› 2ogm

X-ray diffraction
3.5Å resolution

The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519

Released:
DOI: 10.2210/pdb2ogm/pdb
PDB entry 2ogm coloured by chain, front view.
PDB entry 2ogm coloured by chain, side view.
PDB entry 2ogm coloured by chain, top view.
Source organism: Deinococcus radiodurans
Primary publication:
Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity.
Davidovich C, Bashan A, Auerbach-Nevo T, Yaggie RD, Gontarek RR, Yonath A
Proc Natl Acad Sci U S A 104 4291-6 (2007)
PMID: 17360517

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193338 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 211 amino acids
Theoretical weight: 22.48 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXK2 (Residues: 1-211; Coverage: 100%)
Gene names: DR_0311, rplC
Sequence domains: Ribosomal protein L3
23S ribosomal RNA Chain: 0
Molecule details ›
Chain: 0
Length: 2880 nucleotides
Theoretical weight: 933.41 KDa
Source organism: Deinococcus radiodurans
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand G19 1 x G19
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: I222
Unit cell:
a: 170.396Å b: 405.835Å c: 703.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.275 0.275 0.334

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Citations

27 review citations

Antibiotics for emerging pathogens.
Fischbach et al. (2009)
26 more

7 mentions without citation

RNA versatility, flexibility, and thermostability for practice in RNA nanotechnology and biomedical applications.
Haque et al. (2018)
6 more