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Dpo4 extension ternary complex with disordered A opposite an oxoG in anti conformation

X-ray diffraction
2.6Å resolution
PDB entry 3gii coloured by chain, front view.
PDB entry 3gii coloured by chain, side view.
PDB entry 3gii 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: 20553.15 Å2
Buried surface area: 6330.85 Å2
Dissociation area: 1,856.93 Å2
Dissociation energy (ΔGdiss): 33.85 kcal/mol
Dissociation entropy (TΔSdiss): 12.24 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116299

Macromolecules

DNA polymerase IV
Chain: A
Length: 341 amino acids
Theoretical weight: 38.95 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 2-341; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Pfam:
InterPro:
CATH:
DNA polymerase IV in PDB entry 3gii, assembly 1, front view.
DNA polymerase IV in PDB entry 3gii, assembly 1, side view.
DNA polymerase IV in PDB entry 3gii, assembly 1, top view.
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DNA chain D
Name: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3'
Representative chains: D
Source organism: Saccharolobus solfataricus P2 [273057]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 4.07 KDa
5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3' in PDB entry 3gii, assembly 1, front view.
5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3' in PDB entry 3gii, assembly 1, side view.
5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3' in PDB entry 3gii, assembly 1, top view.
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DNA chain E
Name: 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3'
Representative chains: E
Source organism: Saccharolobus solfataricus P2 [273057]
Expression system: Not provided
Length: 19 nucleotides
Theoretical weight: 5.69 KDa
5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' in PDB entry 3gii, assembly 1, front view.
5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' in PDB entry 3gii, assembly 1, side view.
5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' in PDB entry 3gii, assembly 1, top view.
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