› 4ysc

X-ray diffraction
2.03Å resolution

Completely oxidized structure of copper nitrite reductase from Alcaligenes faecalis

Released:
DOI: 10.2210/pdb4ysc/pdb
PDB entry 4ysc coloured by chain, front view.
PDB entry 4ysc coloured by chain, side view.
PDB entry 4ysc coloured by chain, top view.
Source organism: Alcaligenes faecalis
Primary publication:
Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.
Fukuda Y, Tse KM, Nakane T, Nakatsu T, Suzuki M, Sugahara M, Inoue S, Masuda T, Yumoto F, Matsugaki N, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Murphy ME, Inoue T, Iwata S, Mizohata E
Proc Natl Acad Sci U S A 113 2928-33 (2016)
PMID: 26929369

Function and Biology Details

Reaction catalysed: 
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153659 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Copper-containing nitrite reductase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 342 amino acids
Theoretical weight: 37.02 KDa
Source organism: Alcaligenes faecalis
Expression system: Escherichia coli
UniProt:
  • Canonical: P38501 (Residues: 40-376; Coverage: 98%)
Gene names: nir, nirK
Sequence domains:
Structure domains: Cupredoxins - blue copper proteins

Ligands and Environments

2 bound ligands:
Ligand CU 6 x CU
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SACLA BEAMLINE BL3
Spacegroup: P212121
Unit cell:
a: 63.1Å b: 103.8Å c: 147.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.164 0.203
Expression system: Escherichia coli

Quick links

Citations

9 review citations

X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules.
Chapman HN. (2019)
8 more

2 mentions without citation

Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology.
Mizohata et al. (2018)
1 more