samples and problematics, related with both materials and life sciences. Structure refinement including dynamical scattering is also briefly discussed.

Iterative projection algorithms in protein crystallography. II. Application.

Iterative projection algorithms (IPAs) are a promising tool for protein crystallographic phase determination. Although related to traditional density-modification algorithms, IPAs have better convergence properties, and, as a result, can effectively overcome the phase problem given modest levels of structural redundancy. This is illustrated by applying IPAs to determine the electron densities of two protein crystals with fourfold non-crystallographic symmetry, starting with only the experimental diffraction amplitudes, a low-resolution molecular envelope and the position of the non-crystallographic axes. The algorithm returns electron densities that are sufficiently accurate for model building, allowing automated recovery of the known structures. This study indicates that IPAs should find routine application in protein crystallography, being capable of reconstructing electron densities starting with very little initial phase information.

Structural regularities of helicoidally-like biopolymers in the framework of algebraic topology: II. α-Helix and DNA structures

In the framework of algebraic topology the closed sequence of 4-dimensional polyhedra (algebraic polytopes) was defined. This sequence is started by the polytope {240}, discovered by Coxeter, and is determined by the second coordination sphere of 8-dimensional lattice E8. The second polytope of sequence allows to determine a topologically stable rod substructure that appears during multiplication by a non-crystallographic axis 40/11 of the starting union of 4 tetrahedra with common vertex. When positioning the appropriate atoms tin positions of special symmetry of the staring 4 tetrahedra, such helicoid determines an {\alpha}-helix. The third polytope of sequence allows to determine the helicoidally-like union of rods with 12-fold axis, which can be compare with Z-DNA structures. This model is defined as a local lattice rod packing, contained within a surface of helicoidally similar type, which ensures its topological stability, as well as possibility for it to be transformed into other forms of DNA structures. Formation of such structures corresponds to lifting a configuration degeneracy, and the stability of a state - to existence of a point of bifurcation. Furthermore, in the case of DNA structures, a second "security check" possibly takes place in the form of local lattice (periodic) property using the lattices other than the main ones.

A noncrystallographic screw axis parallel to a twin axis can corrupt intensity statistics

A number of methods to detect twinning are based upon the assumption that the statistical properties of diffracted intensities are different for twinned and untwinned specimens. This may not be true for a large portion of the reflections in a twinned specimen if a noncrystallographic screw axis parallel to the twinning axis is present. In this case, up to half of all reflections can obey Wilson statistics, which are typical of untwinned crystals. The distribution corresponding to a whole set of observed intensities is biased towards the Wilson distribution in this case.

High-Resolution Crystal Structure of Spectrin SH3 Domain Fused with a Proline-Rich Peptide

A new chimeric protein, named WT-CIIA, was designed by connecting the proline-rich decapeptide PPPVPPYSAG to the C-terminus of the alpha-spectrin SH3 domain through a natural twelve-residue linker to obtain a single-chain model that would imitate intramolecular SH3-ligand interaction. The crystal structure of this fusion protein was determined at 1.7 Å resolution. The asymmetric unit of the crystal contained two SH3 globules contacting with one PPPVPPY fragment located between them. The domains are related by the twofold non-crystallographic axis and the ligand lies in two opposite orientations with respect to the conservative binding sites of SH3 domains.

The K5 Lyase KflA Combines a Viral Tail Spike Structure with a Bacterial Polysaccharide Lyase Mechanism

K5 lyase A (KflA) is a tail spike protein (TSP) encoded by a K5A coliphage, which cleaves K5 capsular polysaccharide, a glycosaminoglycan with the repeat unit [-4)-betaGlcA-(1,4)- alphaGlcNAc(1-], displayed on the surface of Escherichia coli K5 strains. The crystal structure of KflA reveals a trimeric arrangement, with each monomer containing a right-handed, single-stranded parallel beta-helix domain. Stable trimer formation by the intertwining of strands in the C-terminal domain, followed by proteolytic maturation, is likely to be catalyzed by an autochaperone as described for K1F endosialidase. The structure of KflA represents the first bacteriophage tail spike protein combining polysaccharide lyase activity with a single-stranded parallel beta-helix fold. We propose a catalytic site and mechanism representing convergence with the syn-beta-elimination site of heparinase II from Pedobacter heparinus.

Crystallization and preliminary crystallographic analysis of Gre2p, an NADP(+)-dependent alcohol dehydrogenase from Saccharomyces cerevisiae.

