4nii

X-ray diffraction
1.62Å resolution

Crystal structure of AlkB D135I mutant protein with cofactors bound to dsDNA containing m6A/A

Released:
Source organism: Escherichia coli

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Alpha-ketoglutarate-dependent dioxygenase AlkB Chain: A
Molecule details ›
Chain: A
Length: 205 amino acids
Theoretical weight: 22.83 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P05050 (Residues: 12-216; Coverage: 95%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
5'-D(*TP*AP*GP*GP*TP*AP*AP*(6MA)P*AP*CP*CP*GP*T)-3' Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.07 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 41.374Å b: 75.902Å c: 52.285Å
α: 90° β: 108.6° γ: 90°
R-values:
R R work R free
0.176 0.174 0.209
Expression systems:
  • Escherichia coli
  • Not provided