› 2ykz

X-ray diffraction
0.84Å resolution

RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS AT 0.84 A RESOLUTION: RESTRAINED REFINEMENT

Released:
DOI: 10.2210/pdb2ykz/pdb
PDB entry 2ykz coloured by chain, front view.
PDB entry 2ykz coloured by chain, side view.
PDB entry 2ykz coloured by chain, top view.
Source organism: Achromobacter xylosoxidans
Primary publication:
Carbon monoxide poisoning is prevented by the energy costs of conformational changes in gas-binding haemproteins.
Antonyuk SV, Rustage N, Petersen CA, Arnst JL, Heyes DJ, Sharma R, Berry NG, Scrutton NS, Eady RR, Andrew CR, Hasnain SS
Proc Natl Acad Sci U S A 108 15780-5 (2011)
PMID: 21900609

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132286 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cytochrome c' Chain: A
Molecule details ›
Chain: A
Length: 127 amino acids
Theoretical weight: 13.66 KDa
Source organism: Achromobacter xylosoxidans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00138 (Residues: 1-127; Coverage: 100%)
Sequence domains: Cytochrome C'
Structure domains: Cytochrome c/b562

Ligands and Environments

2 bound ligands:
Ligand HEC 1 x HEC
Ligand SO4 2 x SO4
1 modified residue:
Ligand PCA 1 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P6522
Unit cell:
a: 53.47Å b: 53.47Å c: 181.19Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.106 0.106 0.116
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs.
Quesne et al. (2016)
3 more

2 mentions without citation

Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential.
Blakeley et al. (2015)
1 more