› 3s3d

X-ray diffraction
3.75Å resolution

Structure of Thermus thermophilus cytochrome ba3 oxidase 480s after Xe depressurization

Released:
DOI: 10.2210/pdb3s3d/pdb
PDB entry 3s3d coloured by chain, front view.
PDB entry 3s3d coloured by chain, side view.
PDB entry 3s3d coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase.
Luna VM, Fee JA, Deniz AA, Stout CD
Biochemistry 51 4669-76 (2012)
PMID: 22607023

Function and Biology Details

Reaction catalysed: 
4 ferrocytochrome c + O(2) + 8 H(+)(Side 1) = 4 ferricytochrome c + 4 H(2)O(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-160634 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Cytochrome c oxidase subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 568 amino acids
Theoretical weight: 63.4 KDa
Source organism: Thermus thermophilus HB8
Expression system: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ79 (Residues: 2-562; Coverage: 100%)
Gene names: TTHA1135, cbaA
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Structure domains: Cytochrome c oxidase-like, subunit I domain
Cytochrome c oxidase subunit 2 Chain: B
Molecule details ›
Chain: B
Length: 166 amino acids
Theoretical weight: 18.35 KDa
Source organism: Thermus thermophilus HB8
Expression system: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ80 (Residues: 3-168; Coverage: 99%)
Gene names: TTHA1134, cbaB, ctaC
Sequence domains:
Structure domains:
Cytochrome c oxidase polypeptide 2A Chain: C
Molecule details ›
Chain: C
Length: 33 amino acids
Theoretical weight: 3.64 KDa
Source organism: Thermus thermophilus HB8
Expression system: Thermus thermophilus HB8
UniProt:
  • Canonical: P82543 (Residues: 2-34; Coverage: 97%)
Gene names: TTHA1133, cbaD
Sequence domains: Cytochrome c oxidase subunit IIa family

Ligands and Environments

5 bound ligands:
Ligand CU 1 x CU
Ligand HEM 1 x HEM
Ligand HAS 1 x HAS
Ligand XE 3 x XE
Ligand CUA 1 x CUA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P43212
Unit cell:
a: 110.03Å b: 110.03Å c: 170.23Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.245 0.243 0.293
Expression system: Thermus thermophilus HB8

Quick links

Citations

2 review citations

Oxygen Activation and Energy Conservation by Cytochrome c Oxidase.
Wikström et al. (2018)
1 more

2 mentions without citation

Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase.
Luna et al. (2012)
1 more