› 4csw

X-ray diffraction
2.82Å resolution

Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase

Released:
DOI: 10.2210/pdb4csw/pdb
PDB entry 4csw coloured by chain, front view.
PDB entry 4csw coloured by chain, side view.
PDB entry 4csw coloured by chain, top view.
Source organism: Rhodothermus marinus DSM 4252
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:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112032 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
JmjC domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 406 amino acids
Theoretical weight: 45.8 KDa
Source organism: Rhodothermus marinus DSM 4252
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: D0MK34 (Residues: 1-392; Coverage: 100%)
Gene name: Rmar_0038
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand CIT 1 x CIT
Ligand UN9 2 x UN9
Ligand GOL 1 x GOL
Ligand MN 1 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: C2
Unit cell:
a: 158.3Å b: 87.69Å c: 90.61Å
α: 90° β: 113.1° γ: 90°
R-values:
R R work R free
0.171 0.168 0.21
Expression system: Escherichia coli BL21

Quick links

Citations

22 review citations

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

1 mention without citation

Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8.
Wang et al. (2015)