Publishing structural genomics results: the JCSG Special Issue

Structural analysis of Bacillus pumilus phenolic acid de­carboxylase, a lipocalin-fold enzyme

The crystal structure of phenolic acid decarboxylase from B. pumilus strain UI-670 has been determined and refined at 1.69 Å resolution. The enzyme is a dimer, with each subunit adopting a β-barrel structure belonging to the lipocalin fold.

Unliganded structure of human bis­phosphoglycerate mutase reveals side-chain movements induced by ligand binding

The X-ray structure of human bisphosphoglycerate mutase was solved to 1.94 Å resolution and a bisphosphoglycerate mutase–citrate model was built to explore enzyme–inhibitor interactions.

The homodimeric GBS1074 from Streptococcus agalactiae

The homodimeric nature of the ESAT-6 homologue GBS1074 and the potential for fibre-like assemblies are revealed by the 2 Å resolution crystal structure.

Structure of Plasmodium falciparum ADP-ribosylation factor 1

The crystal structure of GDP-bound ARF1 GTPase of Plasmodium falciparum has been determined at 2.5 Å resolution and compared with the structures of mammalian ARF1s.

Structure of di­hydroorotase from Bacillus anthracis at 2.6 Å resolution

A comparison is made between the structures of dihydroorotase from four different organisms, including B. anthracis dihydroorotase, and reveals substantial variations in the active site, dimer interface and overall tertiary structure.

Structure of the Francisella tularensis enoyl-acyl carrier protein reductase (FabI) in complex with NAD⁺ and triclosan

Structure of the ternary complex of F. tularensis enoyl-acyl carrier protein reductase reveals the structure of the substrate binding loop whose electron density was missing in an earlier structure, and demonstrates a shift in the position of the NAD⁺ cofactor.

Crystallization and preliminary X-ray diffraction analysis of the fructo­furanosidase from Xanthophyllomyces dendrorhous

The invertase from X. dendrorhous has been purified, deglycosylated and crystallized and diffraction data have been collected to 2.3 Å resolution.

Crystallization and preliminary X-ray structural analysis of nucleoside triphosphate hydrolases from Neospora caninum and Toxoplasma gondii

Recombinant nucleoside triphosphate hydrolases from N. caninum and T. gondii have been purified and crystallized for X-ray structure analysis.

Crystallization and preliminary X-ray analysis of a marine diatom-infecting single-stranded RNA virus

A marine diatom-infecting virus was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to space group P6₃22, with unit-cell parameters a = b = 448.67, c = 309.76 Å, and diffracted to 4.0 Å resolution.

Crystallization and diffraction analysis of the serpin IRS-2 from the hard tick Ixodes ricinus

Cleavage of the serpin IRS-2 from the hard tick I. ricinus by contaminating proteolytic activity mimicked the specific processing of the serpin by its target protease and resulted in a more stable form of the serpin which produced crystals that diffracted to 1.8 Å resolution.

Crystallization and preliminary X-ray diffraction analysis of red clover necrotic mosaic virus

Virions of red clover necrotic mosaic virus have been purified and crystallized. The space group was determined to be I23, with unit-cell parameter a = 377.8 Å. The crystals diffracted to 4 Å resolution.

Production, crystallization and preliminary X-ray analysis of CTP:inositol-1-phosphate cytidylyltransferase from Archaeoglobus fulgidus

The expression, purification, crystallization and preliminary X-ray diffraction analysis of CTP:inositol-1-phosphate cytidylyltransferase from A. fulgidus is described.

Purification, crystallization and preliminary X-ray analysis of a fusion of the LIM domains of LMO2 and the LID domain of Ldb1

The crystallization and preliminary diffraction analysis of LMO2 in complex with the LID domain of Ldb1 is described. A three-wavelength anomalous dispersion (MAD) data set was collected to 2.8 Å resolution at the Zn K edge.

Purification, crystallization and preliminary X-ray analysis of the dissimilatory sulfite reductase from Desulfovibrio vulgaris Miyazaki F

Dissimilatory sulfite reductase from Desulfovibrio vulgaris Miyazaki F was purified and crystallized. The crystals belonged to the space group P4₁2₁2 and diffracted to 3.7 Å resolution.

Expression, purification, crystallization and preliminary crystallographic analysis of PA3885 (TpbA) from Pseudomonas aeruginosa PAO1

PA3885 (TpbA), a tyrosine phosphatase, may function as a balancing factor between biofilm formation and motility in the opportunistic pathogen P. aeruginosa. Here, the expression, purification, crystallization and preliminary crystallographic analysis of PA3885 from P. aeruginosa PAO1 are reported.

Crystallization and preliminary X-ray analysis of dimeric and trimeric cytochromes c from horse heart

Dimeric and trimeric cytochromes c were purified and crystallized. X-ray diffraction data sets were collected to resolutions of 2.2 and 2.1 Å, respectively.

Crystallization and preliminary X-ray diffraction studies of a terminal oxygenase of carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1

The terminal oxygenase component (Oxy) of carbazole 1,9a-dioxygenase (CARDO) catalyzes dihydroxylation of the aromatic ring. The Oxy of CARDO from Novosphingobium sp. KA1 was crystallized and the crystals diffracted to a resolution of 2.1 Å.

Purification, crystallization and preliminary X-ray crystallographic analysis of 23S RNA m²G2445 methyltransferase RlmL from Escherichia coli

RlmL, a 23S rRNA m2G2445 methyltransferase from Escherichia coli, was expressed, purified and crystallized, and crystals diffracted to 2.2 Å.

