issue contents

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983

November 2004 issue

Highlighted illustration

Cover illustration: Electron-density map of the protein histone methyltransferase SET 7/9 contoured at 1[sigma] calculated from the peak-wavelength Se-SAD data. Phases were derived by OASIS-2004 and improved by DM. The data were provided by Drs S. J. Gamblin and B. Xiao. The protein was originally determined by J. R. Wilson et al. [(2002), Cell, 111, 105-115] using the MAD method. The refined structure model from the original authors is superimposed on the electron-density map (p. 1987).

research papers


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The structure of human NADH-cytochrome b5 reductase at 1.75 Å resolution is the same as that of rat NADH-cytochrome b5 reductase except for a large main-chain shift caused by a Pro268Thr substitution. Five mutations seem to be related to cytochrome b5.

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Peptidic molecules in the CSD are searched for nests, three-amino-acid residue anion-binding motifs found commonly in proteins. 37 are found. One, in the antibiotic vancomycin, has the function of binding the C-terminal carboxylate group of the bacterial cell wall precursor peptide.

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In the course of investigating the complex of HIV-1 protease with a novel phenylnorstatine inhibitor, two inhibitor molecules were found to be bound to the enzyme, one in a non-productive mode. The contribution of the contacts of this inhibitor molecule at the protein interface to the crystal quality is discussed.


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The effects of radiation damage on iodinated thaumatin crystals have been analysed. It was shown that combination of the anomalous and isomorphous signals in the form of RIPAS (radiation-damage-induced phasing with anomalous scattering) is beneficial for both locating the substructure and subsequent phasing.

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The crystal structure of E. coli argininosuccinate lyase has been determined at 2.44 Å resolution; in this structure, one active site, complexed with two phosphate ions, adopts the closed conformation.

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The D,L-alternating peptide H-(L-Tyr-D-Tyr)4-L-Lys-OH adopts a gramicidin A-like structure. Fragment-search strategies aiming to exploit the high-resolution data available (1.3 Å) were tested.

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De novo crystallization of a ternary complex composed of Y. pestis virulence factors YopN, SycN, and YscB could only be achieved after reductive methylation of surface-exposed lysine residues. This case study also demonstrates that the modification can be safely employed on multiprotein complexes and selenomethionine-substituted samples, underscoring its general potential as a crystallization tool, even in high-throughput settings.

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The influence of the error term on direct-method SAD phasing is examined. A method for automatically tuning the scaling factor in the error term is proposed.

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Structure fragments resulting from automatic model building based on initial direct-method SAD phasing are fed back to the direct-method probability formula in order to strengthen the phasing power and to benefit the automation of structure solution of proteins.

structural genomics papers


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The X-ray crystallographic structure of T. thermophilis RraA has been solved to 2.3 Å resolution.

crystallization papers


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The last step of the shikimate pathway is catalyzed by chorismate synthase (CS). Optimization of crystallization trials allowed the crystallization of homogeneous recombinant CS from M. tuberculosis.

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A thermostable homing endonuclease from Thermoproteus sp. IC-061 has been crystallized. The crystals diffract to 2.7 Å resolution.

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The full-length single-stranded DNA-binding protein (SSB) from the extremophile A. aeolicus has been expressed in Escherichia coli, purified and crystallized and initial X-ray data have been obtained.

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Preliminary crystallographic data of the fusion core of the spike protein of the murine coronavirus mouse hepatitis virus have been obtained.


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Human liver regucalcin, consisting of 299 amino-acid residues, has been overexpressed in Escherichia coli, purified and crystallized by the vapour-diffusion method in the presence of polyethylene glycol 4000 as a precipitant.

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VCBP3, an immunoglobulin-like protein from the protochordate B. floridae with the characteristics of a `primordial' antigen receptor, has been crystallized and complete native data sets have been collected to 2.4 Å resolution. Isomorphous crystals from two different crystallization conditions are consistent with space groups P3121 and P3221, with unit-cell parameters a = b = 58.99, c = 79.21 Å, α = β = 90, γ = 120°.

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The expression, purification, crystallization and preliminary X-ray diffraction studies of the protein TraF from the E. coli F plasmid are reported.

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Vacuolar sorting receptor (VSR) proteins target ligands to the lytic vacuole in a sequence-specific manner. Purification from Drospohila S2 cells, crystallization and preliminary X-ray diffraction studies of Arabidopsis thalia VSR, AtBP80b, have been carried out.

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Glutamate racemase from B. subtilis has been crystallized in the presence of L-glutamate in a form suitable for structure determination.

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Aall-A and Aall-B, two novel heterodimeric snake-venom C-type lectin-like proteins (sv-CLPs), were purified from the venom of D. acutus from Anhui, China, and crystallized.

