› 4koe

X-ray diffraction
3.02Å resolution

Quinolone(Trovafloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae

Released:
DOI: 10.2210/pdb4koe/pdb
PDB entry 4koe coloured by chain, front view.
PDB entry 4koe coloured by chain, side view.
PDB entry 4koe coloured by chain, top view.
Source organism: Streptococcus pneumoniae TIGR4
Entry authors: Laponogov I, Pan X-S, Veselkov DA, Fisher LM, Sanderson MR

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117759 (preferred)
Entry contents:
2 distinct polypeptide molecules
4 distinct DNA molecules
Macromolecules (6 distinct):
DNA topoisomerase 4 subunit A Chains: A, B
Molecule details ›
Chains: A, B
Length: 496 amino acids
Theoretical weight: 56.46 KDa
Source organism: Streptococcus pneumoniae TIGR4
Expression system: Escherichia coli
UniProt:
  • Canonical: P72525 (Residues: 1-488; Coverage: 59%)
Gene names: SP_0855, parC
Sequence domains: DNA gyrase/topoisomerase IV, subunit A
DNA topoisomerase 4 subunit B Chains: C, D
Molecule details ›
Chains: C, D
Length: 268 amino acids
Theoretical weight: 30.42 KDa
Source organism: Streptococcus pneumoniae TIGR4
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59961 (Residues: 404-647; Coverage: 38%)
Gene names: SP_0852, parE
Sequence domains:
Structure domains: Rossmann fold
E-site DNA1 Chain: E
Molecule details ›
Chain: E
Length: 7 nucleotides
Theoretical weight: 2.12 KDa
E-site DNA2 Chain: F
Molecule details ›
Chain: F
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
E-site DNA3 Chain: G
Molecule details ›
Chain: G
Length: 7 nucleotides
Theoretical weight: 2.11 KDa
E-site DNA4 Chain: H
Molecule details ›
Chain: H
Length: 11 nucleotides
Theoretical weight: 3.36 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 6 x MG
Ligand TR6 2 x TR6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P3121
Unit cell:
a: 158.04Å b: 158.04Å c: 210.42Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.177 0.175 0.21
Expression system: Escherichia coli

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