› 5dcr

X-ray diffraction
2.11Å resolution

R2-like ligand-binding oxidase with aerobically reconstituted Mn/Fe cofactor (short soak)

Released:
DOI: 10.2210/pdb5dcr/pdb
Model geometry
Fit model/data
PDB entry 5dcr coloured by chain, front view.
PDB entry 5dcr coloured by chain, side view.
PDB entry 5dcr coloured by chain, top view.
Source organism: Geobacillus kaustophilus HTA426
Primary publication:
Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor.
Griese JJ, Kositzki R, Schrapers P, Branca RM, Nordström A, Lehtiö J, Haumann M, Högbom M
J Biol Chem 290 25254-72 (2015)
PMID: 26324712

Function and Biology Details

Reaction catalysed: 
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177364 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
R2-like ligand binding oxidase Chain: A
Molecule details ›
Chain: A
Length: 316 amino acids
Theoretical weight: 36.96 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5KW80 (Residues: 1-302; Coverage: 100%)
Gene name: GK2771
Sequence domains: Ribonucleotide reductase, small chain
Structure domains: Ribonucleotide Reductase, subunit A

Ligands and Environments

3 bound ligands:
Ligand MN3 1 x MN3
Ligand FE 2 x FE
Ligand PLM 1 x PLM
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06SA
Spacegroup: I222
Unit cell:
a: 56.19Å b: 97.339Å c: 129.764Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.165 0.212
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Dioxygen Activation by Nonheme Diiron Enzymes: Diverse Dioxygen Adducts, High-Valent Intermediates, and Related Model Complexes.
Jasniewski et al. (2018)
15 other articles

1 mention without citation

Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor.
Griese et al. (2015)