› 4bu2

X-ray diffraction
2.78Å resolution

60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG)

Released:
DOI: 10.2210/pdb4bu2/pdb
PDB entry 4bu2 coloured by chain, front view.
PDB entry 4bu2 coloured by chain, side view.
PDB entry 4bu2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Ribosomal oxygenases are structurally conserved from prokaryotes to humans.
Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifton IJ, Ge W, Kershaw NJ, Fox GC, Muniz JRC, Vollmar M, Phillips C, Pilka ES, Kavanagh KL, von Delft F, Oppermann U, McDonough MA, Doherty AJ, Schofield CJ
Nature 510 422-426 (2014)
PMID: 24814345

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184850 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosomal oxygenase 2 Chain: A
Molecule details ›
Chain: A
Length: 442 amino acids
Theoretical weight: 50.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8IUF8 (Residues: 26-465; Coverage: 95%)
Gene names: MDIG, MINA, MINA53, NO52, RIOX2
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand NI 2 x NI
Ligand AKG 1 x AKG
Ligand EDO 4 x EDO
1 modified residue:
Ligand MSE 8 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P4332
Unit cell:
a: 184.632Å b: 184.632Å c: 184.632Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.228 0.233
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

21 review citations

Histone demethylases in chromatin biology and beyond.
Dimitrova et al. (2015)
20 more

4 mentions without citation

Post-translational hydroxylation by 2OG/Fe(II)-dependent oxygenases as a novel regulatory mechanism in bacteria.
van Staalduinen et al. (2014)
3 more