Expression, purification, crystallization and preliminary X-ray analysis of a truncated soluble domain of human glioma pathogenesis-related protein 1

The expression, purification, crystallization and preliminary X-ray diffraction analysis of the soluble domain of human glioma pathogenesis-related protein 1 (sGLIPR1) is presented.

A preliminary X-ray study of human nucleoside diphosphate kinase A under oxidative conditions

In this study, human NDPK-A has been crystallized under oxidative conditions and X-ray data have been collected to 2.80 Å resolution using synchrotron radiation.

Preliminary crystallography confirms that the archaeal DNA-binding and tryptophan-sensing regulator TrpY is a dimer

TrpY was crystallized using the hanging-drop method with ammonium sulfate as the precipitant. The crystals belonged to the tetragonal space group P4₃2₁2 or P4₁2₁2, with unit-cell parameters a = b = 87, c = 147 Å, and diffracted to 2.9 Å resolution.

Crystallization and initial X-ray diffraction analysis of the tellurite-resistance S-adenosyl-L-me­thionine transferase protein TehB from Escherichia coli

The E. coli TehB methyltransferase has been purified and crystallized in the presence of SAM and sinefungin. Diffraction data have been collected to 1.9 Å resolution for both complexes.

Purification, crystallization and preliminary X-ray analysis of 3-hy­droxy-3-methylglutaryl-coenzyme A reductase of Streptococcus pneumoniae

3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase of Streptococcus pneumoniae has been cloned, overexpressed and purified to homogeneity using Ni–NTA affinity chromatography. Crystals were obtained using the hanging-drop vapour-diffusion method.

Purification, crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding region of the Streptococcus gordonii adhesin GspB

The carbohydrate-binding region of GspB from S. gordonii strain M99 was crystallized in space group P2₁2₁2₁ and data were collected to 1.3 Å resolution.

Crystallization and preliminary X-ray analysis of a novel dye-linked L-proline de­hydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix

A novel dye-linked L-proline dehydrogenase from a hyperthermophilic archaeon was successfully isolated and crystallized.

Cloning, expression, purification and crystallization of di­hydrodipicolinate synthase from the psychrophile Shewanella benthica

Dihydrodipicolinate synthase (DHDPS) is an essential oligomeric enzyme of interest to antibiotic discovery research and studies probing the importance of quaternary structure to protein function, stability and dynamics. The cloning, expression, purification and crystallization of DHDPS from the psychrophilic (cold-dwelling) bacterium Shewanella benthica are described.

Expression, purification, crystallization and preliminary crystallographic studies of cis-bi­phenyl-2,3-di­hydrodiol-2,3-de­hydrogenase from Pandoraea pnomenusa B-356

A 29 kDa cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from P. pnomenusa B-356 was purified, crystallized and characterized by the X-ray diffraction method.

Crystallization and preliminary X-ray diffraction analysis of human cytosolic seryl-tRNA synthetase

The crystallization and preliminary X-ray analysis of recombinant human cytosolic seryl-tRNA synthetase (hsSerRS) is reported. Diffraction data were collected to 3.13 Å resolution and the hsSerRS crystal structure is currently being refined and analyzed.

Cloning, expression, purification, crystallization and preliminary crystallographic analysis of Rv1698, an outer membrane channel protein from Mycobacterium tuberculosis

The outer membrane channel protein Rv1698 from M. tuberculosis has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.5 Å resolution.

Crystallization and X-ray diffraction studies of DNA-free and DNA-bound forms of EcoO109I DNA methyltransferase

The crystallization and diffraction studies of EcoO109I DNA methyltransferase are described.

Crystallization and preliminary crystallographic analysis of Achromobacter protease I mutants

Achromobacter protease I (API), a lysine-specific serine protease, exhibits an order of magnitude higher activity than bovine trypsin, while its optimum pH is in the alkaline region at approximately pH 9. Two single point mutants have previously been reported to improve the optimum pH range; determination of the tertiary structure of API mutants would help in understanding these mechanisms.

Crystallization and preliminary crystallographic analysis of the type III secretion translocator chaperone SicA from Salmonella enterica

The SicA protein from the motile enterobacterium S. enterica serovar Typhimurium was overexpressed and crystallized. The crystals diffracted to 3.5 Å resolution and belonged to the monoclinic space group C2, with unit-cell parameters a = 180.4, b = 94.1, c = 131.8 Å, β = 130.9°. The crystallographic asymmetric unit may contain as many as eight molecules, suggesting a unique oligomerization state.

Crystallization, preliminary X-ray diffraction studies and Raman microscopy of the major haemoglobin from the sub-Antarctic fish Eleginops maclovinus in the carbomon­oxy form

The major haemoglobin of the sub-Antarctic fish E. maclovinus is the first sub-Antarctic fish haemoglobin to be crystallized and its structural characterization will shed light on the molecular mechanisms of cold adaptation and the role of the Root effect in fish.

Crystallization of purple nitrous oxide reductase from Pseudomonas stutzeri

The physiologically active form of nitrous oxide reductase was isolated and crystallized under strict exclusion of dioxygen and diffraction data were collected from crystals belonging to two different space groups.

Crystallization and preliminary X-ray diffraction analysis of the protease from Southampton norovirus complexed with a Michael acceptor inhibitor

The crystallization of the recombinant protease from Southampton norovirus is described. Whilst the native crystals were found to diffract only to medium resolution (2.9 Å), cocrystals with a designed covalently bound inhibitor diffracted X-rays to 1.7 Å resolution.

Crystallization and preliminary X-ray analysis of Na-ASP-1, a multi-domain pathogenesis-related-1 protein from the human hookworm parasite Necator americanus. Corrigendum

A correction to the paper by Asojo et al. [(2005), Acta Cryst. F61, 391–394].