› 3bq2

X-ray diffraction
2.7Å resolution

Post-insertion binary complex of Dbh DNA polymerase

Released:
DOI: 10.2210/pdb3bq2/pdb
PDB entry 3bq2 coloured by chain, front view.
PDB entry 3bq2 coloured by chain, side view.
PDB entry 3bq2 coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into the generation of single-base deletions by the Y family DNA polymerase dbh.
Wilson RC, Pata JD
Mol Cell 29 767-79 (2008)
PMID: 18374650

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-116101 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 354 amino acids
Theoretical weight: 40.05 KDa
Source organism: Sulfolobus acidocaldarius
Expression system: Escherichia coli
UniProt:
  • Canonical: Q4JB80 (Residues: 1-354; Coverage: 100%)
Gene names: Saci_0554, dbh
Sequence domains:
Structure domains:
DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DGP*DG)-3') Chain: P
Molecule details ›
Chain: P
Length: 11 nucleotides
Theoretical weight: 3.42 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*DTP*DTP*DCP*DCP*DGP*DCP*DCP*DCP*DGP*DGP*DCP*DTP*DTP*DCP*DC)-3') Chain: T
Molecule details ›
Chain: T
Length: 15 nucleotides
Theoretical weight: 4.47 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P41212
Unit cell:
a: 120.338Å b: 120.338Å c: 68.325Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.234 0.289
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Translesion DNA polymerases.
Goodman et al. (2013)
5 more

2 mentions without citation

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