2R8D Toxin date Sep 10, 2007
title The Structure Of Transporter Associated Domain Corc_hlyc Fro Xylella Fastidiosa Temecula1 Hemolysin In Complex With Mg++
authors M.E.Cuff, L.Volkart, A.Joachimiak, Midwest Center For Structura Genomics (Mcsg)
compound source
Molecule: Hemolysin
Chain: A
Fragment: Corc_hlyc Domain: Residues 349-439
Engineered: Yes
 Organism_scientific: Xylella Fastidiosa
Organism_taxid: 183190
Strain: Temecula1
Atcc: 700964
Gene: Tlyc
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmcsg7
symmetry Space Group: I 2 3
R_factor 0.171 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.061 88.061 88.061 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand MG, MLY, MN, MSE enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (21 Kb) [Save to disk]
  • Biological Unit Coordinates (2r8d.pdb1.gz) 30 Kb
  • LPC: Ligand-Protein Contacts for 2R8D
  • CSU: Contacts of Structural Units for 2R8D
  • Structure Factors (178 Kb)
  • Retrieve 2R8D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2R8D from S2C, [Save to disk]
  • Re-refined 2r8d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2R8D 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 2R8D
  • 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 2R8D, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2r8d] [2r8d_A]
  • SWISS-PROT database: [Q87DZ3]
  • Domain organization of [Q87DZ3_XYLFT] by SWISSPFAM
  • Domain found in 2R8D: [CorC_HlyC ] by SMART
    • Other resources with information on 2R8D
  • Community annotation for 2R8D 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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