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Crystal structure of a salicylic aldehyde base in the pre-insertion site of fragment DNA polymerase I from Bacillus stearothermophilus

X-ray diffraction
3.05Å resolution
PDB entry 2xy7 coloured by chain, front view.
PDB entry 2xy7 coloured by chain, side view.
PDB entry 2xy7 coloured by chain, top view.
Source organisms:
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: 26467.6 Å2
Buried surface area: 5640.33 Å2
Dissociation area: 1,807.2 Å2
Dissociation energy (ΔGdiss): 20.23 kcal/mol
Dissociation entropy (TΔSdiss): 11.34 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-115943

Macromolecules

DNA polymerase I
Chain: A
Length: 580 amino acids
Theoretical weight: 66.18 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: E1C9K5 (Residues: 1-580; Coverage: 100%)
Gene name: polA
Pfam:
InterPro:
CATH:
DNA polymerase I in PDB entry 2xy7, assembly 1, front view.
DNA polymerase I in PDB entry 2xy7, assembly 1, side view.
DNA polymerase I in PDB entry 2xy7, assembly 1, top view.
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DNA chain B
Name: 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP)-3'
Representative chains: B
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 10 nucleotides
Theoretical weight: 3.02 KDa
5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP)-3' in PDB entry 2xy7, assembly 1, front view.
5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP)-3' in PDB entry 2xy7, assembly 1, side view.
5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP)-3' in PDB entry 2xy7, assembly 1, top view.
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DNA chain C
Name: 5'-D(*SAYP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP)-3'
Representative chains: C
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
5'-D(*SAYP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP)-3' in PDB entry 2xy7, assembly 1, front view.
5'-D(*SAYP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP)-3' in PDB entry 2xy7, assembly 1, side view.
5'-D(*SAYP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP)-3' in PDB entry 2xy7, assembly 1, top view.
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