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- PDB-6wva: Takifugu rubripes VKOR-like with vitamin K1 epoxide at non-cataly... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wva | |||||||||||||||||||||
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Title | Takifugu rubripes VKOR-like with vitamin K1 epoxide at non-catalytic state | |||||||||||||||||||||
![]() | Vitamin K epoxide reductase-like protein, termini restrained by green fluorescent protein | |||||||||||||||||||||
![]() | MEMBRANE PROTEIN / Vitamin K epoxide Reductase / VKOR / VKOR-like protein / VKORL | |||||||||||||||||||||
Function / homology | ![]() vitamin-K-epoxide reductase (warfarin-sensitive) / vitamin-K-epoxide reductase (warfarin-sensitive) activity / vitamin K metabolic process / quinone binding / bioluminescence / generation of precursor metabolites and energy / endoplasmic reticulum membrane Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Liu, S. / Sukumar, N. / Li, W. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation. Authors: Liu, S. / Li, S. / Shen, G. / Sukumar, N. / Krezel, A.M. / Li, W. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.2 KB | Display | ![]() |
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PDB format | ![]() | 143.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.4 KB | Display | ![]() |
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Full document | ![]() | 432.5 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wv3C ![]() 6wv4C ![]() 6wv5C ![]() 6wv6C ![]() 6wv7C ![]() 6wv8C ![]() 6wv9C ![]() 6wvbC ![]() 6wvhC ![]() 6wviC ![]() 2b3pS S: Starting model for refinement C: citing same article ( |
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Similar 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
#1: Protein | Mass: 46782.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Gene: GFP, Vkorc1l1 / Production host: ![]() References: UniProt: P42212, UniProt: Q6TEK8, vitamin-K-epoxide reductase (warfarin-sensitive) |
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Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.86 % |
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Crystal grow | Temperature: 295 K / Method: lipidic cubic phase / pH: 7.5 Details: 42% PEG 400, 50 mM ammonium formate, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 19, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→50 Å / Num. obs: 10574 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 85.44 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.075 / Rrim(I) all: 0.147 / Χ2: 1.207 / Net I/σ(I): 7.5 / Num. measured all: 38881 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2B3P Resolution: 3.35→42.32 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 214.22 Å2 / Biso mean: 95.2142 Å2 / Biso min: 29.1 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.35→42.32 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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