› 4khn

X-ray diffraction
2.55Å resolution

Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase

Released:
DOI: 10.2210/pdb4khn/pdb
PDB entry 4khn coloured by chain, front view.
PDB entry 4khn coloured by chain, side view.
PDB entry 4khn coloured by chain, top view.
Source organism: Escherichia phage RB69
Primary publication:
A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site.
Jacewicz A, Trzemecka A, Guja KE, Plochocka D, Yakubovskaya E, Bebenek A, Garcia-Diaz M
OpenAccess logo PLoS One 8 e76700 (2013)
PMID: 24116139

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-117739 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-directed DNA polymerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 903 amino acids
Theoretical weight: 104.52 KDa
Source organism: Escherichia phage RB69
Expression system: Escherichia coli
UniProt:
  • Canonical: Q38087 (Residues: 1-903; Coverage: 100%)
Gene name: 43
Sequence domains:
Structure domains:
DNA (5'-D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 18 nucleotides
Theoretical weight: 5.5 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 13 nucleotides
Theoretical weight: 3.97 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand XG4 4 x XG4
Ligand CA 2 x CA
Ligand SO4 6 x SO4
Ligand GOL 2 x GOL
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 74.258Å b: 119.353Å c: 148.031Å
α: 90° β: 91.64° γ: 90°
R-values:
R R work R free
0.17 0.168 0.211
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 citation in other articles

Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase.
Ren Z. (2016)
3 more

1 mention without citation

A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site.
Jacewicz et al. (2013)