› 3s9h

X-ray diffraction
1.95Å resolution

RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) ternary complex with dUpNpp and a dideoxy-terminated primer in the presence of Ca2+

Released:
DOI: 10.2210/pdb3s9h/pdb
PDB entry 3s9h coloured by chain, front view.
PDB entry 3s9h coloured by chain, side view.
PDB entry 3s9h coloured by chain, top view.
Source organism: Escherichia phage RB69
Primary publication:
Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase.
Xia S, Wang M, Blaha G, Konigsberg WH, Wang J
Biochemistry 50 9114-24 (2011)
PMID: 21923197

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-116867 (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(DE3)
UniProt:
  • Canonical: Q38087 (Residues: 1-903; Coverage: 100%)
Gene name: 43
Sequence domains:
Structure domains:
5'-D(*TP*CP*AP*AP*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: Escherichia phage RB69
Expression system: Not provided
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: Escherichia phage RB69
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 75.05Å b: 119.821Å c: 130.791Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.171 0.213
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases.
Vashishtha et al. (2016)
5 more

1 mention without citation

Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase.
Xia et al. (2011)