› 8dfb

X-ray diffraction
3.17Å resolution

Structure of M. kandleri topoisomerase V in complex with DNA. 39 base pair symmetric DNA complex

Released:
DOI: 10.2210/pdb8dfb/pdb
PDB entry 8dfb coloured by chain, front view.
PDB entry 8dfb coloured by chain, side view.
PDB entry 8dfb coloured by chain, top view.
Source organisms:
Primary publication:
Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism.
Osterman A, Mondragón A
OpenAccess logo Elife 11 (2022)
PMID: 35969036

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-122504 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Helix-hairpin-helix DNA-binding motif class 1 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 854 amino acids
Theoretical weight: 97.11 KDa
Source organism: Methanopyrus kandleri
Expression system: Escherichia coli
UniProt:
  • Canonical: Q977W1 (Residues: 1-854; Coverage: 87%)
Gene names: HA336_03250, top5
Sequence domains:
DNA (40-MER) Chain: U
Molecule details ›
Chain: U
Length: 40 nucleotides
Theoretical weight: 12.3 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (40-MER) Chain: V
Molecule details ›
Chain: V
Length: 40 nucleotides
Theoretical weight: 12.31 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand K 4 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P43212
Unit cell:
a: 121.56Å b: 121.56Å c: 497.191Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.218 0.251
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 citations in other articles

Stability Islands and the Folding Cooperativity of a Seven-Repeat Array from Topoisomerase V.
Petersen et al. (2023)

1 mention without citation

Structures of topoisomerase V in complex with DNA reveal unusual DNA-binding mode and novel relaxation mechanism.
Osterman et al. (2022)