› 4bmo

X-ray diffraction
1.81Å resolution

Crystal Structure of Bacillus cereus Ribonucleotide Reductase di- iron NrdF in Complex with NrdI (1.8 A resolution)

Released:
DOI: 10.2210/pdb4bmo/pdb
PDB entry 4bmo coloured by chain, front view.
PDB entry 4bmo coloured by chain, side view.
PDB entry 4bmo coloured by chain, top view.
Source organism: Bacillus cereus
Primary publication:
Crystal structure of Bacillus cereus class Ib ribonucleotide reductase di-iron NrdF in complex with NrdI.
Hammerstad M, Hersleth HP, Tomter AB, Røhr AK, Andersson KK
ACS Chem Biol 9 526-37 (2014)
PMID: 24295378

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

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109274 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ribonucleoside-diphosphate reductase subunit beta Chain: A
Molecule details ›
Chain: A
Length: 322 amino acids
Theoretical weight: 37.05 KDa
Source organism: Bacillus cereus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q81G55 (Residues: 1-322; Coverage: 100%)
Gene name: BC_1355
Sequence domains: Ribonucleotide reductase, small chain
Structure domains: Ribonucleotide Reductase, subunit A
Protein NrdI Chain: B
Molecule details ›
Chain: B
Length: 119 amino acids
Theoretical weight: 13.54 KDa
Source organism: Bacillus cereus
Expression system: Escherichia coli
UniProt:
  • Canonical: B0YPL1 (Residues: 1-119; Coverage: 100%)
Gene names: B4082_4779, BKK64_22520, BLX06_07420, C1N66_03050, CJ306_07140, CN357_26430, CN475_20520, CN553_06005, CN980_12615, COI69_30475, COI98_10480, CON36_20815, D0437_06525, DR116_0000380, DX932_00180, F8158_28605, F8165_13725, F8172_22390, FC695_16850, FHG65_21670, FXB61_002370, H7U08_16325, JDS76_16260, JTF64_12785, NPM19_00195, QYM23_07005, TQ94_26590, nrdI
Sequence domains: NrdI Flavodoxin like
Structure domains: Rossmann fold

Ligands and Environments


Cofactor: Ligand FMN 1 x FMN
2 bound ligands:
Ligand FE2 2 x FE2
Ligand CL 5 x CL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X10SA
Spacegroup: C2221
Unit cell:
a: 59.49Å b: 124.67Å c: 141.26Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.167 0.209
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Choosing the right metal: case studies of class I ribonucleotide reductases.
Huang et al. (2014)
2 more

2 mentions without citation

Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access.
Grāve et al. (2019)
1 more