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Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4

X-ray diffraction
2.27Å resolution
PDB entry 2c28 coloured by chain, front view.
PDB entry 2c28 coloured by chain, side view.
PDB entry 2c28 coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
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 IV and DNA
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Multimeric state: hetero trimer
Accessible surface area: 19769.76 Å2
Buried surface area: 5284.01 Å2
Dissociation area: 1,685.56 Å2
Dissociation energy (ΔGdiss): 36.95 kcal/mol
Dissociation entropy (TΔSdiss): 12.03 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-115131

Macromolecules

DNA polymerase IV
Chain: A
Length: 358 amino acids
Theoretical weight: 41.09 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Pfam:
InterPro:
CATH:
SCOP:
DNA polymerase IV in PDB entry 2c28, assembly 1, front view.
DNA polymerase IV in PDB entry 2c28, assembly 1, side view.
DNA polymerase IV in PDB entry 2c28, assembly 1, top view.
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DNA chain P
Name: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*C)-3'
Representative chains: P
Source organism: Saccharolobus solfataricus P2 [273057]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 4.1 KDa
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*C)-3' in PDB entry 2c28, assembly 1, front view.
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*C)-3' in PDB entry 2c28, assembly 1, side view.
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*C)-3' in PDB entry 2c28, assembly 1, top view.
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DNA chain T
Name: 5'-D(TP*CP*AP*C 8OGP*GP*AP*AP*TP*CP*CP*TP *TP*CP*CP*CP*CP*C)-3'
Representative chains: T
Source organism: Saccharolobus solfataricus P2 [273057]
Expression system: Not provided
Length: 18 nucleotides
Theoretical weight: 5.39 KDa
5'-D(TP*CP*AP*C 8OGP*GP*AP*AP*TP*CP*CP*TP *TP*CP*CP*CP*CP*C)-3' in PDB entry 2c28, assembly 1, front view.
5'-D(TP*CP*AP*C 8OGP*GP*AP*AP*TP*CP*CP*TP *TP*CP*CP*CP*CP*C)-3' in PDB entry 2c28, assembly 1, side view.
5'-D(TP*CP*AP*C 8OGP*GP*AP*AP*TP*CP*CP*TP *TP*CP*CP*CP*CP*C)-3' in PDB entry 2c28, assembly 1, top view.
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