2VDE Transport Protein date Oct 04, 2007
title Crystal Structure Of The Open State Of Tolc Outer Membrane C Of Mutlidrug Efflux Pumps
authors V.N.Bavro, Z.Pietras, N.Furnham, L.Perez-Cano, J.Fernandez-Recio R.Truer, R.Misra, B.Luisi
compound source
Molecule: Outer Membrane Protein Tolc
Chain: A, B, C
Fragment: Residues 1-450
Synonym: Tolc
Engineered: Yes
Mutation: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: C43, C41
Expression_system_plasmid: Pet41b
symmetry Space Group: P 21 21 21
R_factor 0.266 R_Free 0.315
crystal
cell
length a length b length c angle alpha angle beta angle gamma
128.284 136.176 136.133 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand CL enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceAssembly and channel opening in a bacterial drug efflux machine., Bavro VN, Pietras Z, Furnham N, Perez-Cano L, Fernandez-Recio J, Pei XY, Misra R, Luisi B, Mol Cell. 2008 Apr 11;30(1):114-21. PMID:18406332
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (201 Kb) [Save to disk]
  • Biological Unit Coordinates (2vde.pdb1.gz) 195 Kb
  • LPC: Ligand-Protein Contacts for 2VDE
  • CSU: Contacts of Structural Units for 2VDE
  • Likely Quarternary Molecular Structure file(s) for 2VDE
  • Structure Factors (592 Kb)
  • Retrieve 2VDE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VDE from S2C, [Save to disk]
  • Re-refined 2vde structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VDE 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 2VDE
  • 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 2VDE, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vde_B] [2vde] [2vde_A] [2vde_C]
  • SWISS-PROT database: [P02930]
  • Belongs to the outer membrane factor (omf) family according to TCDB.
  • Domain organization of [TOLC_ECOLI] by SWISSPFAM
  • Other resources with information on 2VDE
  • Community annotation for 2VDE 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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