4dsk

X-ray diffraction
2.18Å resolution

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

Released:
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:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I Chain: A
Molecule details ›
Chain: A
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 (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*CP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.31 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
DNA (5'-D(*TP*CP*AP*CP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 17 nucleotides
Theoretical weight: 5.16 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12B
Spacegroup: P212121
Unit cell:
a: 86.692Å b: 93.339Å c: 106.363Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.185 0.243
Expression systems:
  • Escherichia coli
  • Not provided