› 3dhz

X-ray diffraction
1.63Å resolution

Apo (iron free) structure of C. ammoniagenes R2 protein

Released:
DOI: 10.2210/pdb3dhz/pdb
PDB entry 3dhz coloured by chain, front view.
PDB entry 3dhz coloured by chain, side view.
PDB entry 3dhz coloured by chain, top view.
Source organism: Corynebacterium ammoniagenes
Primary publication:
Structural and mutational studies of the carboxylate cluster in iron-free ribonucleotide reductase R2.
Andersson ME, Högbom M, Rinaldo-Matthis A, Blodig W, Liang Y, Persson BO, Sjöberg BM, Su XD, Nordlund P
Biochemistry 43 7966-72 (2004)
PMID: 15196041

Function and Biology Details

Reaction catalysed: 
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130653 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribonucleoside-diphosphate reductase subunit beta Chains: A, B
Molecule details ›
Chains: A, B
Length: 329 amino acids
Theoretical weight: 37.96 KDa
Source organism: Corynebacterium ammoniagenes
Expression system: Escherichia coli
UniProt:
  • Canonical: O69274 (Residues: 1-329; Coverage: 100%)
Gene name: nrdF
Sequence domains: Ribonucleotide reductase, small chain
Structure domains: Ribonucleotide Reductase, subunit A

Ligands and Environments

1 bound ligand:
Ligand FE2 4 x FE2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I711
Spacegroup: P21
Unit cell:
a: 48.908Å b: 86.537Å c: 70.61Å
α: 90° β: 105.48° γ: 90°
R-values:
R R work R free
0.168 0.165 0.222
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Metal use in ribonucleotide reductase R2, di-iron, di-manganese and heterodinuclear--an intricate bioinorganic workaround to use different metals for the same reaction.
Högbom M. (2011)
1 more

1 mention without citation

Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens.
Srinivas et al. (2018)