Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallization and preliminary crystallographic studies of the hypothetical protein BPSL1038 from Burkholderia pseudomallei.

ABSTRACT: Melioidosis is an infectious disease caused by the pathogenic bacterium Burkholderia pseudomallei. Whole-genome sequencing revealed that the B. pseudomallei genome includes 5855 coding DNA sequences (CDSs), of which ?25% encode hypothetical proteins. A pathogen-associated hypothetical protein, BPSL1038, was overexpressed in Escherichia coli, purified and crystallized using vapour-diffusion methods. A BPSL1038 protein crystal that grew using sodium formate as precipitant diffracted to 1.55?Å resolution. It belonged to space group C2221, with unit-cell parameters a = 85.36, b = 115.63, c = 46.73?Å. The calculated Matthews coefficient (VM) suggests that there are two molecules per asymmetric unit, with a solvent content of 48.8%.

SUBMITTER: Shaibullah S

PROVIDER: S-EPMC4259243 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallization and preliminary crystallographic studies of the hypothetical protein BPSL1038 from Burkholderia pseudomallei.

Shaibullah Sofiyah S Mohd-Sharif Nurhikmah N Ho Kok Lian KL Firdaus-Raih Mohd M Nathan Sheila S Mohamed Rahmah R Ng Chyan Leong CL

Acta crystallographica. Section F, Structural biology communications 20141128 Pt 12

Melioidosis is an infectious disease caused by the pathogenic bacterium Burkholderia pseudomallei. Whole-genome sequencing revealed that the B. pseudomallei genome includes 5855 coding DNA sequences (CDSs), of which ∼25% encode hypothetical proteins. A pathogen-associated hypothetical protein, BPSL1038, was overexpressed in Escherichia coli, purified and crystallized using vapour-diffusion methods. A BPSL1038 protein crystal that grew using sodium formate as precipitant diffracted to 1.55 Å reso ...[more]

PMID: 25484229

Similar Datasets

Overexpression, crystallization and preliminary X-ray crystallographic analysis of hypothetical protein SAV0479 from Staphylococcus aureus Mu50.

Project description:SAV0479, a hypothetical protein from the Mu50 strain of methicillin- and vancomycin-resistant Staphylococcus aureus, was selected for structure and function determination as part of a structural genomics project. Here, the cloning, overexpression, purification and crystallization of SAV0479 are reported. Crystals were obtained by the hanging-drop vapour-diffusion method and diffraction data were collected to a resolution of 2.8 Å. The crystals belonged to space group P3(1)21, with unit-cell parameters a = b = 81.48, c = 82.53 Å. Three monomers of SAV0479 are present in each asymmetric unit.

| S-EPMC3614165 | biostudies-literature

Expression, purification, crystallization and preliminary crystallographic studies of Rhagium inquisitor antifreeze protein.

Project description:Antifreeze proteins (AFPs) are a specialized evolutionary adaptation of a variety of bacteria, fish, arthropods and other organisms to inhibit ice-crystal growth for survival in harsh subzero environments. The recently reported novel hyperactive AFP from Rhagium inquisitor (RiAFP) is the second distinct type of AFP in beetles and its structure could reveal important molecular insights into the evolution of AFPs. For this purpose, RiAFP was overexpressed in Escherichia coli, purified and crystallized at 293?K using a combination of 23% PEG 3350 and 0.2?M ammonium sulfate as a precipitant. X-ray diffraction data were collected to 1.3?Å resolution using a synchrotron-radiation source. The crystals belonged to the trigonal space group P3(1)21 (or P3(2)21), with unit-cell parameters a = b = 46.46, c = 193.21?Å.

| S-EPMC3374510 | biostudies-literature

Cloning, expression, purification, crystallization and preliminary crystallographic studies of BceC, a UDP-glucose dehydrogenase from Burkholderia cepacia IST408.

Project description:Bacteria of the Burkholderia cepacia complex (Bcc) have emerged as important opportunistic pathogens, establishing lung infections in immunocompromised or cystic fibrosis patients. Bcc uses polysaccharide-biofilm production in order to evade the host immune response. The biofilm precursor UDP-glucuronic acid is produced by a twofold NAD(+)-dependent oxidation of UDP-glucose. In B. cepacia IST408 this enzymatic reaction is performed by the UDP-glucose dehydrogenase BceC, a 470-residue enzyme, the production and crystallization of which are described here. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1) and contained four molecules in the asymmetric unit. Their crystallographic analysis at 2.09 A resolution and a molecular-replacement study are reported.

| S-EPMC2833033 | biostudies-literature

Protein preparation, crystallization and preliminary crystallographic studies of Bacillus subtilis glycinamide ribonucleotide transformylase.

Project description:Glycinamide ribonucleotide transformylase (GART) catalyzes the transfer of a formyl group from formyl tetrahydrofolate (FTHF) to glycinamide ribonucleotide (GAR), which is an essential step in the de novo synthesis pathway of purines. In Bacillus subtilis, GART is encoded by the gene purN. In order to study the structure and function of B. subtilis GART, the purN gene was amplified, cloned into an expression vector and expressed in soluble form in Escherichia coli. The protein was purified to homogeneity and crystals suitable for X-ray data collection were obtained. These crystals diffracted to 2.5 A resolution and belonged to space group P3(1)21, with unit-cell parameters a = b = 95.5, c = 64.0 A.

| S-EPMC2705641 | biostudies-literature

Crystallization and preliminary crystallographic studies of Helicobacter pylori arginase.

