› 4dsi

X-ray diffraction
2.05Å resolution

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

Released:
DOI: 10.2210/pdb4dsi/pdb
PDB entry 4dsi coloured by chain, front view.
PDB entry 4dsi coloured by chain, side view.
PDB entry 4dsi 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-117347 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
Length: 581 amino acids
Theoretical weight: 66.25 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 Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
Se-dGTP Chain: C
Molecule details ›
Chain: C
Length: 9 nucleotides
Theoretical weight: 2.69 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand GOL 5 x GOL
Ligand SO4 3 x SO4
Ligand DG 1 x DG
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 88.573Å b: 93.387Å c: 105.928Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.191 0.234
Expression systems:
  • Escherichia coli
  • Not provided

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