› 6fm4

X-ray diffraction
2.7Å 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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119911 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA gyrase subunit A; DNA gyrase subunit B Chains: B, D
Molecule details ›
Chains: B, D
Length: 692 amino acids
Theoretical weight: 78.11 KDa
Source organism: Staphylococcus aureus subsp. aureus N315
Expression system: Escherichia coli
UniProt:
  • Canonical: P66937 (Residues: 409-543, 580-644; Coverage: 31%)
  • Canonical: Q99XG5 (Residues: 2-491; Coverage: 55%)
Gene names: SA0005, SA0006, gyrA, gyrB
Sequence domains:
DNA (5'-5UA*D(P*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') Chain: E
Molecule details ›
Chain: E
Length: 19 nucleotides
Theoretical weight: 5.82 KDa
DNA (5'-5UA*D(P*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*C)-3') Chain: F
Molecule details ›
Chain: F
Length: 18 nucleotides
Theoretical weight: 5.52 KDa

Ligands and Environments

3 bound ligands:
Ligand MN 3 x MN
Ligand 5UA 2 x 5UA
Ligand DU5 1 x DU5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P61
Unit cell:
a: 92.951Å b: 92.951Å c: 407.03Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.228 0.224 0.3
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The Structural Features of Novel Bacterial Topoisomerase Inhibitors That Define Their Activity on Topoisomerase IV.
Kokot et al. (2022)
5 other articles

2 mentions without citation

Dioxane-Linked Amide Derivatives as Novel Bacterial Topoisomerase Inhibitors against Gram-Positive Staphylococcus aureus.
Lu et al. (2020)
1 more