3NPV Lyase date Jun 29, 2010
title Optimization Of The In Silico Designed Kemp Eliminase Ke70 B Computational Design And Directed Evolution
authors O.Khersonsky, D.Rothlisberge, A.M.Wollacott, O.Dym, D.Baker, D.S. Israel Structural Proteomics Center (Ispc)
compound source
Molecule: Deoxyribose Phosphate Aldolase
Chain: B, A
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.143 R_Free 0.170
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.595 53.518 81.702 90.00 110.34 90.00
method X-Ray Diffractionresolution 1.48 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceOptimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution., Khersonsky O, Rothlisberger D, Wollacott AM, Murphy P, Dym O, Albeck S, Kiss G, Houk KN, Baker D, Tawfik DS, J Mol Biol. 2011 Apr 1;407(3):391-412. doi: 10.1016/j.jmb.2011.01.041. Epub 2011 , Jan 28. PMID:21277311
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (165 Kb) [Save to disk]
  • Biological Unit Coordinates (3npv.pdb1.gz) 82 Kb
  • Biological Unit Coordinates (3npv.pdb2.gz) 81 Kb
  • CSU: Contacts of Structural Units for 3NPV
  • Structure Factors (1180 Kb)
  • Retrieve 3NPV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NPV from S2C, [Save to disk]
  • Re-refined 3npv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3NPV 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 3NPV
  • 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 3NPV, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3npv_B] [3npv_A] [3npv]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NPV: [DeoC ] by SMART
    • Other resources with information on 3NPV
  • Community annotation for 3NPV at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science