› 3thv

X-ray diffraction
1.61Å resolution

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddATP-dT in Closed Conformation

Released:
DOI: 10.2210/pdb3thv/pdb
PDB entry 3thv coloured by chain, front view.
PDB entry 3thv coloured by chain, side view.
PDB entry 3thv coloured by chain, top view.
Source organism: Geobacillus
Primary publication:
Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.
Wang W, Hellinga HW, Beese LS
Proc Natl Acad Sci U S A 108 17644-8 (2011)
PMID: 22006298

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-116933 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I Chains: A, D
Molecule details ›
Chains: A, D
Length: 592 amino acids
Theoretical weight: 67.49 KDa
Source organism: Geobacillus
Expression system: Escherichia coli BL21(DE3)
Structure domains:
5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(2DA))-3' Chains: B, E
Molecule details ›
Chains: B, E
Length: 9 nucleotides
Theoretical weight: 2.66 KDa
Source organism: Geobacillus
Expression system: Not provided
5'-D(*C*AP*TP*TP*TP*GP*AP*GP*TP*CP*AP*GP*G)-3' Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 4.01 KDa
Source organism: Geobacillus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand DDS 2 x DDS
Ligand MG 2 x MG
Ligand SO4 3 x SO4
1 modified residue:
Ligand 2DA 2 x 2DA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P212121
Unit cell:
a: 93.81Å b: 109.27Å c: 150.43Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.193 0.224
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

12 review citations

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Šponer et al. (2018)
11 more

4 mentions without citation

An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η.
Yang W. (2014)
3 more