6qx2

X-ray diffraction
3.4Å resolution

3.4A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
9 distinct polypeptide molecules
3 distinct DNA molecules
Macromolecules (12 distinct):
DNA gyrase subunit B Chains: B, S, b, s
Molecule details ›
Chains: B, S, b, s
Length: 186 amino acids
Theoretical weight: 20.85 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 416-638; Coverage: 29%)
Gene name: gyrB
Sequence domains: Toprim domain
DNA gyrase subunit A Chains: A, C, L, R, T, a, c, j, l, r, t
Molecule details ›
Chains: A, C, L, R, T, a, c, j, l, r, t
Length: 490 amino acids
Theoretical weight: 55.54 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99XG5 (Residues: 2-491; Coverage: 55%)
Gene names: SA0006, gyrA
Sequence domains: DNA gyrase/topoisomerase IV, subunit A
DNA gyrase subunit B Chains: D, U, m
Molecule details ›
Chains: D, U, m
Length: 188 amino acids
Theoretical weight: 21.11 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 417-543, 580-638; Coverage: 29%)
Gene name: gyrB
Sequence domains: Toprim domain
DNA gyrase subunit B Chain: K
Molecule details ›
Chain: K
Length: 187 amino acids
Theoretical weight: 21.01 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 416-639; Coverage: 29%)
Gene name: gyrB
Sequence domains: Toprim domain
DNA gyrase subunit A Chain: J
Molecule details ›
Chain: J
Length: 480 amino acids
Theoretical weight: 54.37 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99XG5 (Residues: 11-491; Coverage: 54%)
Gene names: SA0006, gyrA
Sequence domains: DNA gyrase/topoisomerase IV, subunit A
DNA gyrase subunit B Chain: M
Molecule details ›
Chain: M
Length: 189 amino acids
Theoretical weight: 21.27 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 417-543, 580-639; Coverage: 29%)
Gene name: gyrB
Sequence domains: Toprim domain
DNA gyrase subunit B Chain: d
Molecule details ›
Chain: d
Length: 181 amino acids
Theoretical weight: 20.36 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 417-543, 586-637; Coverage: 28%)
Gene name: gyrB
Sequence domains: Toprim domain
DNA gyrase subunit B Chain: k
Molecule details ›
Chain: k
Length: 188 amino acids
Theoretical weight: 21.08 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 416-640; Coverage: 29%)
Gene name: gyrB
Sequence domains: Toprim domain
DNA gyrase subunit B Chain: u
Molecule details ›
Chain: u
Length: 187 amino acids
Theoretical weight: 21.01 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 417-543, 580-637; Coverage: 29%)
Gene name: gyrB
Sequence domains: Toprim domain
DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') Chains: E, F, N, O, W, e, n, v, w
Molecule details ›
Chains: E, F, N, O, W, e, n, v, w
Length: 20 nucleotides
Theoretical weight: 6.15 KDa
DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') Chains: V, o
Molecule details ›
Chains: V, o
Length: 19 nucleotides
Theoretical weight: 5.85 KDa
DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') Chain: f
Molecule details ›
Chain: f
Length: 17 nucleotides
Theoretical weight: 5.2 KDa

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I23
Spacegroup: P21
Unit cell:
a: 187.64Å b: 410.12Å c: 93.94Å
α: 90° β: 120.22° γ: 90°
R-values:
R R work R free
0.178 0.176 0.208
Expression system: Escherichia coli