Project description:Helicobacter pylori arginase is an important factor in evasion of the host's immune system and contributes to persistent infection by this bacterium. It is unique in many aspects compared with other arginases: for example, it has optimal activity with Co(2+) as a cofactor rather than Mn(2+) and has strongest activity at acidic pH instead of alkaline pH. In this study, H. pylori arginase was purified and crystallized in complex with Mn(2+) and a diffraction data set was collected to 2.2 Å resolution. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 94.69, b = 102.24, c = 148.61 Å.

| S-EPMC3107149 | biostudies-literature

Crystallization and preliminary crystallographic studies of L30e, a ribosomal protein from Methanocaldococcus jannaschii (MJ1044).

Project description:In view of the biological significance of understanding the ribosomal machinery of both prokaryotes and eukaryotes, the L30e ribosomal protein from Methanocaldococcus jannaschii was cloned, overexpressed, purified and crystallized using the microbatch-under-oil method with the crystallization conditions 40% PEG 400, 0.1 M MES pH 6.0 and 5% PEG 3000 at 291 K. A diffraction-quality crystal (0.20 x 0.20 x 0.35 mm) was obtained that belonged to the primitive tetragonal space group P4(3), with unit-cell parameters a = 46.1, b = 46.1, c = 98.5 A, and diffracted to a resolution of 1.9 A. Preliminary calculations reveal that the asymmetric unit contains two monomers with a Matthews coefficient (V(M)) of 2.16 A(3) Da(-1).

| S-EPMC2374168 | biostudies-literature

Crystallization and preliminary X-ray crystallographic studies of swine CD8?.

Project description:CD8?? homodimers or CD8?? heterodimers form on the T-cell surface, where they are essential as co-receptors for MHC class I molecules in activation of the CTL response. To date, swine have been found to show the highest percentage of lymphocytes with surface expression of CD8?. Crystallographic analysis of swine CD8? (sCD8?) to 1.8?Å resolution revealed that the crystals belonged to space group P3(2)21, with unit-cell parameters a = 80.97, b = 80.97, c = 95.19?Å. The Matthews coefficient and the solvent content were calculated to be 3.23?Å(3)?Da(-1) and 61.89%, respectively. These results may aid further structural and functional analyses of sCD8?.

| S-EPMC3151120 | biostudies-literature

The multiple roles of hypothetical gene BPSS1356 in Burkholderia pseudomallei.

Project description:Burkholderia pseudomallei is an opportunistic pathogen and the causative agent of melioidosis. It is able to adapt to harsh environments and can live intracellularly in its infected hosts. In this study, identification of transcriptional factors that associate with the β' subunit (RpoC) of RNA polymerase was performed. The N-terminal region of this subunit is known to trigger promoter melting when associated with a sigma factor. A pull-down assay using histidine-tagged B. pseudomallei RpoC N-terminal region as bait showed that a hypothetical protein BPSS1356 was one of the proteins bound. This hypothetical protein is conserved in all B. pseudomallei strains and present only in the Burkholderia genus. A BPSS1356 deletion mutant was generated to investigate its biological function. The mutant strain exhibited reduced biofilm formation and a lower cell density during the stationary phase of growth in LB medium. Electron microscopic analysis revealed that the ΔBPSS1356 mutant cells had a shrunken cytoplasm indicative of cell plasmolysis and a rougher surface when compared to the wild type. An RNA microarray result showed that a total of 63 genes were transcriptionally affected by the BPSS1356 deletion with fold change values of higher than 4. The expression of a group of genes encoding membrane located transporters was concurrently down-regulated in ΔBPSS1356 mutant. Amongst the affected genes, the putative ion transportation genes were the most severely suppressed. Deprivation of BPSS1356 also down-regulated the transcriptions of genes for the arginine deiminase system, glycerol metabolism, type III secretion system cluster 2, cytochrome bd oxidase and arsenic resistance. It is therefore obvious that BPSS1356 plays a multiple regulatory roles on many genes.

| S-EPMC4057154 | biostudies-literature

Crystallization and preliminary X-ray crystallographic studies of casein kinase I-like protein from rice.

Project description:Casein kinase I (CKI) is a serine/threonine protein kinase that performs various functions in the cell, such as DNA repair, cell-cycle regulation, cytokinesis, vesicular trafficking, morphogenesis and circadian-rhythm regulation. CKI proteins contain a highly conserved catalytic domain at the N-terminus and a highly diverse regulatory domain that is responsible for substrate specificity at the C-terminus. In this study, CKI from rice (riceCKI) was overexpressed in Escherichia coli with an engineered C-terminal His tag. RiceCKI was then purified to homogeneity and crystallized at 293 K. X-ray diffraction data were collected to a resolution of 2.0 Å from a crystal belonging to the monoclinic space group C2, with unit-cell parameters a = 108.83, b = 69.60, c = 55.85 Å, β = 109.47°. The asymmetric unit was estimated to contain one monomer.

| S-EPMC3310535 | biostudies-literature

Crystallization and preliminary crystallographic studies of the butyrolactone autoregulator receptor protein (BarA) from Streptomyces virginiae.

Project description:The Streptomyces butyrolactone autoregulator receptor protein (BarA) is a DNA-binding protein that regulates the biosynthesis of the antibiotic virginiamycin. In this study, BarA from S. virginiae was overexpressed in Escherichia coli, purified and crystallized. Crystals of purified protein have been grown that diffracted to beyond 3.0 A resolution at 100 K using synchrotron radiation. The protein crystals belonged to the hexagonal space group P6(5)22, with unit-cell parameters a = b = 128.0, c = 286.2 A. With four molecules per asymmetric unit, the crystal volume per unit protein mass (V(M)) was 3.2 A(3) Da(-1) and the solvent content was 62%.

| S-EPMC2882764 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data