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Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA

X-ray diffraction
2.28Å resolution
PDB entry 2w9b coloured by chain, front view.
PDB entry 2w9b coloured by chain, side view.
PDB entry 2w9b coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Assembly composition:
hetero trimer (preferred)
Entry contents: 2 distinct polypeptide molecules
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: 20151.7 Å2
Buried surface area: 5241.24 Å2
Dissociation area: 1,726.88 Å2
Dissociation energy (ΔGdiss): 31.49 kcal/mol
Dissociation entropy (TΔSdiss): 12.04 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-218926
Assembly 2
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Assembly Name: DNA polymerase IV and DNA
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Multimeric state: hetero trimer
Accessible surface area: 20251.61 Å2
Buried surface area: 5419.4 Å2
Dissociation area: 1,790.41 Å2
Dissociation energy (ΔGdiss): 29.5 kcal/mol
Dissociation entropy (TΔSdiss): 12.07 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-218926

Macromolecules

DNA polymerase IV
Chain: A
Length: 358 amino acids
Theoretical weight: 41.11 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:
DNA polymerase IV in PDB entry 2w9b, assembly 1, front view.
DNA polymerase IV in PDB entry 2w9b, assembly 1, side view.
DNA polymerase IV in PDB entry 2w9b, assembly 1, top view.
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DNA polymerase IV
Chain: B
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:
DNA polymerase IV in PDB entry 2w9b, assembly 2, front view.
DNA polymerase IV in PDB entry 2w9b, assembly 2, side view.
DNA polymerase IV in PDB entry 2w9b, assembly 2, top view.
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DNA chains C, D
Name: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOCP)-3'
Representative chains: C, D
Length: 14 nucleotides
Theoretical weight: 4.37 KDa
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOCP)-3' in PDB entry 2w9b, assembly 1, front view.
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOCP)-3' in PDB entry 2w9b, assembly 1, side view.
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOCP)-3' in PDB entry 2w9b, assembly 1, top view.
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DNA chains E, F
Name: 5'-D(*TP*CP*AP*TP*M2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'
Representative chains: E, F
Length: 18 nucleotides
Theoretical weight: 5.42 KDa
5'-D(*TP*CP*AP*TP*M2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' in PDB entry 2w9b, assembly 1, front view.
5'-D(*TP*CP*AP*TP*M2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' in PDB entry 2w9b, assembly 1, side view.
5'-D(*TP*CP*AP*TP*M2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' in PDB entry 2w9b, assembly 1, top view.
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