+Open data
-Basic information
Entry | Database: PDB / ID: 3gh9 | ||||||
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Title | Crystal structure of EDTA-treated BdbD (Oxidised) | ||||||
Components | Disulfide bond formation protein D | ||||||
Keywords | OXIDOREDUCTASE / BdbD / DsbA / Trx-like / Competence / Disulfide bond / 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: 1.69 Å | ||||||
Authors | Crow, A. / Lewin, A. / Hederstedt, L. / Le-Brun, N.E. | ||||||
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 | 3gh9.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gh9.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/3gh9 ftp://data.pdbj.org/pub/pdb/validation_reports/gh/3gh9 | HTTPS FTP |
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-Related structure data
Related structure data | 3eu3SC 3eu4C 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) / Strain: 1A1 / Gene: bdbD, BSU33480, yvgV / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: O32218 |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-UNX / |
#4: 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: 1.9 Å3/Da / Density % sol: 35.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25-27 % PEG2000, 100mM Ammonium Acetate, 100mM MES, pH6.5, 100uM EDTA, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798 Å |
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→36.79 Å / Num. all: 18095 / Num. obs: 18095 / % possible obs: 92.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Rsym value: 0.052 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.69→1.78 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.286 / % possible all: 66.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EU3 Resolution: 1.69→36.79 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.992 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.407 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.136 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→36.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.734 Å / Total num. of bins used: 20
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