› 2rdi

X-ray diffraction
1.92Å resolution

Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms

Released:
DOI: 10.2210/pdb2rdi/pdb
PDB entry 2rdi coloured by chain, front view.
PDB entry 2rdi coloured by chain, side view.
PDB entry 2rdi coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4.
Wong JH, Fiala KA, Suo Z, Ling H
J Mol Biol 379 317-30 (2008)
PMID: 18448122

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188998 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 342 amino acids
Theoretical weight: 39.12 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q97W02 (Residues: 1-341; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand PEG 1 x PEG
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: C2
Unit cell:
a: 92.927Å b: 51.069Å c: 86.026Å
α: 90° β: 98.08° γ: 90°
R-values:
R R work R free
0.207 0.205 0.247
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Structural diversity of the Y-family DNA polymerases.
Pata JD. (2010)
5 more

17 mentions without citation

An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η.
Yang W. (2014)
16 more