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Yorodumi- PDB-2fhq: Crystal Structure of General Stress Protein from Bacteroides thet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fhq | ||||||
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Title | Crystal Structure of General Stress Protein from Bacteroides thetaiotaomicron | ||||||
Components | putative general stress protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta structure / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information General stress protein, FMN-binding split barrel domain / Pyridoxamine 5'-phosphate oxidase like / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å | ||||||
Authors | Kim, Y. / Hatzos, C. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published / Year: 2006 Title: Crystal Structure of General Stress Protein from Bacteroides thetaiotaomicron Authors: Kim, Y. / Hatzos, C. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fhq.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fhq.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 2fhq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/2fhq ftp://data.pdbj.org/pub/pdb/validation_reports/fh/2fhq | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15934.468 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: GenBank: 29338736, UniProt: Q8A7U5*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.86 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.20M magnesium chloride, 0.1M bis-tris pH 5.5, 25%w/v polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97922 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2005 / Details: mirrors |
Radiation | Monochromator: double crystal monochrmoator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→50 Å / Num. all: 20346 / Num. obs: 19822 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.88→1.95 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.34 / Num. unique all: 1184 / % possible all: 53.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.87→26.89 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.065 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.104 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→26.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.874→1.922 Å / Total num. of bins used: 20
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