1njm

X-ray diffraction
3.6Å resolution

The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (4 distinct):
50S ribosomal protein L16 Chain: K
Molecule details ›
Chain: K
Length: 141 amino acids
Theoretical weight: 16.13 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RXJ5 (Residues: 1-141; Coverage: 100%)
Gene names: DR_0318, rplP
Sequence domains: Ribosomal protein L16p/L10e
50S ribosomal protein L25 Chain: T
Molecule details ›
Chain: T
Length: 237 amino acids
Theoretical weight: 25.42 KDa
Source organism: Deinococcus radiodurans
UniProt:
  • Canonical: Q9RX88 (Residues: 1-237; Coverage: 100%)
Gene names: DR_0427, ctc, rplY
Sequence domains:
23S ribosomal RNA Chain: 0
Molecule details ›
Chain: 0
Length: 2880 nucleotides
Theoretical weight: 933.41 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
tRNA acceptor stem mimic Chain: 5
Molecule details ›
Chain: 5
Length: 35 nucleotides
Theoretical weight: 11.39 KDa

Ligands and Environments

1 bound ligand:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: I222
Unit cell:
a: 169.6Å b: 409.4Å c: 695.1Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.284 0.284 0.308