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Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

X-ray diffraction
1.51Å resolution
PDB entry 3o1p coloured by chain, front view.
PDB entry 3o1p coloured by chain, side view.
PDB entry 3o1p coloured by chain, top view.
Source organism: Escherichia coli K-12
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: Alpha-ketoglutarate-dependent dioxygenase AlkB and DNA
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Multimeric state: hetero trimer
Accessible surface area: 12550.2 Å2
Buried surface area: 4149.96 Å2
Dissociation area: 1,662.28 Å2
Dissociation energy (ΔGdiss): 4.26 kcal/mol
Dissociation entropy (TΔSdiss): 20.26 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116632

Macromolecules

Alpha-ketoglutarate-dependent dioxygenase AlkB
Chain: A
Length: 206 amino acids
Theoretical weight: 22.96 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P05050 (Residues: 12-216; Coverage: 95%)
Gene names: JW2200, aidD, alkB, b2212
InterPro:
CATH: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
Alpha-ketoglutarate-dependent dioxygenase AlkB in PDB entry 3o1p, assembly 1, front view.
Alpha-ketoglutarate-dependent dioxygenase AlkB in PDB entry 3o1p, assembly 1, side view.
Alpha-ketoglutarate-dependent dioxygenase AlkB in PDB entry 3o1p, assembly 1, top view.
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DNA chain B
Name: DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(EDA)P*AP*CP*CP*GP*T)-3')
Representative chains: B
Source organism: Escherichia coli K-12 [83333]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 4.08 KDa
DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(EDA)P*AP*CP*CP*GP*T)-3') in PDB entry 3o1p, assembly 1, front view.
DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(EDA)P*AP*CP*CP*GP*T)-3') in PDB entry 3o1p, assembly 1, side view.
DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(EDA)P*AP*CP*CP*GP*T)-3') in PDB entry 3o1p, assembly 1, top view.
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DNA chain C
Name: DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3')
Representative chains: C
Source organism: Escherichia coli K-12 [83333]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3') in PDB entry 3o1p, assembly 1, front view.
DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3') in PDB entry 3o1p, assembly 1, side view.
DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3') in PDB entry 3o1p, assembly 1, top view.
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