› 8ilh

X-ray diffraction
2.1Å resolution

The crystal structure of dG(Se-Sp)-DNA:Pol X product binary complex

Released:
DOI: 10.2210/pdb8ilh/pdb
PDB entry 8ilh coloured by chain, front view.
PDB entry 8ilh coloured by chain, side view.
PDB entry 8ilh coloured by chain, top view.
Source organisms:
Primary publication:
Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom.
Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z
OpenAccess logo Int J Mol Sci 24 (2023)
PMID: 37958741

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-270528 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Repair DNA polymerase X Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 177 amino acids
Theoretical weight: 20.52 KDa
Source organism: African swine fever virus BA71V
Expression system: Escherichia coli
UniProt:
  • Canonical: P42494 (Residues: 1-174; Coverage: 100%)
Gene names: Ba71V-97, O174L
Sequence domains:
DNA (5'-D(*CP*GP*GP*AP*TP*CP*C)-3') Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 7 nucleotides
Theoretical weight: 2.1 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MG 8 x MG
Ligand SO4 8 x SO4
Ligand 8EB 1 x 8EB
Ligand GMS 3 x GMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P21
Unit cell:
a: 60.471Å b: 87.28Å c: 87.056Å
α: 90° β: 91.15° γ: 90°
R-values:
R R work R free
0.183 0.181 0.227
Expression systems:
  • Escherichia coli
  • Not provided

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