2YGT Toxin date Apr 20, 2011
title Clostridium Perfringens Delta-Toxin
authors J.Huyet, C.E.Naylor, M.Gibert, M.R.Popoff, A.K.Basak
compound source
Molecule: Delta Toxin
Chain: A
Fragment: Residues 29-318
Engineered: Yes
Organism_scientific: Clostridium Perfringens
Organism_taxid: 1502
Strain: Cp24-03
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Codonplus Ril
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet28a
symmetry Space Group: P 21 21 2
R_factor 0.179 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
112.932 49.664 58.477 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand GOL, IMD, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural Insights into Delta Toxin Pore Formation., Huyet J, Naylor CE, Savva CG, Gibert M, Popoff MR, Basak AK, PLoS One. 2013 Jun 21;8(6):e66673. Print 2013. PMID:23805259
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (2ygt.pdb1.gz) 94 Kb
  • LPC: Ligand-Protein Contacts for 2YGT
  • CSU: Contacts of Structural Units for 2YGT
  • Structure Factors (98 Kb)
  • Retrieve 2YGT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YGT from S2C, [Save to disk]
  • Re-refined 2ygt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YGT 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 2YGT
  • 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 2YGT, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ygt_A] [2ygt]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2YGT
  • Community annotation for 2YGT at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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