1DV4 Ribosome date Jan 19, 2000
title Partial Structure Of 16s Rna Of The Small Ribosomal Subunit Thermus Thermophilus
authors A.Tocilj, F.Schlunzen, D.Janell, M.Gluhmann, H.Hansen, J.Harms, A. H.Bartels, I.Agmon, F.Franceschi, A.Yonath
compound source
Molecule: 16s Ribosomal Rna
Chain: A
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Ribosomal Protein S5
Chain: E
Fragment: Residues 4-148
Synonym: Bs5

Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422

Molecule: Ribosomal Protein S7
Chain: G
Fragment: Residues 12-146

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 41 21 2
R_factor
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
407.100 407.100 176.008 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.50 Å
ligand WO2 enzyme
note 1DV4 supersedes 1C59
Gene
Ontology
ChainFunctionProcessComponent
E


G


Primary referenceThe small ribosomal subunit from Thermus thermophilus at 4.5 A resolution: pattern fittings and the identification of a functional site., Tocilj A, Schlunzen F, Janell D, Gluhmann M, Hansen HA, Harms J, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A, Proc Natl Acad Sci U S A 1999 Dec 7;96(25):14252-7. PMID:10588692
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (1dv4.pdb1.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 1DV4
  • CSU: Contacts of Structural Units for 1DV4
  • Likely Quarternary Molecular Structure file(s) for 1DV4
  • Retrieve 1DV4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DV4 from S2C, [Save to disk]
  • View 1DV4 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 1DV4
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dv4a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1dv4e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1dv4g_, region G [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1dv4_G] [1dv4] [1dv4_A] [1dv4_E]
  • SWISS-PROT database: [P02357] [P17291]
  • Domain organization of [RS5_BACST] [RS7_THET8] by SWISSPFAM
  • Other resources with information on 1DV4
  • Community annotation for 1DV4 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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