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Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA , dCTP, and zinc (closed form).

X-ray diffraction
1.9Å resolution
PDB entry 3ez5 coloured by chain, front view.
PDB entry 3ez5 coloured by chain, side view.
PDB entry 3ez5 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: 27213.61 Å2
Buried surface area: 7161.37 Å2
Dissociation area: 1,679.38 Å2
Dissociation energy (ΔGdiss): 26.8 kcal/mol
Dissociation entropy (TΔSdiss): 10.62 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116229
Assembly 2
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Assembly Name: DNA polymerase I and DNA
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Multimeric state: hetero trimer
Accessible surface area: 27008.85 Å2
Buried surface area: 7113.94 Å2
Dissociation area: 1,678.98 Å2
Dissociation energy (ΔGdiss): 26.56 kcal/mol
Dissociation entropy (TΔSdiss): 10.64 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116229

Macromolecules

DNA polymerase I
Chains: A, D
Length: 580 amino acids
Theoretical weight: 66.2 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P52026 (Residues: 299-876; Coverage: 66%)
Gene names: pol, polA
Pfam:
InterPro:
CATH:
DNA polymerase I in PDB entry 3ez5, assembly 1, front view.
DNA polymerase I in PDB entry 3ez5, assembly 1, side view.
DNA polymerase I in PDB entry 3ez5, assembly 1, top view.
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DNA chains B, E
Name: 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3'
Representative chains: B, E
Source organism: Geobacillus stearothermophilus [1422]
Expression system: Not provided
Length: 9 nucleotides
Theoretical weight: 2.69 KDa
5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3' in PDB entry 3ez5, assembly 1, front view.
5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3' in PDB entry 3ez5, assembly 1, side view.
5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3' in PDB entry 3ez5, assembly 1, top view.
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DNA chains C, F
Name: 5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3'
Representative chains: C, F
Source organism: Geobacillus stearothermophilus [1422]
Expression system: Not provided
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3' in PDB entry 3ez5, assembly 1, front view.
5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3' in PDB entry 3ez5, assembly 1, side view.
5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3' in PDB entry 3ez5, assembly 1, top view.
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