PDBe 4zhn

X-ray diffraction
1.33Å resolution

Crystal Structure of AlkB T208A mutant protein in complex with Co(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T

Entry authors: Ergel B, Yu B, Vorobiev SM, Forouhar F, Hunt JF, Northeast Structural Genomics Consortium (NESG)

Function and Biology Details

Reaction catalysed:
DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA-base + formaldehyde + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Alpha-ketoglutarate-dependent dioxygenase AlkB Chain: A
Molecule details ›
Chain: A
Length: 211 amino acids
Theoretical weight: 23.58 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
  • Canonical: P05050 (Residues: 12-216; Coverage: 95%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
methylated trinucleotide DNA T-meA-T Chain: B
Molecule details ›
Chain: B
Length: 3 nucleotides
Theoretical weight: 892 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P43
Unit cell:
a: 41.373Å b: 41.373Å c: 116.569Å
α: 90° β: 90° γ: 90°
R R work R free
0.119 0.118 0.147
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided