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

X-ray diffraction
3.6Å resolution
PDB entry 1njm coloured by chain, front view.
PDB entry 1njm coloured by chain, side view.
PDB entry 1njm coloured by chain, top view.
Source organism: Deinococcus radiodurans
Assembly composition:
hetero tetramer (preferred)
Entry contents: 2 distinct polypeptide molecules
2 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Large ribosomal protein and RNA
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Multimeric state: hetero tetramer
Accessible surface area: 391380.06 Å2
Buried surface area: 2953.91 Å2
Dissociation area: 1,099.97 Å2
Dissociation energy (ΔGdiss): 25.97 kcal/mol
Dissociation entropy (TΔSdiss): 12.02 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-193331

Macromolecules

Large ribosomal subunit protein uL16
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
Pfam: Ribosomal protein L16p/L10e
InterPro:
SCOP: Large subunit
Large ribosomal subunit protein uL16 in PDB entry 1njm, assembly 1, front view.
Large ribosomal subunit protein uL16 in PDB entry 1njm, assembly 1, side view.
Large ribosomal subunit protein uL16 in PDB entry 1njm, assembly 1, top view.
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Large ribosomal subunit protein bL25
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
Pfam:
InterPro:
SCOP: Large subunit
Large ribosomal subunit protein bL25 in PDB entry 1njm, assembly 1, front view.
Large ribosomal subunit protein bL25 in PDB entry 1njm, assembly 1, side view.
Large ribosomal subunit protein bL25 in PDB entry 1njm, assembly 1, top view.
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RNA chain 0
Name: 23S ribosomal RNA
Representative chains: 0
Length: 2880 nucleotides
Theoretical weight: 933.41 KDa
Rfam: Bacterial large subunit ribosomal RNA
23S ribosomal RNA in PDB entry 1njm, assembly 1, front view.
23S ribosomal RNA in PDB entry 1njm, assembly 1, side view.
23S ribosomal RNA in PDB entry 1njm, assembly 1, top view.
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RNA chain 5
Name: tRNA acceptor stem mimic
Representative chains: 5
Length: 35 nucleotides
Theoretical weight: 11.39 KDa
tRNA acceptor stem mimic in PDB entry 1njm, assembly 1, front view.
tRNA acceptor stem mimic in PDB entry 1njm, assembly 1, side view.
tRNA acceptor stem mimic in PDB entry 1njm, assembly 1, top view.
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