5cdm

X-ray diffraction
2.5Å resolution

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118472 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA gyrase subunit B Chains: B, D
Molecule details ›
Chains: B, D
Length: 190 amino acids
Theoretical weight: 21.33 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P66937 (Residues: 416-543, 580-639; Coverage: 29%)
Gene names: SA0005, gyrB
Sequence domains:
DNA gyrase subunit A Chains: A, C
Molecule details ›
Chains: A, C
Length: 482 amino acids
Theoretical weight: 54.78 KDa
Source organism: Staphylococcus aureus
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 (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
Molecule details ›
Chains: E, F
Length: 8 nucleotides
Theoretical weight: 2.45 KDa
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: I, N
Molecule details ›
Chains: I, N
Length: 12 nucleotides
Theoretical weight: 3.65 KDa

Ligands and Environments

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P61
Unit cell:
a: 93.884Å b: 93.884Å c: 412.482Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.165 0.163 0.192
Expression system: Escherichia coli