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Yorodumi- PDB-2f9s: 2nd Crystal Structure Of A Soluble Domain Of ResA In The Oxidised Form -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f9s | ||||||
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Title | 2nd Crystal Structure Of A Soluble Domain Of ResA In The Oxidised Form | ||||||
Components | Thiol-disulfide oxidoreductase resA | ||||||
Keywords | OXIDOREDUCTASE / Thioredoxin-like protein | ||||||
Function / homology | Function and homology information cytochrome complex assembly / disulfide oxidoreductase activity / antioxidant activity / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.401 Å | ||||||
Authors | Colbert, C.L. / Wu, Q. / Erbel, P.J.A. / Gardner, K.H. / Deisenhofer, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: Mechanism of substrate specificity in Bacillus subtilis ResA, a thioredoxin-like protein involved in cytochrome c maturation Authors: Colbert, C.L. / Wu, Q. / Erbel, P.J.A. / Gardner, K.H. / Deisenhofer, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f9s.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f9s.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 2f9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f9s_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 2f9s_full_validation.pdf.gz | 442.7 KB | Display | |
Data in XML | 2f9s_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 2f9s_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/2f9s ftp://data.pdbj.org/pub/pdb/validation_reports/f9/2f9s | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | monomer is the biological assembly |
-Components
#1: Protein | Mass: 17247.762 Da / Num. of mol.: 2 / Fragment: Soluble extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: resa / Plasmid: pET21 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P35160 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 100mM Tris HCl; 2.2M Ammonium Sulfate; 2mM L-Cysteine, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: SBC / Detector: CCD / Date: Nov 11, 2003 | ||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.401→52.7 Å / Num. all: 69296 / Num. obs: 69296 / % possible obs: 0.986 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rsym value: 0.051 / Net I/σ(I): 17.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.401→1.45 Å / Mean I/σ(I) obs: 1.5 / Rsym value: 0.353 / % possible all: 0.959 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.401→52.7 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.708 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.048 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.087 Å2
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Refine analyze | Luzzati sigma a obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.401→52.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.437 Å / Total num. of bins used: 20 /
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