Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the program Zanuda.

Journal ArticleResearch Support, Non-U.S. Gov'tThe presence of pseudo-symmetry in a macromolecular crystal and its interplay with twinning may lead to an incorrect space-group (SG) assignment. Moreover, if the pseudo-symmetry is very close to an exact crystallographic symmetry, the structure can be solved and partially refined in the wrong SG. Typically, in such incorrectly determined structures all or some of the pseudo-symmetry operations are, in effect, taken for crystallographic symmetry operations and vice versa. A mistake only becomes apparent when the R(free) ceases to decrease below 0.39 and further model rebuilding and refinement cannot improve the refinement statistics. If pseudo-symmetry includes pseudo-translation, the uncertainty in SG assignment may be associated with an incorrect choice of origin, as demonstrated by the series of examples provided here. The program Zanuda presented in this article was developed for the automation of SG validation. Zanuda runs a series of refinements in SGs compatible with the observed unit-cell parameters and chooses the model with the highest symmetry SG from a subset of models that have the best refinement statistics.STFC UKCCP4BBSR

Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps

Journal ArticleThe molecular-replacement method has been extended to locate molecules and their fragments in an electron-density map. The approach is based on a new spherically averaged phased translation function. The position of the centre of mass of a search model is found prior to determination of its orientation. The orientation is subsequently found by a phased rotation function. The technique also allows superposition of distantly related macromolecules. The method has been implemented in a computer program MOLREP and successfully tested using experimental data sets

NCS-constrained exhaustive search using oligomeric models

Copyright © 2008 International Union of CrystallographyThe efficiency of the cross-rotation function step of molecular replacement (MR) is intrinsically limited as it uses only a fraction of the Patterson vectors. Along with general techniques extending the boundaries of the method, there are approaches that utilize specific features of a given structure. In special cases, where the directions of noncrystallographic symmetry axes can be unambiguously derived from the self-rotation function and the structure of the homologue protein is available in a related oligomeric state, the cross-rotation function step of MR can be omitted. In such cases, a small number of yet unknown parameters defining the orientation of the oligomer and/or its internal organization can be optimized using an exhaustive search. Three difficult MR cases are reported in which these parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches.NI

Crystallization and preliminary x-ray diffraction studies of a novel bacterial esterase.

Journal ArticleResearch Support, Non-U.S. Gov'tA novel bacterial esterase has been crystallized in two forms suitable for X-ray diffraction studies. Crystals have been obtained by vapour-phase diffusion at 290 K using ammonium sulfate as precipitant. The first crystals grew in space group C2 with unit-cell parameters a = 134.7, b = 55.8, c = 110.3 A, beta = 125.1 degrees. A monoclinic data set has been collected to 2.0 A resolution. Microseeding yielded a second crystal form which grew in space group P212121 with unit-cell parameters a = 57.1, b = 115.4, c = 130.4 A. Native data from these crystals have been collected to 1.6 A resolution. A molecular envelope has been determined using an uranyl acetate derivative for phase calculation.BBSRCSmithKline Beecham PharmaceuticalsEuropean Unio

Crystallization and preliminary X-ray diffraction studies of pyrrolidone carboxyl peptidase from the hyperthermophilic archaeon Thermococcus litoralis.

Journal ArticleResearch Support, Non-U.S. Gov'tPyrrolidone carboxyl peptidase from the hyperthermophilic archaeon Thermococcus litoralis has been crystallized in a form suitable for X-ray diffraction from ammonium sulfate or ammonium dihydrogen orthophosphate using the vapour-phase diffusion method. Crystals from both precipitants are of the orthorhombic space group P21212 with unit-cell dimensions a = 94.06, b = 149.06, c = 73.54 A. A complete data set to 2.8 A resolution has been collected from crystals grown from ammonium sulfate.BBSR

Crystallization and preliminary X-ray diffraction studies of a novel alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.

