2OJR Protein Binding date Jan 13, 2007
title Structure Of Ubiquitin Solved By Sad Using The Lanthanide-Bi
authors N.R.Silvaggi, K.N.Allen
compound source
Molecule: Ubiquitin
Chain: A
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21-De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Modified Pet-11a
symmetry Space Group: P 32 2 1
R_factor 0.216 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.870 57.870 115.260 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand TB enzyme
Primary referenceDouble-Lanthanide-Binding Tags for Macromolecular Crystallographic Structure Determination., Silvaggi NR, Martin LJ, Schwalbe H, Imperiali B, Allen KN, J Am Chem Soc. 2007 Jun 6;129(22):7114-7120. Epub 2007 May 12. PMID:17497863
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (23 Kb) [Save to disk]
  • Biological Unit Coordinates (2ojr.pdb1.gz) 18 Kb
  • LPC: Ligand-Protein Contacts for 2OJR
  • CSU: Contacts of Structural Units for 2OJR
  • Likely Quarternary Molecular Structure file(s) for 2OJR
  • Structure Factors (135 Kb)
  • Retrieve 2OJR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OJR from S2C, [Save to disk]
  • Re-refined 2ojr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2OJR 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 2OJR
  • 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 2OJR, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ojr_A] [2ojr]
  • SWISS-PROT database: [P62988]
  • Domain organization of [UBIQ_HUMAN] by SWISSPFAM
  • Domain found in 2OJR: [UBQ ] by SMART
    • Other resources with information on 2OJR
  • Community annotation for 2OJR 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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