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Yorodumi- PDB-3fkf: thiol-disulfide oxidoreductase from Bacteroides fragilis NCTC 9343 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fkf | ||||||
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Title | thiol-disulfide oxidoreductase from Bacteroides fragilis NCTC 9343 | ||||||
Components | thiol-disulfide oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / thiol disulfide oxidoreductase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information Domain of unknown function DUF4369 / Domain of unknown function (DUF4369) / Thioredoxin-like / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Duke, N.E.C. / Freeman, L. / Tesar, C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: thiol-disulfide oxidoreductase from Bacteroides fragilis NCTC 9343 Authors: Duke, N.E.C. / Freeman, L. / Tesar, C. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fkf.cif.gz | 123.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fkf.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 3fkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/3fkf ftp://data.pdbj.org/pub/pdb/validation_reports/fk/3fkf | 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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Details | asymmetric unit contains four monomers |
-Components
#1: Protein | Mass: 16825.062 Da / Num. of mol.: 4 / Fragment: residues 203-347 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5L7K1, EC: 1.8.4.7 #2: Chemical | ChemComp-ACT / #3: 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: 3.3 Å3/Da / Density % sol: 62.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.10 M sodium acetate, pH 4.6 2.5 M ammonium sulphate 25% v/v glycerol included in cryoprotectant, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.978828 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Oct 10, 2008 / Details: Si (111) double crystal monochromator, mirror |
Radiation | Monochromator: Si (111) double crystal monochromator, mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978828 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→88.39 Å / Num. all: 45778 / Num. obs: 43234 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 24.364 |
Reflection shell | Resolution: 2.2→2.257 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.029 / % possible all: 90.27 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→88.39 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.656 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.194 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.522 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→88.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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