2JA9 Rna-Binding Protein date Nov 24, 2006
title Structure Of The N-Terminal Deletion Of Yeast Exosome Component Rrp40
authors A.Oddone, E.Lorentzen, J.Basquin, A.Gasch, V.Rybin, E.Conti, M.Sattler
compound source
Molecule: Exosome Complex Exonuclease Rrp40
Chain: A
Fragment: Residues 62-236
Synonym: Rrp40, Ribosomal Rna-Processing Protein 40
Ec: 3.1.13.-
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: I 41 3 2
R_factor 0.189 R_Free 0.206
crystal
cell
length a length b length c angle alpha angle beta angle gamma
153.510 153.510 153.510 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand
enzyme Hydrolase E.C.3.1.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural and biochemical characterization of the yeast exosome component Rrp40., Oddone A, Lorentzen E, Basquin J, Gasch A, Rybin V, Conti E, Sattler M, EMBO Rep. 2007 Jan;8(1):63-9. Epub 2006 Dec 8. PMID:17159918
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (34 Kb) [Save to disk]
  • Biological Unit Coordinates (2ja9.pdb1.gz) 58 Kb
  • CSU: Contacts of Structural Units for 2JA9
  • Likely Quarternary Molecular Structure file(s) for 2JA9
  • Structure Factors (222 Kb)
  • Retrieve 2JA9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2JA9 from S2C, [Save to disk]
  • Re-refined 2ja9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2JA9 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 2JA9
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2JA9, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ja9_A] [2ja9]
  • SWISS-PROT database: [Q08285]
  • Domain organization of [RRP40_YEAST] by SWISSPFAM
  • Domain found in 2JA9: [S1 ] by SMART
    • Other resources with information on 2JA9
  • Community annotation for 2JA9 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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