Journal ArticleResearch Support, Non-U.S. Gov'tA novel alcohol dehydrogenase enzyme has been cloned from the hyperthermophilic archaeon Aeropyrum pernix and overexpressed in Escherichia coli. This zinc-containing enzyme has been crystallized by the sitting-drop vapour-diffusion method using PEG 600 as precipitant. The crystals diffract to 1.5 A resolution and belong to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 100.7, b = 103.2, c = 67.5 A. The asymmetric unit contains two enzyme monomers. Two synchrotron data sets have been collected: one at a wavelength near the absorption edge of zinc and one at a remote wavelength. Three strong zinc-ion positions were visible in the anomalous Patterson map. Two additional weaker zinc ions have been identified by anomalous Fourier synthesis.BBSRCEuropean Community (Access to Research Infrastructure Action of the Improving Human Potential Programme to EMBL Hamburg Outstation

Crystallization and preliminary X-ray diffraction analysis of L-aminoacylase from the hyperthermophilic archaeon Thermococcus litoralis.

Journal ArticleResearch Support, Non-U.S. Gov'tThe enzyme L-aminoacylase catalyses the hydrolysis of N-acyl-L-amino acids from peptides or proteins. The recombinant enzyme from the hyperthermophilic archaeon Thermococcus litoralis has been purified to homogeneity. This zinc-containing enzyme has been crystallized from ammonium sulfate using the sitting-drop vapour-diffusion method. The crystals diffract to 2.8 A resolution and belong to the rhombohedral space group R32, with unit-cell parameters a = b = 102.4, c = 178.5 A, gamma = 120 degrees in a hexagonal lattice setting. The asymmetric unit contains one enzyme monomer, containing a single zinc ion. Two synchrotron data sets have been collected at a remote wavelength and at the maximum f'wavelength for zinc. This has allowed the position of the metal to be identified in anomalous Patterson maps.BBSRCTMR/LSF programme to the EMBL Hamburg Outstatio

Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity

Copyright © 2013 International Union of CrystallographyThe crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases.University of Exeter - PhD GTA bursaryWellcome TrustBiotechnology and Biological Sciences Research Council (BBSRC)Engineering and Physical Sciences Research Council (EPSRC

Crystallization and preliminary X-ray analysis of human thioredoxin peroxidase-B from red blood cells.

Journal ArticleResearch Support, Non-U.S. Gov'tTwo different crystal forms of human thioredoxin peroxidase-B have been grown by vapour diffusion using polyethylene glycol 400 as a precipitant. Monoclinic P21 crystals were grown from freshly purified protein, whilst orthorhombic P212121 crystals were grown from purified protein that had been stored in ammonium sulfate, but otherwise under the same conditions. The diffraction from both crystal forms was observed to extend to beyond 2.0 A resolution using synchrotron radiation. Complete native data sets to 1.8 and 3. 7 A have been collected from the monoclinic and orthorhombic crystals, respectively.EU (HCMP Access to Large Scale Facilities grant

Crystallization and preliminary X-ray diffraction studies of the oxygenating subunit of 3,6-diketocamphane monooxygenase from Pseudomonas putida.

Journal ArticleResearch Support, Non-U.S. Gov'tThe oxygenating constituent of the 3,6-diketocamphane monooxygenase isozyme from Pseudomonas putida NCIMB 10007 has been crystallized under two different conditions. Crystals were initially grown from polyethylene glycol (PEG) 8000 and sodium acetate using the vapour-phase diffusion method. The crystals were of orthorhombic P212121 space group, with cell dimensions a = 55.8, b = 94.5 and c = 163.7 A and diffracted to 2.8 A resolution. More recently, improved crystals, which diffracted beyond 2 A, have been grown from ammonium sulfate. These crystals also belong to the orthorhombic P212121 space group, with cell dimensions of a = 54.6, b = 93.2 and c = 154. 1 A. A full native data set to 2.5 A resolution has been collected from the ammonium sulfate grown crystals.BBSR