› 4dwi

X-ray diffraction
1.85Å resolution

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

Released:
DOI: 10.2210/pdb4dwi/pdb
PDB entry 4dwi coloured by chain, front view.
PDB entry 4dwi coloured by chain, side view.
PDB entry 4dwi 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-117363 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 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 (5'-D(*AP*CP*TP*GP*GP*AP*TP*CP*CP*A)-3') Chains: B, C
Molecule details ›
Chains: B, C
Length: 10 nucleotides
Theoretical weight: 3.03 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand GOL 4 x GOL
Ligand SO4 6 x SO4
Ligand 9MG 1 x 9MG
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P212121
Unit cell:
a: 88.051Å b: 93.545Å c: 105.543Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.214 0.263
Expression systems:
  • Escherichia coli
  • Not provided

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