› 2dtu

X-ray diffraction
2.37Å resolution

Crystal structure of the beta hairpin loop deletion variant of RB69 gp43 in complex with DNA containing an abasic site analog

Released:
DOI: 10.2210/pdb2dtu/pdb
PDB entry 2dtu coloured by chain, front view.
PDB entry 2dtu coloured by chain, side view.
PDB entry 2dtu coloured by chain, top view.
Source organism: Escherichia phage RB69
Primary publication:
Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family.
Hogg M, Aller P, Konigsberg W, Wallace SS, Doublié S
J Biol Chem 282 1432-44 (2007)
PMID: 17098747

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115187 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-directed DNA polymerase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 896 amino acids
Theoretical weight: 103.76 KDa
Source organism: Escherichia phage RB69
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q38087 (Residues: 1-903; Coverage: 99%)
Gene name: 43
Sequence domains:
Structure domains:
5'-D(*CP*GP*(3DR)P*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3' Chains: E, G, I, K
Molecule details ›
Chains: E, G, I, K
Length: 18 nucleotides
Theoretical weight: 5.37 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided
5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*GP*A)-3' Chains: F, H, J, L
Molecule details ›
Chains: F, H, J, L
Length: 15 nucleotides
Theoretical weight: 4.63 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21
Unit cell:
a: 133.074Å b: 123.061Å c: 164.564Å
α: 90° β: 96.78° γ: 90°
R-values:
R R work R free
0.223 0.223 0.268
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

10 review citations

POLD1: Central mediator of DNA replication and repair, and implication in cancer and other pathologies.
Nicolas et al. (2016)
9 more

3 mentions without citation

Dynamics: the missing link between structure and function of the viral RNA-dependent RNA polymerase?
Cameron et al. (2009)
2 more