› 6l46

Hybrid

High-resolution neutron and X-ray joint refined structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans

Released:
DOI: 10.2210/pdb6l46/pdb
PDB entry 6l46 coloured by chain, front view.
PDB entry 6l46 coloured by chain, side view.
PDB entry 6l46 coloured by chain, top view.
Source organism: Geobacillus thermodenitrificans
Primary publication:
High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase.
Fukuda Y, Hirano Y, Kusaka K, Inoue T, Tamada T
OpenAccess logo Proc Natl Acad Sci U S A 117 4071-4077 (2020)
PMID: 32041886

Function and Biology Details

Biochemical function:
  • not assigned
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-245302 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Copper-containing nitrite reductase Chain: A
Molecule details ›
Chain: A
Length: 323 amino acids
Theoretical weight: 35.52 KDa
Source organism: Geobacillus thermodenitrificans
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

5 bound ligands:
Ligand CU 4 x CU
Ligand NA 1 x NA
Ligand CL 1 x CL
Ligand MPD 1 x MPD
Ligand DOD 458 x DOD
No modified residues

Experiments and Validation Details

Experimental Method: X-ray diffraction, Neutron Diffraction
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A, J-PARC MLF BEAMLINE BL-03
Spacegroup: R3
Unit cell:
a: 114.212Å b: 114.212Å c: 83.688Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.098 0.097 0.112
Expression system: Escherichia coli BL21(DE3)

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Citations

6 citation in other articles

An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Rose et al. (2021)
5 more

3 mentions without citation

Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography.
Schröder et al. (2021)
2 more