› 2xct

X-ray diffraction
3.35Å resolution

The twinned 3.35A structure of S. aureus Gyrase complex with Ciprofloxacin and DNA

Released:
DOI: 10.2210/pdb2xct/pdb
PDB entry 2xct coloured by chain, front view.
PDB entry 2xct coloured by chain, side view.
PDB entry 2xct coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus N315
Primary publication:
Type IIA topoisomerase inhibition by a new class of antibacterial agents.
Bax BD, Chan PF, Eggleston DS, Fosberry A, Gentry DR, Gorrec F, Giordano I, Hann MM, Hennessy A, Hibbs M, Huang J, Jones E, Jones J, Brown KK, Lewis CJ, May EW, Saunders MR, Singh O, Spitzfaden CE, Shen C, Shillings A, Theobald AJ, Wohlkonig A, Pearson ND, Gwynn MN
Nature 466 935-40 (2010)
PMID: 20686482

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-115925 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
DNA gyrase subunit A; DNA gyrase subunit B Chains: B, D, S, U
Molecule details ›
Chains: B, D, S, U
Length: 692 amino acids
Theoretical weight: 78.11 KDa
Source organism: Staphylococcus aureus subsp. aureus N315
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P66937 (Residues: 410-543, 580-644; Coverage: 31%)
  • Canonical: Q99XG5 (Residues: 2-491; Coverage: 55%)
Gene names: SA0005, SA0006, gyrA, gyrB
Sequence domains:
Structure domains: Rossmann fold
5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3' Chains: E, V
Molecule details ›
Chains: E, V
Length: 8 nucleotides
Theoretical weight: 2.47 KDa
5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3' Chains: F, W
Molecule details ›
Chains: F, W
Length: 8 nucleotides
Theoretical weight: 2.45 KDa
5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3' Chains: G, X
Molecule details ›
Chains: G, X
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3' Chains: H, Y
Molecule details ›
Chains: H, Y
Length: 12 nucleotides
Theoretical weight: 3.62 KDa

Ligands and Environments

2 bound ligands:
Ligand MN 8 x MN
Ligand CPF 4 x CPF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P21
Unit cell:
a: 88.984Å b: 123.166Å c: 170.418Å
α: 90° β: 90.25° γ: 90°
R-values:
R R work R free
0.169 0.166 0.236
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

54 review citations

Drugging topoisomerases: lessons and challenges.
Pommier Y. (2013)
53 more

73 mentions without citation

Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target.
Robinson et al. (2012)
72 more