issue contents

Journal logoSTRUCTURAL BIOLOGY
COMMUNICATIONS
ISSN: 2053-230X

June 2014 issue

Highlighted illustration

Cover illustration: GlmU (N-acetylglucosamine-1-phosphate uridyltransferase) bound to three magnesium ions and ATP (Vithani et al., p. 703).

IYCr crystallization series


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Automation is the response to overcoming the crystallization bottleneck in biological crystallography. This review provides a summary of the current methods and technologies applied in automated platforms for the setup of initial and follow-up crystallization experiments.

structural communications


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The crystal structure of the His170Tyr mutant of thermostable pNPPase from Geobacillus stearothermophilus has been determined at 2.0 Å resolution, with Na+ and SO42− bound in the active site, showing a half-closed cap conformation.

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The structure of GlmU for M. tuberculosis is determined in complex with GlcNAc-1-P, a non-canonical nucleotide substrate – ATP and three Mg2+ ions. ATP is bound at the active site in an unusual conformation.


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High-resolution crystal structures of cyclophilin D in complex with PEG 400 in primitive orthorhombic and primitive tetragonal forms are reported.

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A 2.9 Å resolution crystal structure of transportin SR2 (TRN-SR2), a β-karyopherin involved in the nuclear import of HIV, in complex with the small GTPase Ran was determined. GTP-loaded Ran binds to the N-terminal part of the α-helical solenoid-like fold of TRN-SR2.

crystallization communications


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CsyB from A. oryzae has been overexpressed in E. coli, purified and crystallized. Diffraction data have been collected to a resolution of 1.71 Å.

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AntE, a crotonyl-CoA carboxylase/reductase involved in the biosynthesis of antimycin A from Streptomyces sp. NRRL 2288, has been overexpressed in E. coli, purified and crystallized. Diffraction data have been collected to a resolution of 2.29 Å.

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Native and selenomethionine-labelled PotA proteins from T. maritima were expressed, purified and crystallized, and X-ray diffraction data were collected to 2.7 Å resolution.

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The crystallization and preliminary X-ray diffraction analysis of a complex between bovine CD8αα and the bovine MHC class I molecule (BoLA-I, BoLA-2*02201) at 1.7 Å resolution revealed that the crystal belonged to space group P21, with unit-cell parameters a = 53.9, b = 103.8, c = 61.8 Å, α = γ = 90, β = 96°, and contained one complex in the asymmetric unit. The Matthews coefficient and solvent content were calculated as 2.41 Å3 Da−1 and 48.9%, respectively.

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Carboxyl-terminal region 4 of SigR (σR4) from S. coelicolor A3(2) has been crystallized (space group P43212, unit-cell parameters a = b = 42.14, c = 102.02 Å). Diffraction data were collected to 2.60 Å resolution using synchrotron radiation.

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The cysQ gene from Mycobacterium tuberculosis was cloned and the expressed protein, a 3′-phosphoadenosine-5′'-phosphatase, was purified and crystallized. X-ray diffraction data were collected to 1.7 Å resolution.

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A family 46 carbohydrate-binding module (BhCBM46) from B. halodurans endo-β-1,4-glucanase B (CelB) was purified and crystallized, and data were collected for the native form and a selenomethionine derivative to 2.46 and 2.3 Å resolution, respectively.

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Mutations in the defective pollen wall (dpw) gene cause abnormalities in the development of anthers and pollen grains of O. sativa. In this study, DPWΔ80 protein was cloned and expressed in E. coli. Purified DPWΔ80 in complex with its cofactor NADPH formed crystals. Diffraction data were collected to 3.4 Å resolution.

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The ArsI C-As lyase from Thermomonospora curvata was expressed, purified and crystallized. The crystals diffracted to 1.46 Å and belong to space group P43212 or its enantiomer P41212.

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The minimal Uba5 fragment necessary for high-efficiency activation of Ufm1 was identified, expressed, purified and crystallized, and diffraction data were collected to 2.95 Å resolution.

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The full-length proximal thread matrix protein 1 (PTMP1) from M. galloprovincialis was recombinantly produced, purified and crystallized. Diffraction analysis of the obtained crystals showed that they belonged to space group P21 and diffracted to 1.95 Å resolution.

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The crystallization and preliminary X-ray diffraction analysis of H. jecorina Cel7A in two new crystalline forms are reported.

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A ferredoxin/flavodoxin-NADP(H) oxidoreductase (FNR) from B. cereus (Bc0385) belonging to the thioredoxin reductase-like class of FNRs has been cloned, overexpressed, purified and crystallized. Diffraction data have been collected to 2.5 Å resolution.

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A dehydroascorbate reductase (DHAR) from rice (O. sativa L. japonica) was overexpressed, purified and crystallized. The crystals belonged to space group P21 and a complete native data set was obtained to a resolution of 1.9 Å.

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The crystallization of HER3-ecd in complex with a novel anti-HER3 antibody 9E12 was carried out and data were collected to 2.1 Å.

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A bacterial Asn-transamidosome composed of two GatCABs, one AspRS dimer and two tRNAAsns from P. aeruginosa was crystallized and the crystal diffracted to 3.73 Å resolution.

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The extracellular catalytic domain of mouse Enpp6 was expressed in mammalian cells, purified and crystallized. An X-ray diffraction data set was collected to 1.8 Å resolution.

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(R)-Carbonyl reductase from C. parapsilosis was crystallized in the presence of its cofactor NAD+. Preliminary X-ray diffration analysis was performed.

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Sm21.7, an S. mansoni tegumental protein that reduces the worm burden in a murine immunization model, was cloned, expressed and purified. Its C-terminal domain was crystallized and a native crystal diffracted to 2.05 Å resolution. An NaI derivative used for SIRAS phasing diffracted to 1.95 Å resolution.

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The LH2 complex from the purple photosynthetic bacterium M. purpuratum was purified and was crystallized using the sitting-drop vapour-diffusion method. X-ray diffraction data collection from the crystals revealed that the complex is an octamer.

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A 2.0 Å resolution neutron data set and a 1.6 Å resolution X-ray data set were collected for joint X-ray/neutron refinement of the ecDHFR–folate–NADP+ complex in order to study the reaction mechanism of dihydrofolate reductase.

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This paper describes the growth of large crystals of and the collection of neutron time-of-flight data from an H/D-exchanged crystal of the bacterial phosphate-binding protein PBP.

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The enzyme 2,4′-dihydroxyacetophenone dioxygenase (or DAD) catalyses the conversion of 2,4′-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid with the incorporation of molecular oxygen. By the use of limited proteolysis, the DAD enzyme from Alcaligenes sp. 4HAP has been crystallized in a form that diffracts synchrotron radiation to a resolution of 2.2 Å.

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A Fic protein from the pathogenic bacterium C. difficile R20291 has been cloned, expressed and purified. The purified protein was characterized by mass spectrometry and circular-dichroism spectroscopy, and was crystallized. In addition, a diffraction data set was collected and processed to 1.68 Å resolution.

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The crystallization and preliminary X-ray crystallographic analysis of a plant PPO exhibiting monophenolase activity from J. regia (jrPPO1) in its active form (Asp101–Arg445) are reported.
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