2VO9 Hydrolase date Feb 09, 2008
title Crystal Structure Of The Enzymatically Active Domain Of The Monocytogenes Bacteriophage 500 Endolysin Ply500
authors I.P.Korndoerfer, A.Kanitz, A.Skerra
compound source
Molecule: L-Alanyl-D-Glutamate Peptidase
Chain: A, B, C
Fragment: Catalytic Domain, Residues 1-167
Synonym: Ead500
Ec: 3.4.24.-
Engineered: Yes
Organism_scientific: Bacteriophage A500
Organism_taxid: 40522
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm83
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Peace500.7
symmetry Space Group: C 2 2 21
R_factor 0.196 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.787 95.180 182.578 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand SO4, ZN enzyme Hydrolase E.C.3.4.24 BRENDA
note 2VO9 supersedes 1XP2
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceStructural analysis of the L-alanoyl-D-glutamate endopeptidase domain of Listeria bacteriophage endolysin Ply500 reveals a new member of the LAS peptidase family., Korndorfer IP, Kanitz A, Danzer J, Zimmer M, Loessner MJ, Skerra A, Acta Crystallogr D Biol Crystallogr. 2008 Jun;64(Pt 6):644-50. Epub 2008, May 14. PMID:18560152
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (2vo9.pdb1.gz) 28 Kb
  • Biological Unit Coordinates (2vo9.pdb2.gz) 28 Kb
  • Biological Unit Coordinates (2vo9.pdb3.gz) 27 Kb
  • LPC: Ligand-Protein Contacts for 2VO9
  • CSU: Contacts of Structural Units for 2VO9
  • Likely Quarternary Molecular Structure file(s) for 2VO9
  • Structure Factors (347 Kb)
  • Retrieve 2VO9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VO9 from S2C, [Save to disk]
  • Re-refined 2vo9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VO9 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 2VO9
  • 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 2VO9, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vo9] [2vo9_B] [2vo9_A] [2vo9_C]
  • SWISS-PROT database: [Q37979]
  • Domain organization of [AEPE_BPA50] by SWISSPFAM
  • Other resources with information on 2VO9
  • Community annotation for 2VO9 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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