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The M. oreades agglutinin (MOA) has been crystallized. Crystals diffract anisotropically to 2.5 Å resolution. A complete X-ray data set has been obtained to 3.0 Å resolution.

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The ectoplasmic region of apical membrane antigen 1 from P. vivax has been expressed and crystallized in two crystal forms. Phases have been obtained by the MAD technique using a Pt derivative.

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The water-forming NADH oxidase from L. sanfranciscensis has been crystallized in space group P212121 and X-ray diffraction data to 1.85 Å resolution have been collected.

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The retinoic acid receptor β ligand-binding domain has been expressed and crystallized bound to a synthetic retinoid (TTNPB) with or without a co-activator peptide (SRC-1).

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Crystals of infestin 4, a factor XIIa Kazal-type inhibitor from T. infestans, diffracted to 1.8 Å resolution and belong to the orthorhombic space group P212121, with unit-cell parameters a = 25.89, b = 45.64, c = 57.41 Å.

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Crystals of the complex between the P. vivax sexual stage 25 kDa protein Pvs25 and a malaria transmission-blocking Fab diffract X-rays to 3.5 Å. Two complex molecules are predicted per asymmetric unit.

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Mexicain, a cysteine protease, has been extracted from the latex of the tropical plant Pileusmexicanus, purified and crystallized. The crystals belong to the space group P21 and they diffract X-rays to 2.1 Å resolution.

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Pyridoxal 4-dehydrogenase from Microbacterium luteolum has been crystallized by the sitting-drop vapour-diffusion method. The crystals were monoclinic and belonged to space group C2, with unit-cell parameters a = 107.0, b = 56.7, c = 130.2 Å, β = 103.6°. Diffraction data were collected from a single crystal to 2.0 Å.

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The catalytic domain of one of three sialidases encoded by the C. perfringens genome has been subcloned and crystallized. The diffraction of this 50 kDa domain to beyond 0.92 Å will allow detailed mechanistic enzymology of this enzyme superfamily.


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Sulfite dehydrogenase from S. novella has been crystallized. Crystals diffract to at least 1.8 Å resolution and belong to space group P21212, with unit-cell parameters a = 97.5, b = 92.5, c = 55.9 Å.

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Crystals of wild-type and two mutants of apo tryptophanase from E. coli belong to space group F222 and diffract to 1.9 Å.

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A protein disulfide oxidoreductase from A. aeolicus has been crystallized for the first time. Crystals belong to space group R32 and diffract to 2.4 Å resolution.

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The hook is a short, highly curved segment of the bacterial flagellum, working as a universal joint, and is a helical assembly of about 120 copies of a single protein FlgE (42 kDa). The expression, purification, crystallization and diffraction data collection of a 31KDa fragment of FlgE, which is otherwise extremely difficult to crystallize because of its strong polymerization ability, are reported.

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Chitosanase from Bacillus sp. strain K17, which belongs to glycoside hydrolase family 8 and exhibits subclass II specificity, has been crystallized in two forms corresponding to the active and inactive states.

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Mouse autocrine motility factor has been crystallized in the absence and presence of carbohydrate phosphate inhibitors. Diffraction data have been collected using synchrotron radiation.

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A stable domain of the vesicular stomatitis virus phosphoprotein was crystallized. The crystals belonged to space group P41212 or P43212, with unit-cell parameters a = b = 74.50, c = 156.84 Å, and diffraction data were collected to 2.75 Å.

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The production and crystallization of recombinant E. coli glutamate-5-kinase, the enzyme that catalyzes the first and feedback-controlled step of proline biosynthesis and a member of the amino-acid kinase enzyme family, is reported. In addition to the catalytic machinery, this enzyme contains a PUA putative RNA-binding domain that endows it with gene-expression regulatory properties.

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Crystals of the catalytic fragment of human 2′,3′-cyclic nucleotide 3′-phosphodiesterase (hCNP-CF) have been obtained. The crystals diffract X-rays to 1.8 Å resolution.

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PEX1 N-terminal domain crystals have been prepared. The crystals belong to space group P31 or P32, with unit-cell parameters a = b = 63.5, c = 33.5 Å, and contain one protein molecule per crystallographic asymmetric unit. An intensity data set was collected to a resolution of 2.05 Å.

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Purification, identification and preliminary crystallographic studies on an allergy-related protein from V. unguiculata seeds were carried out. The protein, crystals of which diffract to about 2.1 Å resolution, does not indicate homology with any protein with known crystal structure.


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A proteolyzed form of horse PLRP2 has been crystallized by the hanging-drop vapour-diffusion method in complex with DDAO. Native data have been collected to 2.9 Å resolution.

short communications


addenda and errata


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