› 3bvd

X-ray diffraction
3.37Å resolution

Structure of Surface-engineered Cytochrome ba3 Oxidase from Thermus thermophilus under Xenon Pressure, 100psi 5min

Released:
DOI: 10.2210/pdb3bvd/pdb
PDB entry 3bvd coloured by chain, front view.
PDB entry 3bvd coloured by chain, side view.
PDB entry 3bvd coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Crystallographic studies of Xe and Kr binding within the large internal cavity of cytochrome ba3 from Thermus thermophilus: structural analysis and role of oxygen transport channels in the heme-Cu oxidases.
Luna VM, Chen Y, Fee JA, Stout CD
Biochemistry 47 4657-65 (2008)
PMID: 18376849

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 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: 63.43 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: 168 amino acids
Theoretical weight: 18.58 KDa
Source organism: Thermus thermophilus HB8
Expression system: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ80 (Residues: 1-168; Coverage: 100%)
Gene names: TTHA1134, cbaB, ctaC
Sequence domains:
Structure domains:
Cytochrome c oxidase polypeptide 2A Chain: C
Molecule details ›
Chain: C
Length: 34 amino acids
Theoretical weight: 3.77 KDa
Source organism: Thermus thermophilus HB8
Expression system: Thermus thermophilus HB8
UniProt:
  • Canonical: P82543 (Residues: 1-34; Coverage: 100%)
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 7 x XE
Ligand CUA 1 x CUA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-1
Spacegroup: P41212
Unit cell:
a: 119.726Å b: 119.726Å c: 153.535Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.292 0.292 0.336
Expression system: Thermus thermophilus HB8

Quick links

Citations

10 review citations

Cytochrome c oxidase: exciting progress and remaining mysteries.
Brzezinski et al. (2008)
9 more

5 mentions without citation

High resolution structure of the ba3 cytochrome c oxidase from Thermus thermophilus in a lipidic environment.
Tiefenbrunn et al. (2011)
4 more