- PDB-5ir6: The structure of bd oxidase from Geobacillus thermodenitrificans -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5ir6
Title
The structure of bd oxidase from Geobacillus thermodenitrificans
Components
Bd-type quinol oxidase subunit I
Bd-type quinol oxidase subunit II
Putative membrane protein
Keywords
OXIDOREDUCTASE / bd oxidase / terminal oxidase
Function / homology
Function and homology information
cytochrome complex / aerobic electron transport chain / membrane => GO:0016020 / electron transfer activity / membrane / metal ion binding / plasma membrane Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.73829 Å / Relative weight: 1
Reflection
Resolution: 3.8→49 Å / Num. obs: 16612 / % possible obs: 99.6 % / Redundancy: 32.1 % / Rrim(I) all: 0.014 / Rsym value: 0.096 / Net I/σ(I): 21.2
Reflection shell
Resolution: 3.8→3.9 Å / Redundancy: 32.3 % / Mean I/σ(I) obs: 3.7 / Rpim(I) all: 0.2 / Rsym value: 1.75 / % possible all: 98.9
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0073
refinement
XDS
datareduction
XSCALE
datascaling
SHELX
phasing
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 3.8→20 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.893 / SU B: 62.819 / SU ML: 0.813 / Cross valid method: THROUGHOUT / ESU R Free: 0.81 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.3252
807
4.9 %
RANDOM
Rwork
0.30261
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obs
0.30361
15690
98.91 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å