› 4bxf

X-ray diffraction
2.05Å resolution

60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II), 2-oxoglutarate (2OG) and 60S ribosomal protein L27A (RPL27A G37C) peptide fragment

Released:
DOI: 10.2210/pdb4bxf/pdb
PDB entry 4bxf coloured by chain, front view.
PDB entry 4bxf coloured by chain, side view.
PDB entry 4bxf 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:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155509 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ribosomal oxygenase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 442 amino acids
Theoretical weight: 50.37 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:
Large ribosomal subunit protein uL15 Chains: C, D
Molecule details ›
Chains: C, D
Length: 19 amino acids
Theoretical weight: 2.28 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P46776 (Residues: 32-50; Coverage: 13%)
Gene name: RPL27A

Ligands and Environments

2 bound ligands:
Ligand MN 2 x MN
Ligand AKG 2 x AKG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 70.34Å b: 88.39Å c: 167.18Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.22 0.221
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

22 review citations

2-Oxoglutarate-Dependent Oxygenases.
Islam et al. (2018)
21 more

4 mentions without citation

Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+-binding.
Guo et al. (2018)
3 more