› 5cdo

X-ray diffraction
3.15Å resolution

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118474 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
DNA gyrase subunit A Chains: A, C, R, T
Molecule details ›
Chains: A, C, R, T
Length: 482 amino acids
Theoretical weight: 54.78 KDa
Source organism: Staphylococcus aureus subsp. aureus N315
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99XG5 (Residues: 9-490; Coverage: 54%)
Gene names: SA0006, gyrA
Sequence domains: DNA gyrase/topoisomerase IV, subunit A
DNA gyrase subunit B Chains: B, D, S, U
Molecule details ›
Chains: B, D, S, U
Length: 188 amino acids
Theoretical weight: 21.11 KDa
Source organism: Staphylococcus aureus subsp. aureus N315
Expression system: Escherichia coli
UniProt:
  • Canonical: P66937 (Residues: 417-543, 580-638; Coverage: 29%)
Gene names: SA0005, gyrB
Sequence domains:
DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') Chains: E, F, V, W
Molecule details ›
Chains: E, F, V, W
Length: 20 nucleotides
Theoretical weight: 6.15 KDa

Ligands and Environments

7 bound ligands:
Ligand SO4 3 x SO4
Ligand NA 5 x NA
Ligand GOL 5 x GOL
Ligand MN 4 x MN
Ligand 53M 2 x 53M
Ligand 53L 1 x 53L
Ligand 50M 1 x 50M
1 modified residue:
Ligand PTR 4 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P21
Unit cell:
a: 90.472Å b: 170.211Å c: 124.579Å
α: 90° β: 102.75° γ: 90°
R-values:
R R work R free
0.216 0.215 0.246
Expression system: Escherichia coli

Quick links

Citations

9 review citations

The Current Case of Quinolones: Synthetic Approaches and Antibacterial Activity.
Naeem et al. (2016)
8 more

3 mentions without citation

DNA Topoisomerase Inhibitors: Trapping a DNA-Cleaving Machine in Motion.
Bax et al. (2019)
2 more