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Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate and methylated trinucleotide T-meC-T

X-ray diffraction
1.6Å resolution
PDB entry 3i49 coloured by chain, front view.
PDB entry 3i49 coloured by chain, side view.
PDB entry 3i49 coloured by chain, top view.
Source organism: Escherichia coli K-12
Assembly composition:
hetero dimer (preferred)
Entry contents: 1 distinct polypeptide molecule
1 distinct DNA molecule

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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 dimer
Accessible surface area: 9224.24 Å2
Buried surface area: 1582.21 Å2
Dissociation area: 546.1 Å2
Dissociation energy (ΔGdiss): 4.49 kcal/mol
Dissociation entropy (TΔSdiss): 6.61 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116393

Macromolecules

Alpha-ketoglutarate-dependent dioxygenase AlkB
Chain: A
Length: 211 amino acids
Theoretical weight: 23.61 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 3i49, assembly 1, front view.
Alpha-ketoglutarate-dependent dioxygenase AlkB in PDB entry 3i49, assembly 1, side view.
Alpha-ketoglutarate-dependent dioxygenase AlkB in PDB entry 3i49, assembly 1, top view.
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DNA chain B
Name: DNA (5'-D(P*TP*(ME6)P*T)-3')
Representative chains: B
Source organism: Escherichia coli K-12 [83333]
Expression system: Not provided
Length: 3 nucleotides
Theoretical weight: 868 Da
DNA (5'-D(P*TP*(ME6)P*T)-3') in PDB entry 3i49, assembly 1, front view.
DNA (5'-D(P*TP*(ME6)P*T)-3') in PDB entry 3i49, assembly 1, side view.
DNA (5'-D(P*TP*(ME6)P*T)-3') in PDB entry 3i49, assembly 1, top view.
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