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2.65 structure of S.aureus DNA gyrase and artificially nicked DNA

X-ray diffraction
2.65Å resolution
PDB entry 5cdr coloured by chain, front view.
PDB entry 5cdr coloured by chain, side view.
PDB entry 5cdr coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus N315
Assembly composition:
hetero heptamer (preferred)
Entry contents: 2 distinct polypeptide molecules
3 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA gyrase and DNA
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Multimeric state: hetero heptamer
Accessible surface area: 57472.58 Å2
Buried surface area: 21891.67 Å2
Dissociation area: 1,310.28 Å2
Dissociation energy (ΔGdiss): 17.38 kcal/mol
Dissociation entropy (TΔSdiss): 9.4 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-118477

Macromolecules

DNA gyrase subunit A
Chains: A, C
Length: 483 amino acids
Theoretical weight: 54.74 KDa
Source organism: Staphylococcus aureus subsp. aureus N315
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99XG5 (Residues: 9-491; Coverage: 54%)
Gene names: SA0006, gyrA
Pfam: DNA gyrase/topoisomerase IV, subunit A
InterPro:
DNA gyrase subunit A in PDB entry 5cdr, assembly 1, front view.
DNA gyrase subunit A in PDB entry 5cdr, assembly 1, side view.
DNA gyrase subunit A in PDB entry 5cdr, assembly 1, top view.
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DNA gyrase subunit B
Chains: B, D
Length: 190 amino acids
Theoretical weight: 21.35 KDa
Source organism: Staphylococcus aureus subsp. aureus N315
Expression system: Escherichia coli
UniProt:
  • Canonical: P66937 (Residues: 417-543, 580-640; Coverage: 29%)
Gene names: SA0005, gyrB
Pfam:
InterPro:
DNA gyrase subunit B in PDB entry 5cdr, assembly 1, front view.
DNA gyrase subunit B in PDB entry 5cdr, assembly 1, side view.
DNA gyrase subunit B in PDB entry 5cdr, assembly 1, top view.
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DNA chain E
Name: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*)-3')
Representative chains: E
Length: 8 nucleotides
Theoretical weight: 2.45 KDa
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*)-3') in PDB entry 5cdr, assembly 1, front view.
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*)-3') in PDB entry 5cdr, assembly 1, side view.
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*)-3') in PDB entry 5cdr, assembly 1, top view.
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DNA chain G
Name: DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
Representative chains: G
Length: 13 nucleotides
Theoretical weight: 3.97 KDa
DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') in PDB entry 5cdr, assembly 1, front view.
DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') in PDB entry 5cdr, assembly 1, side view.
DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') in PDB entry 5cdr, assembly 1, top view.
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DNA chain F
Name: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
Representative chains: F
Length: 20 nucleotides
Theoretical weight: 6.13 KDa
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') in PDB entry 5cdr, assembly 1, front view.
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') in PDB entry 5cdr, assembly 1, side view.
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') in PDB entry 5cdr, assembly 1, top view.
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