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Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines

X-ray diffraction
1.9Å resolution
PDB entry 4elv coloured by chain, front view.
PDB entry 4elv coloured by chain, side view.
PDB entry 4elv 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, thermostable and DNA
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Multimeric state: hetero trimer
Accessible surface area: 25254.29 Å2
Buried surface area: 7023.28 Å2
Dissociation area: 2,067.17 Å2
Dissociation energy (ΔGdiss): 19.99 kcal/mol
Dissociation entropy (TΔSdiss): 11.89 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117425

Macromolecules

DNA polymerase I, thermostable
Chain: A
Length: 540 amino acids
Theoretical weight: 60.94 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P19821 (Residues: 293-832; Coverage: 65%)
Gene names: pol1, polA
Pfam:
InterPro:
CATH:
DNA polymerase I, thermostable in PDB entry 4elv, assembly 1, front view.
DNA polymerase I, thermostable in PDB entry 4elv, assembly 1, side view.
DNA polymerase I, thermostable in PDB entry 4elv, assembly 1, top view.
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DNA chain B
Name: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(0R8))-3')
Representative chains: B
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 12 nucleotides
Theoretical weight: 3.74 KDa
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(0R8))-3') in PDB entry 4elv, assembly 1, front view.
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(0R8))-3') in PDB entry 4elv, assembly 1, side view.
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(0R8))-3') in PDB entry 4elv, assembly 1, top view.
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DNA chain C
Name: DNA (5'-D(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
Representative chains: C
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 16 nucleotides
Theoretical weight: 4.96 KDa
DNA (5'-D(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') in PDB entry 4elv, assembly 1, front view.
DNA (5'-D(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') in PDB entry 4elv, assembly 1, side view.
DNA (5'-D(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') in PDB entry 4elv, assembly 1, top view.
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