3SYB Membrane Protein date Jul 16, 2011
title Crystal Structure Of Pseudomonas Aeruginosa Occd3 (Opdp)
authors B.Van Den Berg, E.Eren
compound source
Molecule: Glycine-Glutamate Dipeptide Porin Opdp
Chain: A
Fragment: Unp Residues 26-484
Engineered: Yes
 Organism_scientific: Pseudomonas Aeruginosa
Organism_taxid: 287
Gene: Opdp, Pa4501
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.214 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.930 159.828 82.064 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand C8E, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • channel activity
  • porin activity
  • dipeptide transmembrane tran...


    • Primary referenceSubstrate Specificity within a Family of Outer Membrane Carboxylate Channels., Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, van den Berg B, PLoS Biol. 2012 Jan;10(1):e1001242. Epub 2012 Jan 17. PMID:22272184
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (3syb.pdb1.gz) 65 Kb
  • Biological Unit Coordinates (3syb.pdb2.gz) 128 Kb
  • LPC: Ligand-Protein Contacts for 3SYB
  • CSU: Contacts of Structural Units for 3SYB
  • Structure Factors (149 Kb)
  • Retrieve 3SYB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SYB from S2C, [Save to disk]
  • Re-refined 3syb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3SYB 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 3SYB
  • 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 3SYB, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3syb] [3syb_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3SYB
  • Community annotation for 3SYB at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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