› 3cq8

X-ray diffraction
2.5Å resolution

Ternary complex of the L415F mutant RB69 exo(-)polymerase

Released:
DOI: 10.2210/pdb3cq8/pdb
PDB entry 3cq8 coloured by chain, front view.
PDB entry 3cq8 coloured by chain, side view.
PDB entry 3cq8 coloured by chain, top view.
Source organism: Escherichia phage RB69
Primary publication:
Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity.
Zhong X, Pedersen LC, Kunkel TA
OpenAccess logo Nucleic Acids Res 36 3892-904 (2008)
PMID: 18503083

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 domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116150 (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: 104.69 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(*DAP*DCP*DAP*DGP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*DTP*DCP*DCP*DGP*DCP*DG)-3') Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.55 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided
DNA (5'-D(*DGP*DCP*DGP*DGP*DAP*DCP*DTP*DGP*DCP*DTP*DTP*DAP*DCP*DC)-3') Chain: P
Molecule details ›
Chain: P
Length: 14 nucleotides
Theoretical weight: 4.26 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand CA 6 x CA
Ligand NA 3 x NA
Ligand TTP 1 x TTP
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 80.84Å b: 117.006Å c: 127.823Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.212 0.281
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

DNA polymerase delta in DNA replication and genome maintenance.
Prindle et al. (2012)
1 more

1 mention without citation

Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity.
Zhong et al. (2008)