issue contents

Journal logoSTRUCTURAL BIOLOGY
COMMUNICATIONS
ISSN: 2053-230X

October 2014 issue

Highlighted illustration

Cover illustration: The crystal structure of group B streptococcus glyceraldehyde-3-phosphate dehydrogenase from Streptococcus agalactiae in complex with NAD at 2.46 Å resolution (Ayres et al., p. 1333).

IYCr crystallization series


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The PDB is looked at to find data to answer the question `How well do our current screens cover crystallization space?' and to try to find answers to the more general question about the most efficient strategy to employ in a crystallization campaign.

structural communications


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The crystal structure of the N-terminal domain of lactoferrin-binding protein B (LbpB) from N. meningitidis is reported. Docking of the structure with lactoferrin suggests roles for LbpB in both host iron acquisition and neutralization of the toxic effects of the lactoferricin peptide.

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The structure of a short-chain dehydrogenase encoded within genomic islands of A. baumannii strains has been solved to 2.4 Å resolution. This classical SDR incorporates a flexible helical subdomain. The NADP-binding site and catalytic side chains are identified.

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A controversy has existed in the literature between crystallographic and spectroscopic data on the binding mode of cyanate to carbonic anhydrase II (CA II). To settle this ambiguity, the X-ray crystal structures of the complexes of wild-type and V207I variant CA II with cyanate were redetermined to 1.7 and 1.5 Å resolution, respectively. The data clearly support that cyanate binds directly to the catalytic zinc and not as an outer sphere ligand mimicking the binding of CO2.

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The structure of the A. fumigatus old yellow enzyme EasA was determined to 1.8 Å resolution. This enzyme catalyzes the reduction of chanoclavine-I aldehyde to dihydrochanoclavine aldehyde and works in conjunction with festuclavine synthase at the branchpoint for ergot alkaloid pathways.

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The crystal structure of group B streptococcus glyceraldehyde-3-phosphate dehydrogenase from Streptococcus agalactiae in complex with NAD is reported at 2.46 Å resolution.

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The structure of homoserine O-acetyltransferase (HTA) from the human pathogen Staphylococcus aureus has been determined. Despite a similar overall fold and active site architecture to other α/β-hydrolases, this more compact HTA structure has a more narrow access to the active site than can confer important specificity differences.

crystallization communications


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The cryptic polo-box (CPB) domain of the polo-like kinase ZYG-1 from C. elegans was cloned, overexpressed, purified and crystallized. Anomalous X-ray diffraction data were collected to 2.54 Å resolution.

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IL-18 and its two receptors, IL-18Rα and IL-18Rβ, were purified for crystallization and biochemical analysis. IL-18 was crystallized in free, IL-18Rα-bound and IL-18Rα/IL-18Rβ-bound states and complete X-ray data sets suitable for further structural analysis were obtained from each crystal.

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Crystals of the Pax9 paired domain bound to a DC5 enhancer DNA element that diffract anisotropically to 3.0 Å resolution are reported.

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The integral membrane lysine permease from P. aeruginosa was cloned and overexpressed in E. coli as a GFP-fusion protein. Crystals of the tag-less transporter diffracted to 7.5 Å resolution.

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Cystathionine β-lyase from multidrug-resistant A. baumannii OXA-23 (AbCBL), an enzyme involved in the methionine-metabolism pathway and a novel antibacterial drug target, was cloned, expressed, purified and crystallized. Preliminary X-ray crystallography was performed to analyse the AbCBL crystal.

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The cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of 7-keto-8-aminopelargonic acid (KAPA) synthase from M. smegmatis are described..

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FBPA I from E. coli was expressed, purified and crystallized. The crystals diffracted to 2.0 Å resolution and belonged to space group C2.

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The Ets1–Runx1–CBFβ–DNA complex, a higher-order TF–DNA complex formed on the T-cell receptor α gene enhancer, was crystallized.

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The crystallization and preliminary crystallographic analysis of CrArsM, an arsenic(III) S-adenosylmethionine methyltransferase from C. reinhardtii, is described.

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Crystallization experiments of the BRPF1 bromodomain in complex with its H4K12ac and H2AK5ac histone ligands yielded crystals that are suitable for high-resolution X-ray diffraction analysis. These structures will be solved in order to elucidate the molecular mechanism of histone recognition.

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The chemolithoautotrophic nitrifying thaumarchaeon Ca. Nitrososphaera gargensis with unusual metabolic pathways was enriched by cultivation over six years. A novel α/β-hydrolase was identified, isolated and crystallized for further functional analysis.

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Lin1840 from L. innocua has been overexpressed in E. coli, purified and crystallized. Diffraction data have been collected to a resolution of 1.8 Å.

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McbB, a multifunctional enzyme responsible for catalysing Pictet–Spengler cyclization, decarboxylation and oxidation reactions in the biosynthesis of β-carboline, was expressed and crystallized. The crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 66.06, b = 85.48, c = 106.19 Å, α = 90.00, β = 106.77, γ = 90.00°.

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A crystal was obtained of the complex between reduced terminal oxygenase and oxidized ferredoxin components of carbazole 1,9a-dioxygenase. The crystal belonged to space group P21 and diffracted to 2.25 Å resolution.

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Cyclolavandulyl diphosphate synthase, which catalyzes both the condensation of two molecules of C5 dimethylallyl diphosphate and the subsequent cyclization, has been crystallized and X-ray diffraction data have been collected and analyzed.

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The CIDE domain of Drep2 was purified and crystallized in space group P212121, with unit-cell parameters a = 50.28, b = 88.70, c = 113.37 Å. The crystals diffracted to a resolution of 2.3 Å.

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The SMase D from L. gaucho venom was expressed, purified, crystallized and diffraction data were collected to 2.6 Å resolution.

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The first crystal structure for an intracellular poly(3-hydroxybutyrate) depolymerase at 1.42 Å resolution was determined by molecular replacement using a search model with 24% sequence identity.

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The thiosulfate dehydrogenase TsdA from A. vinosum was recombinantly expressed, purified and crystallized. The crystals belonged to space group C2, with unit-cell parameters a = 79.2, b = 69.9, c = 57.9 Å, β = 129.3°, and diffracted to a resolution of 1.98 Å.

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A crystal of the full-length response regulator spr1814 of S. pneumoniae in complex with a phosphoryl analogue was obtained and diffraction data were collected to 1.9 Å resolution.

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The C-terminal domain of C. trachomatis CdsD was purified and crystallized. The preliminary X-ray diffraction studies are presented.

laboratory communications


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All seven possible single-site lysine-to-serine mutations of ubiquitin were tested for crystallization behavior and were found to yield crystallization `hit rates' varying by two orders of magnitude. High-resolution structures of three mutants revealed that mutations can exert both promoting and permissive effects on crystallization.

obituaries


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