3DDL Transport Protein date Jun 05, 2008
title Crystallographic Structure Of Xanthorhodopsin, A Light-Drive With Dual Chromophore
authors J.Stagno, H.Luecke, B.Schobert, J.K.Lanyi, E.S.Imasheva, J.M.Wang S.P.Balashov
compound source
Molecule: Xanthorhodopsin
Chain: A, B
 Organism_scientific: Salinibacter Ruber
Organism_taxid: 146919
symmetry Space Group: P 1
R_factor 0.247 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.740 59.490 59.720 76.35 74.93 64.08
method X-Ray Diffractionresolution 1.90 Å
ligand PCW, PX4, RET, SXN, UNL enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • ion channel activity
  • light-activated ion channel ...


    • Primary referenceCrystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore., Luecke H, Schobert B, Stagno J, Imasheva ES, Wang JM, Balashov SP, Lanyi JK, Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16561-5. Epub 2008 Oct 15. PMID:18922772
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (96 Kb) [Save to disk]
  • Biological Unit Coordinates (3ddl.pdb1.gz) 45 Kb
  • Biological Unit Coordinates (3ddl.pdb2.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 3DDL
  • CSU: Contacts of Structural Units for 3DDL
  • Likely Quarternary Molecular Structure file(s) for 3DDL
  • Structure Factors (349 Kb)
  • Retrieve 3DDL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DDL from S2C, [Save to disk]
  • Re-refined 3ddl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3DDL 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 3DDL
  • 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 3DDL, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ddl_B] [3ddl_A] [3ddl]
  • SWISS-PROT database: [Q2S2F8]
  • Belongs to the ion-translocating microbial rhodopsin (mr) family according to TCDB.
  • Domain organization of [Q2S2F8_SALRD] by SWISSPFAM
  • Domain found in 3DDL: [Bac_rhodopsin ] by SMART
    • Other resources with information on 3DDL
  • Community annotation for 3DDL 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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