› 3qep

X-ray diffraction
1.8Å resolution

RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dTTP Opposite Difluorotoluene Nucleoside

Released:
DOI: 10.2210/pdb3qep/pdb
PDB entry 3qep coloured by chain, front view.
PDB entry 3qep coloured by chain, side view.
PDB entry 3qep coloured by chain, top view.
Source organisms:
Primary publication:
Hydrogen-bonding capability of a templating difluorotoluene nucleotide residue in an RB69 DNA polymerase ternary complex.
Xia S, Konigsberg WH, Wang J
J Am Chem Soc 133 10003-5 (2011)
PMID: 21667997

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-116759 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-directed DNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 903 amino acids
Theoretical weight: 104.49 KDa
Source organism: Escherichia phage RB69
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q38087 (Residues: 1-903; Coverage: 100%)
Gene name: 43
Sequence domains:
Structure domains:
DNA (5'-D(*TP*CP*GP*(DFT)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.53 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand TTP 1 x TTP
Ligand CA 7 x CA
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 75.133Å b: 119.774Å c: 130.481Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.167 0.204
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

1 review citation

RB69 DNA polymerase structure, kinetics, and fidelity.
Xia et al. (2014)
9 other articles

3 mentions without citation

The steric hypothesis for DNA replication and fluorine hydrogen bonding revisited in light of structural data.
Egli M. (2012)
2 more