Gre2p [Genes de respuesta a estres (stress-response gene)] from Saccharomyces cerevisiae is a monomeric enzyme of 342 amino acids with a molecular weight of 38.1 kDa. The enzyme catalyses both the stereospecific reduction of keto compounds and the oxidation of various hydroxy compounds and alcohols by the simultaneous consumption of the cofactor NADPH and formation of NADP(+). Crystals of a Gre2p complex with NADP(+) were grown using PEG 8000 as a precipitant. They belong to the monoclinic space group P2(1). The current diffraction resolution is 3.2 A. In spite of the monomeric nature of Gre2p in solution, packing and self-rotation calculations revealed the existence of two Gre2p protomers per asymmetric unit related by a twofold noncrystallographic axis.

PAS-mediated Dimerization of Soluble Guanylyl Cyclase Revealed by Signal Transduction Histidine Kinase Domain Crystal Structure

Signal transduction histidine kinases (STHK) are key for sensing environmental stresses, crucial for cell survival, and attain their sensing ability using small molecule binding domains. The N-terminal domain in an STHK from Nostoc punctiforme is of unknown function yet is homologous to the central region in soluble guanylyl cyclase (sGC), the main receptor for nitric oxide (NO). This domain is termed H-NOXA (or H-NOBA) because it is often associated with the heme-nitric oxide/oxygen binding (H-NOX) domain. A structure-function approach was taken to investigate the role of H-NOXA in STHK and sGC. We report the 2.1 A resolution crystal structure of the dimerized H-NOXA domain of STHK, which reveals a Per-Arnt-Sim (PAS) fold. The H-NOXA monomers dimerize in a parallel arrangement juxtaposing their N-terminal helices and preceding residues. Such PAS dimerization is similar to that previously observed for EcDOS, AvNifL, and RmFixL. Deletion of 7 N-terminal residues affected dimer organization. Alanine scanning mutagenesis in sGC indicates that the H-NOXA domains of sGC could adopt a similar dimer organization. Although most putative interface mutations did decrease sGCbeta1 H-NOXA homodimerization, heterodimerization of full-length heterodimeric sGC was mostly unaffected, likely due to the additional dimerization contacts of sGC in the coiled-coil and catalytic domains. Exceptions are mutations sGCalpha1 F285A and sGCbeta1 F217A, which each caused a drastic drop in NO stimulated activity, and mutations sGCalpha1 Q368A and sGCbeta1 Q309A, which resulted in both a complete lack of activity and heterodimerization. Our structural and mutational results provide new insights into sGC and STHK dimerization and overall architecture.

Molecular Mechanism of Allosteric Substrate Activation in a Thiamine Diphosphate-dependent Decarboxylase

Thiamine diphosphate-dependent enzymes are involved in a wide variety of metabolic pathways. The molecular mechanism behind active site communication and substrate activation, observed in some of these enzymes, has since long been an area of debate. Here, we report the crystal structures of a phenylpyruvate decarboxylase in complex with its substrates and a covalent reaction intermediate analogue. These structures reveal the regulatory site and unveil the mechanism of allosteric substrate activation. This signal transduction relies on quaternary structure reorganizations, domain rotations, and a pathway of local conformational changes that are relayed from the regulatory site to the active site. The current findings thus uncover the molecular mechanism by which the binding of a substrate in the regulatory site is linked to the mounting of the catalytic machinery in the active site in this thiamine diphosphate-dependent enzyme.

UnusualO-coordination of caffeine in tetrakis(μ-3,5-dinitrobenzoato-κ2O:O′)bis[(caffeine-κO)copper(II)

The title compound {systematic name: tetra­kis(μ-3,5-dinitro­benzoato-κ2O:O′)bis­[(3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione-κO2)copper(II)]}, [Cu2(C7H3N2O6)4(C8H10N4O2)2], consists of paddle-wheel dimeric tetra­kis(μ-3,5-dinitro­benzoato-κ2O:O′)dicopper(II) units with O-coordinated caffeine mol­ecules in both apical positions. The entire dimeric mol­ecule lies on a tetra­gonal inversion \overline{4} axis, and thus one nitro­benzoate anion with one Cu atom in a special position belong to the independent part of the mol­ecule. The caffeine ligand bonded to the Cu atom is disordered on a local twofold non-crystallographic axis coincident with the \overline{4} axis. A π–π stacking inter­action is observed between the caffeine rings and adjacent symmetry-related benzene rings of the 3,5-dinitro­benzoate anions.

