› 3qno

X-ray diffraction
1.88Å resolution

RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite 3tCo

Released:
DOI: 10.2210/pdb3qno/pdb
PDB entry 3qno coloured by chain, front view.
PDB entry 3qno coloured by chain, side view.
PDB entry 3qno coloured by chain, top view.
Source organism: Escherichia phage RB69
Primary publication:
Using a fluorescent cytosine analogue tC(o) to probe the effect of the Y567 to Ala substitution on the preinsertion steps of dNMP incorporation by RB69 DNA polymerase.
Xia S, Beckman J, Wang J, Konigsberg WH
Biochemistry 51 4609-17 (2012)
PMID: 22616982

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-116778 (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: 901 amino acids
Theoretical weight: 104.3 KDa
Source organism: Escherichia phage RB69
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q38087 (Residues: 1-901; Coverage: 100%)
Gene name: 43
Sequence domains:
Structure domains:
DNA Tempalte Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.59 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided
DNA Primer Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ATP 1 x ATP
Ligand CA 4 x CA
2 modified residues:
Ligand YCO 1 x YCO
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 74.882Å b: 120.495Å c: 130.85Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.174 0.212
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

1 review citation

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

1 mention without citation

Using a fluorescent cytosine analogue tC(o) to probe the effect of the Y567 to Ala substitution on the preinsertion steps of dNMP incorporation by RB69 DNA polymerase.
Xia et al. (2012)