1NJM Ribosome date Jan 02, 2003
title The Crystal Structure Of The 50s Large Ribosomal Subunit From Deinococcus Radiodurans Complexed With A Trna Acceptor Stem Mimic (Asm) And The Antibiotic Sparsomycin
authors A.Bashan, I.Agmon, R.Zarivatch, F.Schluenzen, J.M.Harms, R.Berisio, H.Bartels, H.A.Hansen, A.Yonath
compound source
Molecule: 23s Ribosomal Rna
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: Trna Acceptor Stem Mimic
Chain: 5
Engineered: Yes

Synthetic: Yes
Other_details: The Terminal C Of Asm Was Coupled Via A Phosphodiester Bond To The 5 Oh Of The N6-Dimethyl Moiety Of Puromycin;

Molecule: 50s Ribosomal Protein L16
Chain: K

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: General Stress Protein Ctc
Chain: T

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299
symmetry Space Group: I 2 2 2
R_factor 0.284 R_Free 0.308
length a length b length c angle alpha angle beta angle gamma
169.600 409.400 695.100 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand PPU, SPS enzyme


Primary referenceStructural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression., Bashan A, Agmon I, Zarivach R, Schluenzen F, Harms J, Berisio R, Bartels H, Franceschi F, Auerbach T, Hansen HA, Kossoy E, Kessler M, Yonath A, Mol Cell 2003 Jan;11(1):91-102. PMID:12535524
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1038 Kb) [Save to disk]
  • Biological Unit Coordinates (1njm.pdb1.gz) 1033 Kb
  • LPC: Ligand-Protein Contacts for 1NJM
  • CSU: Contacts of Structural Units for 1NJM
  • Likely Quarternary Molecular Structure file(s) for 1NJM
  • Retrieve 1NJM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NJM from S2C, [Save to disk]
  • View 1NJM in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1NJM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1NJM, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1njm0_, region 0 [Jmol] [rasmolscript] [script source]
        - Domain d1njmk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1njmt_, region T [Jmol] [rasmolscript] [script source]
  • Fold representative 1njm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1njm_5] [1njm_0] [1njm_K] [1njm] [1njm_T]
  • SWISS-PROT database: [Q9RXJ5] [Q9RX88]
  • Domain organization of [RL16_DEIRA] [RL25_DEIRA] by SWISSPFAM
  • Other resources with information on 1NJM
  • Community annotation for 1NJM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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