1VEV Hydrolase date Apr 06, 2004
title Crystal Structure Of Peptide Deformylase From Leptospira Int (Lipdf) At Ph6.5
authors Z.Zhou, X.Song, Y.Li, W.Gong
compound source
Molecule: Peptide Deformylase
Chain: A, B
Synonym: Lipdf, Pdf, Polypeptide Deformylase
Ec: 3.5.1.88
Engineered: Yes
Organism_scientific: Leptospira Interrogans
Organism_taxid: 173
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 41 21 2
R_factor 0.258 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.192 82.192 201.040 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.51 Å
ligand FMT, MES, ZN enzyme Hydrolase E.C.3.5.1.88 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceNovel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift., Zhou Z, Song X, Gong W, J Biol Chem. 2005 Dec 23;280(51):42391-6. Epub 2005 Oct 20. PMID:16239225
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (63 Kb) [Save to disk]
  • Biological Unit Coordinates (1vev.pdb1.gz) 58 Kb
  • Biological Unit Coordinates (1vev.pdb2.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 1VEV
  • CSU: Contacts of Structural Units for 1VEV
  • Likely Quarternary Molecular Structure file(s) for 1VEV
  • Structure Factors (375 Kb)
  • Retrieve 1VEV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VEV from S2C, [Save to disk]
  • Re-refined 1vev structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VEV 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 1VEV
  • 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 1VEV, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vev] [1vev_B] [1vev_A]
  • SWISS-PROT database: [Q93LE9]
  • Domain organization of [DEF_LEPIN] by SWISSPFAM
  • Other resources with information on 1VEV
  • Community annotation for 1VEV 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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