+Open data
-Basic information
Entry | Database: PDB / ID: 4nv5 | ||||||
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Title | C50A mutant of Synechococcus VKOR, C2 crystal form (dehydrated) | ||||||
Components | VKORC1/thioredoxin domain protein | ||||||
Keywords | OXIDOREDUCTASE / four helix bundle / thioredoxin-like protein / Membrane | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on CH or CH2 groups; With a disulfide as acceptor / quinone binding / oxidoreductase activity / membrane Similarity search - Function | ||||||
Biological species | Synechococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Liu, S. / Cheng, W. / Fowle Grider, R. / Shen, G. / Li, W. | ||||||
Citation | Journal: Nat Commun / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nv5.cif.gz | 205.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nv5.ent.gz | 174.8 KB | Display | PDB format |
PDBx/mmJSON format | 4nv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nv5_validation.pdf.gz | 794.3 KB | Display | wwPDB validaton report |
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Full document | 4nv5_full_validation.pdf.gz | 802.8 KB | Display | |
Data in XML | 4nv5_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 4nv5_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/4nv5 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/4nv5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 31652.775 Da / Num. of mol.: 2 / Mutation: C50A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: JA-2-3B'a(2-13) / Gene: CYB_2278 / Plasmid: PET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2JJF6 #2: Chemical | |
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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: 4.5 Å3/Da / Density % sol: 72.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 12% PEG3350, 0.1M sodium cacodylate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2012 | |||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.79→50 Å / Num. all: 27621 / Num. obs: 27546 / % possible obs: 99.8 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 3.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.2 | |||||||||||||||
Reflection shell | Resolution: 2.79→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→37.8 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.899 / SU B: 18.712 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 77.599 Å2
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Refinement step | Cycle: LAST / Resolution: 2.79→37.8 Å
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Refine LS restraints |
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