Structural and Functional Organization of the ESCRT-I Trafficking Complex

The endosomal sorting complex required for transport (ESCRT) complexes are central to receptor downregulation, lysosome biogenesis, and budding of HIV. The yeast ESCRT-I complex contains the Vps23, Vps28, and Vps37 proteins, and its assembly is directed by the C-terminal steadiness box of Vps23, the N-terminal half of Vps28, and the C-terminal half of Vps37. The crystal structures of a Vps23:Vps28 core subcomplex and the Vps23:Vps28:Vps37 core were solved at 2.1 and 2.8 A resolution. Each subunit contains a structurally similar pair of helices that form the core. The N-terminal domain of Vps28 has a hydrophobic binding site on its surface that is conformationally dynamic. The C-terminal domain of Vps28 binds the ESCRT-II complex. The structure shows how ESCRT-I is assembled by a compact core from which the Vps23 UEV domain, the Vps28 C domain, and other domains project to bind their partners.

Acanthamoeba polyphaga mimivirus NDK: preliminary crystallographic analysis of the first viral nucleoside diphosphate kinase.

The complete sequence of the largest known double-stranded DNA virus, Acanthamoeba polyphaga mimivirus, has recently been determined [Raoult et al. (2004), Science, 306, 1344-1350] and revealed numerous genes not expected to be found in a virus. A comprehensive structural and functional study of these gene products was initiated [Abergel et al. (2005), Acta Cryst. F61, 212-215] both to better understand their role in the virus physiology and to obtain some clues to the origin of DNA viruses. Here, the preliminary crystallographic analysis of the viral nucleoside diphosphate kinase protein is reported. The crystal belongs to the cubic space group P2(1)3, with unit-cell parameter 99.425 A. The self-rotation function confirms that there are two monomers per asymmetric unit related by a twofold non-crystallographic axis and that the unit cell thus contains four biological entities.

Preliminary investigation of the three-dimensional structure of Salmonella typhimurium uridine phosphorylase in the crystalline state.

Uridine phosphorylase (UPh) catalyzes the phosphorolytic cleavage of the C-N glycosidic bond of uridine to ribose 1-phosphate and uracil in the pyrimidine-salvage pathway. The crystal structure of the Salmonella typhimurium uridine phosphorylase (StUPh) has been determined at 2.5 A resolution and refined to an R factor of 22.1% and an Rfree of 27.9%. The hexameric StUPh displays 32 point-group symmetry and utilizes both twofold and threefold non-crystallographic axes. A phosphate is bound at the active site and forms hydrogen bonds to Arg91, Arg30, Thr94 and Gly26 of one monomer and Arg48 of an adjacent monomer. The hexameric StUPh model reveals a close structural relationship to Escherichia coli uridine phosphorylase (EcUPh).

Crystal structure of thermostable catechol 2,3-dioxygenase determined by multiwavelength anomalous dispersion method

The selenomethionyl derivative of the thermostable catechol 2,3-dioxygenase (SeMet-TC23O) is expressed, purified and crystallized. By using multiwave length anomalous dispersion (MAD) phasing techniques, the crystal structure of TC23O at 0.3 nm resolutions is determined. TC23O is a homotetramer. Each monomer is composed of N-terminal and C-terminal domains (residues 1∼153 and 153∼319, respectively). The two domains are proximately symmetric by a non-crystallographic axis. Each domain contains two characteristic motifs which are found in almost all of extradial dioxygenases.

Phasing from an envelope.

Solution of the phase problem is central to crystallographic structure determination. Conventional molecular-replacement methods are ineffective in the absence of knowledge of the structure of a homologous protein. A recent method utilizing the low-resolution molecular shape determined from solution X-ray scattering data has been shown to be successful in locating the molecular shape within the crystallographic unit cell for the cases of the trimeric nitrite reductase (AxNiR, 105 kDa) and the dimeric superoxide dismutase (SOD, 32 kDa). This was achieved by performing a direct real-space search for orientation and translation using the orientation of the non-crystallographic axis obtained by performing a self-rotation on the crystallographic data. This effectively reduces the potential six-dimensional search to a four-dimensional one (Eulerian angle gamma and three translational parameters). The program FSEARCH incorporating this method has been generalized to handle molecules from all space groups. The program can also be used in general six-dimensional cases for a molecular-replacement solution given a predetermined envelope from any source, such as electron-microscopic images or solution scattering, provided that the envelope can be converted to the standard CCP4 map format or expressed in terms of spherical harmonics. It is hoped that this method will greatly facilitate the ab initio structure determination of proteins and provide a good foundation for further structure refinement.

Implementation of cluster analysis for ab initio phasing using the molecular envelope from solution X-ray scattering.

