› 6sf5

X-ray diffraction
1.9Å resolution

Mn-containing form of the ribonucleotide reductase NrdB protein from Leeuwenhoekiella blandensis

Released:
DOI: 10.2210/pdb6sf5/pdb
Model geometry
Fit model/data
PDB entry 6sf5 coloured by chain, front view.
PDB entry 6sf5 coloured by chain, side view.
PDB entry 6sf5 coloured by chain, top view.
Source organism: Leeuwenhoekiella blandensis
Primary publication:
Class Id ribonucleotide reductase utilizes a Mn2(IV,III) cofactor and undergoes large conformational changes on metal loading.
Rozman Grinberg I, Berglund S, Hasan M, Lundin D, Ho FM, Magnuson A, Logan DT, Sjöberg BM, Berggren G
OpenAccess logo J Biol Inorg Chem 24 863-877 (2019)
PMID: 31414238

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-107251 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ribonucleoside-diphosphate reductase Chains: A, B
Molecule details ›
Chains: A, B
Length: 348 amino acids
Theoretical weight: 40.58 KDa
Source organism: Leeuwenhoekiella blandensis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A3XHF9 (Residues: 100-427; Coverage: 77%)
Gene name: MED217_17135
Sequence domains: Ribonucleotide reductase, small chain

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: P212121
Unit cell:
a: 57.06Å b: 80.602Å c: 158.228Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.175 0.195
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

The periodic table of ribonucleotide reductases.
Ruskoski et al. (2021)
4 other articles

2 mentions without citation

Why is manganese so valuable to bacterial pathogens?
Čapek et al. (2023)
1 more

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO