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- PDB-3kp8: The thioredoxin-like domain of a VKOR homolog from Synechococcus sp. -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kp8 | ||||||
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Title | The thioredoxin-like domain of a VKOR homolog from Synechococcus sp. | ||||||
![]() | VKORC1/thioredoxin domain protein | ||||||
![]() | OXIDOREDUCTASE / Blood Coagulation / Disulfide formation / Redox partner | ||||||
Function / homology | ![]() Oxidoreductases; Acting on CH or CH2 groups; With a disulfide as acceptor / quinone binding / oxidoreductase activity / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, W. / Schulman, S. / Dutton, R.J. / Boyd, D. / Beckwith, J. / Rapoport, T.A. | ||||||
![]() | ![]() Title: Structure of a bacterial homologue of vitamin K epoxide reductase. Authors: Li, W. / Schulman, S. / Dutton, R.J. / Boyd, D. / Beckwith, J. / Rapoport, T.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 | ![]() | 43.8 KB | Display | ![]() |
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PDB format | ![]() | 34.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.8 KB | Display | ![]() |
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Full document | ![]() | 422.9 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11570.846 Da / Num. of mol.: 1 / Fragment: residues 186-283 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.59 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7.8 Details: 0.6M sodium potassium tartrate, 10% PEG MME 5000, pH 7.8, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.66→50 Å / Num. all: 11831 / Num. obs: 11819 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
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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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.564 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→33.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.704 Å / Total num. of bins used: 20
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