Solution of the phase problem is central to crystallographic structure determination. The conventional methods of isomorphous replacement (MIR or SIR) and molecular replacement are ineffective in the absence of a suitable isomorphous heavy-atom derivative or knowledge of the structure of a homologous protein. A recent method utilizing the low-resolution molecular shape determined from solution X-ray scattering data has shown to be successful in locating the molecular shape within the crystallographic unit cell in the case of the trimer nitrite reductase (NiR, 105 kDa) [Hao et al. (1999), Acta Cryst. D55, 243-246]. This was achieved by performing a direct real-space search for orientation and translation using knowledge of the orientation of the polar angles of the non-crystallographic axis obtained by performing a self-rotation on crystallographic data. This effectively reduces the potential six-dimensional search to a four-dimensional one (Eulerian angle gamma and three translational parameters). In the case of NiR, the direct four-dimensional search produced a clear solution that was in good agreement with the known structure. The program FSEARCH incorporating this method has been generalized to handle molecules from all space groups and in particular those in possession of non-crystallographic symmetry. However, the method employed was initially unsuccessful when applied to the small dimeric molecule superoxide dismutase (SOD, 32 kDa) owing to the absence of strong reflections at low resolution caused by saturation at the detector. The determined solution deviated greatly from that of the known structure [Hough & Hasnain (1999), J. Mol. Biol. 287, 579-592]. It was found that once these absent reflections were replaced by a series of randomly generated intensity values and cluster analysis was performed on the output, the signal-to-noise ratio was improved and a most probable solution was found. The electron-density map of the stochastically determined solution agrees well with the known structure; the phase error calculated from this map was 67 degrees within 14 A resolution.

Facile Synthesis and Molecular Structure of [Ni(PPh2NHPh)4

NiCl₂ · 6 H₂O readily reacts with PPh₂NHPh in the presence of zinc dust to yield the homoleptic nickel(0) tetrakis-phosphine complex [Ni(PPh₂NHPh)₄] (1). 1 crystallises triclinic P1 (no. 2), with a = 14.656(1), b = 17.124(2), c = 17.424(1) A, α = 95.998(1), β = 111.845(1), γ= 111.402(1)°, V = 3630.04(5) A3, Z = 2, R values [I > 2σ(I)]: R1 = 0.0554, all data: wR2 = 0.1720. The nickel atom is coordinated in a distorted tetrahedral fashion by four phosphorus atoms, resembling a compressed tetrahedron along one of the non-crystallographic S₄ axes.

The decameric structure of bovine pancreatic trypsin inhibitor (BPTI) crystallized from thiocyanate at 2.7 A resolution.

The structure of a monoclinic form of bovine pancreatic trypsin inhibitor (BPTI) crystallized from a thiocyanate solution has been determined and refined at 2.7 A resolution. The space group is P21 with a = 71.56, b = 73.83, c = 64.47 A, beta = 93.9 degrees and Z = 20. The ten independent molecules were located by a multi-body molecular-replacement search as developed in the AMoRe program, starting from a single monomer model (PDB code: 6PTI). The molecular arrangement of the subunits is a decamer resulting from the combination of two orthogonal fivefold and twofold non-crystallographic axes. This builds a globular micelle-like particle which minimizes hydrophobic interactions with the solvent. The refinement was conducted with non-crystallographic symmetry constraints up to a final residual of R = 0.20 (Rfree= 0.26). The root-mean-square deviations from ideal geometry were 0.015 A and 1.6 degrees on bond distances and bond angles, respectively. Several sites for thiocyanate ions were analyzed.

Plastic deformation of metamorphic pyrite: new evidence from electron-backscatter diffraction and forescatter orientation-contrast imaging

Application of new scanning electron microscope techniques to the study of deformed metamorphic pyrite reveals evidence for plastic deformation not readily recognised by more traditional methods. Specifically, use of forescatter solid-state detectors in conjunction with tilted polished specimens of pyritic ore produces high quality crystallographic orientation contrast images, which map the distribution of deformation domains within grains. Use of electron-backscatter diffraction allows quantification of the crystallographic misorientations shown by the orientation contrast images. Combination of these techniques shows that the pyrite studied deforms by slip on {100} and more rarely {110} systems. Slip is often associated with distributed rotation of up to 20° about and more rarely axes. Pyrites may have simple histories involving rotation about a single axis, or more complex histories involving rotation about different axes, and more rarely , in different domains of the same pyrite grain, or sequential rotations about quite different systems, typically distributed rotation about followed by discrete rotation about a non-crystallographic axis.