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

X-ray diffraction
2.05Å resolution
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
Assembly composition:
hetero trimer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA polymerase I and DNA
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Multimeric state: hetero trimer
Accessible surface area: 27396.78 Å2
Buried surface area: 6607.22 Å2
Dissociation area: 1,376.29 Å2
Dissociation energy (ΔGdiss): 22.31 kcal/mol
Dissociation entropy (TΔSdiss): 9.91 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117347

Macromolecules

DNA polymerase I
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
Pfam:
InterPro:
CATH:
DNA polymerase I in PDB entry 4dsi, assembly 1, front view.
DNA polymerase I in PDB entry 4dsi, assembly 1, side view.
DNA polymerase I in PDB entry 4dsi, assembly 1, top view.
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DNA chain B
Name: DNA
Representative chains: B
Source organism: Geobacillus stearothermophilus [1422]
Expression system: Not provided
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
DNA in PDB entry 4dsi, assembly 1, front view.
DNA in PDB entry 4dsi, assembly 1, side view.
DNA in PDB entry 4dsi, assembly 1, top view.
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DNA chain C
Name: Se-dGTP
Representative chains: C
Source organism: Geobacillus stearothermophilus [1422]
Expression system: Not provided
Length: 9 nucleotides
Theoretical weight: 2.69 KDa
Se-dGTP in PDB entry 4dsi, assembly 1, front view.
Se-dGTP in PDB entry 4dsi, assembly 1, side view.
Se-dGTP in PDB entry 4dsi, assembly 1, top view.
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