› 6koe

X-ray diffraction
3.75Å resolution

X-ray Structure of the proton-pumping cytochrome aa3-600 menaquinol oxidase from Bacillus subtilis

Released:
DOI: 10.2210/pdb6koe/pdb
Model geometry
Fit model/data
PDB entry 6koe coloured by chain, front view.
PDB entry 6koe coloured by chain, side view.
PDB entry 6koe coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Structure of the cytochrome aa3 -600 heme-copper menaquinol oxidase bound to inhibitor HQNO shows TM0 is part of the quinol binding site.
Xu J, Ding Z, Liu B, Yi SM, Li J, Zhang Z, Liu Y, Li J, Liu L, Zhou A, Gennis RB, Zhu J
Proc Natl Acad Sci U S A 117 872-876 (2020)
PMID: 31888984

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152758 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Quinol oxidase subunit 1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 655 amino acids
Theoretical weight: 74.72 KDa
Source organism: Bacillus subtilis
Expression system: Bacillus subtilis
UniProt:
  • Canonical: P34956 (Residues: 1-649; Coverage: 100%)
Gene names: BSU38160, ipa-38d, qoxB
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Quinol oxidase subunit 2 Chains: B, F
Molecule details ›
Chains: B, F
Length: 296 amino acids
Theoretical weight: 33.59 KDa
Source organism: Bacillus subtilis
Expression system: Bacillus subtilis
UniProt:
  • Canonical: P34957 (Residues: 26-321; Coverage: 100%)
Gene names: BSU38170, ipa-37d, qoxA
Sequence domains:
Quinol oxidase subunit 3 Chains: C, G
Quinol oxidase subunit 4 Chains: D, H

Ligands and Environments

3 bound ligands:
Ligand HEA 4 x HEA
Ligand CU 2 x CU
Ligand HQO 2 x HQO
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P21
Unit cell:
a: 112.988Å b: 162.11Å c: 149.509Å
α: 90° β: 109.02° γ: 90°
R-values:
R R work R free
0.347 0.347 0.368
Expression system: Bacillus subtilis

Quick links

Citations

4 review citations

Architecture of bacterial respiratory chains.
Kaila et al. (2021)
3 more

1 mention without citation

Structure of the cytochrome aa 3 -600 heme-copper menaquinol oxidase bound to inhibitor HQNO shows TM0 is part of the quinol binding site.
Xu et al. (2020)

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO