› 5ytm

X-ray diffraction
1.5Å resolution

C135A mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans determined by in-ouse source

Released:
DOI: 10.2210/pdb5ytm/pdb
PDB entry 5ytm coloured by chain, front view.
PDB entry 5ytm coloured by chain, side view.
PDB entry 5ytm coloured by chain, top view.
Source organism: Geobacillus thermodenitrificans
Primary publication:
Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans.
Fukuda Y, Matsusaki T, Tse KM, Mizohata E, Murphy MEP, Inoue T
Acta Crystallogr D Struct Biol 74 769-777 (2018)
PMID: 30082512

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-245268 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Copper-containing nitrite reductase Chain: A
Molecule details ›
Chain: A
Length: 323 amino acids
Theoretical weight: 35.49 KDa
Source organism: Geobacillus thermodenitrificans
Expression system: Escherichia coli BL21(DE3)
Structure domains: Cupredoxins - blue copper proteins

Ligands and Environments

4 bound ligands:
Ligand CU 4 x CU
Ligand ACY 2 x ACY
Ligand MRD 1 x MRD
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: R3
Unit cell:
a: 115.078Å b: 115.078Å c: 84.043Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.119 0.117 0.153
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase.
Fukuda et al. (2020)