› 5c5j

X-ray diffraction
2.1Å resolution

Poymerase Nucleotide complex

Released:
DOI: 10.2210/pdb5c5j/pdb
PDB entry 5c5j coloured by chain, front view.
PDB entry 5c5j coloured by chain, side view.
PDB entry 5c5j coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Reactive Oxygen Species Play an Important Role in the Bactericidal Activity of Quinolone Antibiotics.
Kottur J, Nair DT
Angew Chem Int Ed Engl 55 2397-400 (2016)
PMID: 26757158

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118462 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA polymerase IV Chains: A, F
Molecule details ›
Chains: A, F
Length: 352 amino acids
Theoretical weight: 39.59 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: Q47155 (Residues: 2-351; Coverage: 100%)
Gene names: JW0221, b0231, dinB, dinP
Sequence domains:
Structure domains:
DNA (5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3') Chains: B, C, G, H
Molecule details ›
Chains: B, C, G, H
Length: 18 nucleotides
Theoretical weight: 5.49 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand 8GT 1 x 8GT
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21
Unit cell:
a: 86.45Å b: 57.38Å c: 110.64Å
α: 90° β: 94.51° γ: 90°
R-values:
R R work R free
0.225 0.222 0.274
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

The Role of Reactive Oxygen Species in Antibiotic-Mediated Killing of Bacteria.
Van Acker et al. (2017)
5 more

1 mention without citation

Autonomous aggregation suppression by acidic residues explains why chaperones favour basic residues.
Houben et al. (2020)