3SY7 Membrane Protein date Jul 15, 2011
title Improved Crystal Structure Of Pseudomonas Aeruginosa Oprd
authors B.Van Den Berg, E.Eren
compound source
Molecule: Porin D
Chain: A
Fragment: Unp Residues 24-443
Synonym: Imipenembasic Amino Acid-Specific Outer Membrane Outer Membrane Protein D2;
Ec: 3.4.21.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Pseudomonas Aeruginosa
Organism_taxid: 287
Gene: Oprd, Pa0958
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.196 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
136.408 103.892 47.544 90.00 107.68 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand C8E enzyme Hydrolase E.C.3.4.21 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • channel activity
  • porin activity


  • 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] (131 Kb) [Save to disk]
  • Biological Unit Coordinates (3sy7.pdb1.gz) 125 Kb
  • LPC: Ligand-Protein Contacts for 3SY7
  • CSU: Contacts of Structural Units for 3SY7
  • Structure Factors (278 Kb)
  • Retrieve 3SY7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SY7 from S2C, [Save to disk]
  • Re-refined 3sy7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SY7 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 3SY7
  • 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 3SY7, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3sy7_A] [3sy7]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3SY7
  • Community annotation for 3SY7 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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