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Open data
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Basic information
Entry | Database: PDB / ID: 4nv6 | ||||||
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Title | C212A mutant of Synechococcus VKOR | ||||||
![]() | VKORC1/thioredoxin domain protein | ||||||
![]() | OXIDOREDUCTASE / four helix bundle / thioredoxin-like protein / Membrane | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Liu, S. / Cheng, W. / Fowle Grider, R. / Shen, G. / Li, W. | ||||||
![]() | ![]() Title: Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer. Authors: Liu, S. / Cheng, W. / Fowle Grider, R. / Shen, G. / 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 | ![]() | 110.5 KB | Display | ![]() |
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PDB format | ![]() | 91.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 568.2 KB | Display | ![]() |
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Full document | ![]() | 570.5 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nv2C ![]() 4nv5C ![]() 4nsz 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: 31652.775 Da / Num. of mol.: 1 / Mutation: C212A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-U10 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density % sol: 79.85 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: A 20mg/ml protein solution was mixed overnight with 15mg/ml DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine), and 0.5% DDM. This mixture was crystallized with a buffer containing 11% PEG1500, ...Details: A 20mg/ml protein solution was mixed overnight with 15mg/ml DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine), and 0.5% DDM. This mixture was crystallized with a buffer containing 11% PEG1500, 8% glycerol, 5% ethanol, 0.1M MgCl2, 0.1M NaCl, and 0.1M sodium cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 4.19→50 Å / Num. all: 5743 / Num. obs: 5732 / % possible obs: 99.9 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 4.19→4.27 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 2.3 / Num. unique all: 282 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.19→45.683 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 23.4539 Å / Origin y: -48.6099 Å / Origin z: 2.5404 Å
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Refinement TLS group | Selection details: ALL |