- PDB-4nv2: C50A mutant of Synechococcus VKOR, C2221 crystal form -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4nv2
Title
C50A mutant of Synechococcus VKOR, C2221 crystal form
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
VKOR domain / Vitamin K epoxide reductase-like VKOR/LOT1 / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / de novo design (two linked rop proteins) / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...VKOR domain / Vitamin K epoxide reductase-like VKOR/LOT1 / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / de novo design (two linked rop proteins) / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 3.6→3.66 Å / Redundancy: 6 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 1.6 / % possible all: 95.1
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Processing
Software
Name
Version
Classification
HKL-2000
datacollection
PARROT
phasing
REFMAC
5.7.0029
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.61→31.67 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.834 / SU B: 79.561 / SU ML: 0.529 / Cross valid method: THROUGHOUT / ESU R Free: 0.681 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.32224
719
9.9 %
RANDOM
Rwork
0.27411
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obs
0.2787
6578
94.67 %
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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