› 4dsj

X-ray diffraction
2.86Å resolution

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA, dGTP and Calcium

Released:
DOI: 10.2210/pdb4dsj/pdb
PDB entry 4dsj coloured by chain, front view.
PDB entry 4dsj coloured by chain, side view.
PDB entry 4dsj coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Entry authors: Gan JH, Abdur R, Liu HH, Sheng J, Caton-Willians J, Soares AS, Huang Z

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-117348 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I Chains: A, B
Molecule details ›
Chains: A, B
Length: 579 amino acids
Theoretical weight: 66.1 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: E1C9K5 (Residues: 2-580; Coverage: 100%)
Gene name: polA
Sequence domains: DNA polymerase family A
Structure domains:
DNA Chains: C, E
Molecule details ›
Chains: C, E
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
dGTP Chains: D, F
Molecule details ›
Chains: D, F
Length: 10 nucleotides
Theoretical weight: 3.02 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DGT 1 x DGT
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12B
Spacegroup: P212121
Unit cell:
a: 60.016Å b: 112.07Å c: 229.45Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.213 0.277
Expression systems:
  • Escherichia coli
  • Not provided

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