› 2x0x

X-ray diffraction
2.3Å resolution

Ribonucleotide reductase R1 subunit of E. coli to 2.3 A resolution

Released:
DOI: 10.2210/pdb2x0x/pdb
PDB entry 2x0x coloured by chain, front view.
PDB entry 2x0x coloured by chain, side view.
PDB entry 2x0x coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Site-specific incorporation of 3-nitrotyrosine as a probe of pKa perturbation of redox-active tyrosines in ribonucleotide reductase.
Yokoyama K, Uhlin U, Stubbe J
J Am Chem Soc 132 8385-97 (2010)
PMID: 20518462

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 analysis Details

Assemblies composition:
hetero dodecamer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-132534 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ribonucleoside-diphosphate reductase 1 subunit alpha Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 761 amino acids
Theoretical weight: 85.88 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P00452 (Residues: 1-761; Coverage: 100%)
Gene names: JW2228, b2234, dnaF, nrdA
Sequence domains:
Structure domains: Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Ribonucleoside-diphosphate reductase 1 subunit beta Chains: D, E, F, P
Molecule details ›
Chains: D, E, F, P
Length: 20 amino acids
Theoretical weight: 2.27 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
UniProt:
  • Canonical: P69924 (Residues: 357-376; Coverage: 5%)
Gene names: JW2229, b2235, ftsB, nrdB

Ligands and Environments

1 bound ligand:
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: R32
Unit cell:
a: 223.877Å b: 223.877Å c: 336.467Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.185 0.183 0.224
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Biochemistry and theory of proton-coupled electron transfer.
Migliore et al. (2014)
6 more

6 mentions without citation

Equilibration of tyrosyl radicals (Y356•, Y731•, Y730•) in the radical propagation pathway of the Escherichia coli class Ia ribonucleotide reductase.
Yokoyama et al. (2011)
5 more