2DYJ Ribosomal Protein date Sep 14, 2006
title Crystal Structure Of Ribosome-Binding Factor A From Thermus Thermophilus Hb8
authors M.Kawazoe, C.Takemoto, R.Nakayama-Ushikoshi, T.Terada, M.Shirouz S.Yokoyama, Riken Structural Genomicsproteomics Initiative
compound source
Molecule: Ribosome-Binding Factor A
Chain: A, B
Engineered: Yes
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Ttha0907
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11b
symmetry Space Group: P 1 21 1
R_factor 0.199 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
28.426 65.838 43.173 90.00 96.18 90.00
method X-Ray Diffractionresolution 1.84 Å
note 2DYJ is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural aspects of RbfA action during small ribosomal subunit assembly., Datta PP, Wilson DN, Kawazoe M, Swami NK, Kaminishi T, Sharma MR, Booth TM, Takemoto C, Fucini P, Yokoyama S, Agrawal RK, Mol Cell. 2007 Nov 9;28(3):434-45. PMID:17996707
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk]
  • Biological Unit Coordinates (2dyj.pdb1.gz) 16 Kb
  • Biological Unit Coordinates (2dyj.pdb2.gz) 16 Kb
  • CSU: Contacts of Structural Units for 2DYJ
  • Likely Quarternary Molecular Structure file(s) for 2DYJ
  • Structure Factors (102 Kb)
  • Retrieve 2DYJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DYJ from S2C, [Save to disk]
  • Re-refined 2dyj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2DYJ 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 2DYJ
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2DYJ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dyj] [2dyj_A] [2dyj_B]
  • SWISS-PROT database: [Q5SJV1]
  • Domain organization of [Q5SJV1_THET8] by SWISSPFAM
    • Other resources with information on 2DYJ
  • Community annotation for 2DYJ 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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