PDBe 4y3o

X-ray diffraction
2.2Å resolution

Crystal structure of Ribosomal oxygenase NO66 in complex with substrate Rpl8 peptide and Ni(II) and cofactor N-oxalyglycine

Released:
Source organism: Homo sapiens
Primary publication:
Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8.
OpenAccess logo Acta Crystallogr. D Biol. Crystallogr. 71 1955-64 (2015)
PMID: 26327385

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ribosomal oxygenase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 466 amino acids
Theoretical weight: 52.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H6W3 (Residues: 176-641; Coverage: 73%)
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: 11 amino acids
Theoretical weight: 1.1 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62917 (Residues: 212-222; Coverage: 4%)
Gene name: RPL8

Ligands and Environments


No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2
Unit cell:
a: 88.5Å b: 202.93Å c: 85.68Å
α: 90° β: 118.94° γ: 90°
R-values:
R R work R free
0.206 0.203 0.262
Expression systems:
  • Escherichia coli
  • Not provided