PDBe 4ccm

X-ray diffraction
2.51Å resolution

60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1)

Released:

Function and Biology Details

Reaction catalysed:
(1a) [protein]-N(6),N(6)-dimethyl-L-lysine + 2-oxoglutarate + O(2) = [protein]-N(6)-methyl-L-lysine + succinate + formaldehyde + CO(2)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ribosomal oxygenase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 467 amino acids
Theoretical weight: 53.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H6W3 (Residues: 183-641; Coverage: 72%)
Gene names: C14orf169, MAPJD, NO66, RIOX1
Sequence domains: Cupin superfamily protein
Structure domains:
60S ribosomal protein L8 Chains: C, D
Molecule details ›
Chains: C, D
Length: 35 amino acids
Theoretical weight: 3.74 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62917 (Residues: 205-239; Coverage: 14%)
Gene name: RPL8

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: C2
Unit cell:
a: 154.77Å b: 83.5Å c: 96.87Å
α: 90° β: 100.2° γ: 90°
R-values:
R R work R free
0.228 0.228 0.236
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided