+Open data
-Basic information
Entry | Database: PDB / ID: 3eu4 | ||||||
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Title | Crystal Structure of BdbD from Bacillus subtilis (oxidised) | ||||||
Components | BdbD | ||||||
Keywords | OXIDOREDUCTASE / bdbdb / oxidised / disulfide bridge / partially broken disulfide / Competence / Redox-active center | ||||||
Function / homology | Function and homology information establishment of competence for transformation / oxidoreductase activity / membrane raft / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Crow, A. / Moller, M.C. / Hederstedt, L. / Le Brun, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal Structure and Biophysical Properties of Bacillus subtilis BdbD: AN OXIDIZING THIOL:DISULFIDE OXIDOREDUCTASE CONTAINING A NOVEL METAL SITE Authors: Crow, A. / Lewin, A. / Hecht, O. / Carlsson Moller, M. / Moore, G.R. / Hederstedt, L. / Le Brun, N.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eu4.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eu4.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 3eu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eu4_validation.pdf.gz | 429 KB | Display | wwPDB validaton report |
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Full document | 3eu4_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | 3eu4_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 3eu4_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/3eu4 ftp://data.pdbj.org/pub/pdb/validation_reports/eu/3eu4 | HTTPS FTP |
-Related structure data
Related structure data | 3eu3SC 3gh9C 3ghaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23043.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: bdbD, BSU33480, yvgV / Plasmid: pET21a-based / Production host: Escherichia coli (E. coli) / References: UniProt: O32218 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.45 % |
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Crystal grow | pH: 6.5 Details: 25% PEG2000, 0.1M ammonium acetate, 0.1M MES, pH6.5, cryo-protected with 20% Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→52.2 Å / Num. all: 7198 / Num. obs: 7198 / % possible obs: 94.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rsym value: 0.046 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 7.3 / Rsym value: 0.119 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EU3 Resolution: 2.3→52.2 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.95 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.758 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, THE DEPOSITORS ASSERT THAT NO BACKBONE TORSION (RAMACHANDRAN PLOT) OUTLIERS ARE PRESENT AS JUDGED BY THE STANDARDS EMPLOYED BY MOLPROBITY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, THE DEPOSITORS ASSERT THAT NO BACKBONE TORSION (RAMACHANDRAN PLOT) OUTLIERS ARE PRESENT AS JUDGED BY THE STANDARDS EMPLOYED BY MOLPROBITY (V3.15), OR PROCHECK (V3.4.4).
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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: 19.203 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→52.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.361 Å / Total num. of bins used: 20
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