› 3px4

X-ray diffraction
1.58Å resolution

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (wobble) in Ajar Conformation

Released:
DOI: 10.2210/pdb3px4/pdb
PDB entry 3px4 coloured by chain, front view.
PDB entry 3px4 coloured by chain, side view.
PDB entry 3px4 coloured by chain, top view.
Source organism: Geobacillus kaustophilus
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

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-116722 (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 kaustophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5KWC1 (Residues: 287-878; Coverage: 67%)
Gene names: GK2730, polA
Sequence domains:
Structure domains:
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 9 nucleotides
Theoretical weight: 2.64 KDa
Source organism: Geobacillus kaustophilus
Expression system: Not provided
DNA (5'-D(*CP*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 4.04 KDa
Source organism: Geobacillus kaustophilus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand DCT 2 x DCT
Ligand MG 1 x MG
Ligand SO4 2 x SO4
1 modified residue:
Ligand DOC 2 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P212121
Unit cell:
a: 93.68Å b: 109.19Å c: 150.46Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.211 0.239
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

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

4 mentions without citation

Recent progress in dissecting molecular recognition by DNA polymerases with non-native substrates.
Pugliese et al. (2017)
3 more