› 1n48

X-ray diffraction
2.2Å resolution

Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion

Released:
DOI: 10.2210/pdb1n48/pdb
PDB entry 1n48 coloured by chain, front view.
PDB entry 1n48 coloured by chain, side view.
PDB entry 1n48 coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Entry authors: Ling H, Boudsocq F, Woodgate R, Yang W

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114228 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 352 amino acids
Theoretical weight: 40.26 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3' Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.11 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
5'-D(*CP*AP*(3DR)P*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.62 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 3 x CA
Ligand ATP 1 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200HB
Spacegroup: P212121
Unit cell:
a: 75.546Å b: 88.458Å c: 92.389Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.204 0.23
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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