› 5hrk

X-ray diffraction
2.9Å resolution

The crystal structure of AsfvPolX(H115F mutant): 1nt-gap(P) DNA2:dGTP ternary complex

Released:
DOI: 10.2210/pdb5hrk/pdb
PDB entry 5hrk coloured by chain, front view.
PDB entry 5hrk coloured by chain, side view.
PDB entry 5hrk coloured by chain, top view.
Source organisms:
Entry authors: Chen YQ, Zhang J, Gan JH

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118762 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Repair DNA polymerase X Chains: A, B
Molecule details ›
Chains: A, B
Length: 178 amino acids
Theoretical weight: 20.62 KDa
Source organism: African swine fever virus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P42494 (Residues: 1-174; Coverage: 100%)
Gene names: Ba71V-97, O174L
Sequence domains:
Structure domains:
DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 9 nucleotides
Theoretical weight: 2.78 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3') Chains: E, H
Molecule details ›
Chains: E, H
Length: 18 nucleotides
Theoretical weight: 5.46 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3') Chains: D, G
Molecule details ›
Chains: D, G
Length: 8 nucleotides
Theoretical weight: 2.46 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand DGT 2 x DGT
Ligand MN 4 x MN
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2
Unit cell:
a: 106.726Å b: 87.196Å c: 82.616Å
α: 90° β: 97.59° γ: 90°
R-values:
R R work R free
0.235 0.233 0.272
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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