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

X-ray diffraction
3.17Å resolution
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:
Assembly composition:
hetero tetramer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Helix-hairpin-helix DNA-binding motif class 1 domain-containing protein and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 80876.46 Å2
Buried surface area: 23965.89 Å2
Dissociation area: 9,340.95 Å2
Dissociation energy (ΔGdiss): 106.46 kcal/mol
Dissociation entropy (TΔSdiss): 32.75 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-122504

Macromolecules

Helix-hairpin-helix DNA-binding motif class 1 domain-containing protein
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
Pfam:
InterPro:
Helix-hairpin-helix DNA-binding motif class 1 domain-containing protein in PDB entry 8dfb, assembly 1, front view.
Helix-hairpin-helix DNA-binding motif class 1 domain-containing protein in PDB entry 8dfb, assembly 1, side view.
Helix-hairpin-helix DNA-binding motif class 1 domain-containing protein in PDB entry 8dfb, assembly 1, top view.
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DNA chain U
Name: DNA (40-MER)
Representative chains: U
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 40 nucleotides
Theoretical weight: 12.3 KDa
DNA (40-MER) in PDB entry 8dfb, assembly 1, front view.
DNA (40-MER) in PDB entry 8dfb, assembly 1, side view.
DNA (40-MER) in PDB entry 8dfb, assembly 1, top view.
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DNA chain V
Name: DNA (40-MER)
Representative chains: V
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 40 nucleotides
Theoretical weight: 12.31 KDa
DNA (40-MER) in PDB entry 8dfb, assembly 1, front view.
DNA (40-MER) in PDB entry 8dfb, assembly 1, side view.
DNA (40-MER) in PDB entry 8dfb, assembly 1, top view.
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