3NPW Lyase date Jun 29, 2010
title In Silico Designed Of An Improved Kemp Eliminase Ke70 Mutant 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: A, B
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.220 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.386 82.872 127.964 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.14 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] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (3npw.pdb1.gz) 38 Kb
  • Biological Unit Coordinates (3npw.pdb2.gz) 36 Kb
  • CSU: Contacts of Structural Units for 3NPW
  • Structure Factors (465 Kb)
  • Retrieve 3NPW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NPW from S2C, [Save to disk]
  • Re-refined 3npw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3NPW 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 3NPW
  • 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 3NPW, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3npw_B] [3npw_A] [3npw]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NPW: [DeoC ] by SMART
    • Other resources with information on 3NPW
  • Community annotation for 3NPW 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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