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- PDB-3fkf: thiol-disulfide oxidoreductase from Bacteroides fragilis NCTC 9343 -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fkf | ||||||
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Title | thiol-disulfide oxidoreductase from Bacteroides fragilis NCTC 9343 | ||||||
![]() | thiol-disulfide oxidoreductase | ||||||
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Function / homology | ![]() Domain of unknown function DUF4369 / Domain of unknown function (DUF4369) / ![]() ![]() ![]() ![]() Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Duke, N.E.C. / Freeman, L. / Tesar, C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.9 KB | Display | ![]() |
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PDB format | ![]() | 102.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | asymmetric unit contains four monomers |
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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.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ACT / ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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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