› 3r1r

X-ray diffraction
3Å resolution

RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH AMPPNP OCCUPYING THE ACTIVITY SITE FROM ESCHERICHIA COLI

Released:
DOI: 10.2210/pdb3r1r/pdb
PDB entry 3r1r coloured by chain, front view.
PDB entry 3r1r coloured by chain, side view.
PDB entry 3r1r coloured by chain, top view.
Source organisms:
Primary publication:
Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding.
Eriksson M, Uhlin U, Ramaswamy S, Ekberg M, Regnström K, Sjöberg BM, Eklund H
Structure 5 1077-92 (1997)
PMID: 9309223

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 domains:

Structure analysis Details

Assemblies composition:
hetero trimer
hetero dimer (preferred)
hetero pentadecamer
hetero dodecamer
hetero nonamer
homo hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-132526 (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
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 ATP 3 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12B
Spacegroup: R32
Unit cell:
a: 224.61Å b: 224.61Å c: 336.63Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.263 not available 0.287
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

24 review citations

Ribonucleotide reductases.
Nordlund et al. (2006)
23 more

16 mentions without citation

X-ray Scattering Studies of Protein Structural Dynamics.
Meisburger et al. (2017)
15 more