5ECD Hydrolase date Oct 20, 2015
title Structure Of The Shigella Flexneri Vapc Mutant D98n Crystal
authors K.Xu
compound source
Molecule: Trna(Fmet)-Specific Endonuclease Vapc
Chain: A, B
Synonym: Rnase Vapc,Toxin Vapc
Ec: 3.1.-.-
Engineered: Yes
Mutation: Yes
 Organism_scientific: Shigella Flexneri
Organism_taxid: 623
Gene: Vapc, Mvpa, Stborf2, Cp0245
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: H 3
R_factor 0.161 R_Free 0.197
crystal
cell
length a length b length c angle alpha angle beta angle gamma
121.450 121.450 51.740 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.75 Å
ligand EPE enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity
  • ribonuclease activity


    • Primary referenceStructural analysis on the active site architecture of the VapC toxin from Shigella flexneri., Xu K, Dedic E, Brodersen DE, Proteins. 2016 Feb 2. doi: 10.1002/prot.25002. PMID:26833558
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (5ecd.pdb1.gz) 98 Kb
  • LPC: Ligand-Protein Contacts for 5ECD
  • CSU: Contacts of Structural Units for 5ECD
  • Structure Factors (488 Kb)
  • Retrieve 5ECD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ECD from S2C, [Save to disk]
  • Re-refined 5ecd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5ECD 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 5ECD
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ecd] [5ecd_B] [5ecd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5ECD
  • Community annotation for 5ECD at PDBWiki (http://pdbwiki.org)

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