› 8ylu

Electron Microscopy
2.8Å resolution

structure of phage T6 topoisomerase II central domain bound with DNA

Released:
DOI: 10.2210/pdb8ylu/pdb
PDB entry 8ylu coloured by chain, front view.
PDB entry 8ylu coloured by chain, side view.
PDB entry 8ylu coloured by chain, top view.
Source organisms:
Entry authors: Chen YT, Xin YH
Related structures: EMD-39391

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-269220 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA topoisomerase medium subunit Chains: A, B
Molecule details ›
Chains: A, B
Length: 452 amino acids
Theoretical weight: 51.95 KDa
Source organism: Escherichia phage T4
Expression system: Escherichia coli
UniProt:
  • Canonical: P07065 (Residues: 1-442; Coverage: 100%)
Gene name: 52
Sequence domains: DNA gyrase/topoisomerase IV, subunit A
DNA topoisomerase (ATP-hydrolyzing) Chains: C, D
Molecule details ›
Chains: C, D
Length: 611 amino acids
Theoretical weight: 69.24 KDa
Source organism: Salmonella phage Chi
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A346FJ89 (Residues: 1-605; Coverage: 100%)
Gene name: EcT6_00003
Sequence domains:
DNA(5'-D(P*TP*GP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*TP*AP)) Chain: E
Molecule details ›
Chain: E
Length: 22 nucleotides
Theoretical weight: 6.76 KDa
DNA (5'-D(P*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*CP*A)-3') Chain: F
Molecule details ›
Chain: F
Length: 22 nucleotides
Theoretical weight: 6.73 KDa

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.8Å
Relevant EMDB volumes: EMD-39391
Expression system: Escherichia coli

Quick links