3D47 Lyase date May 14, 2008
title Crystal Structure Of L-Rhamnonate Dehydratase From Salmonell Typhimurium Complexed With Mg And D-Malate
authors A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, J.A.Gerlt, S.C. York Sgx Research Center For Structural Genomics (Nysgxrc)
compound source
Molecule: Putative Galactonate Dehydratase
Chain: A, B, C, D, E, F, G, H
Engineered: Yes
 Organism_scientific: Salmonella Typhimurium Lt2
Organism_taxid: 99287
Strain: Lt2 Sgsc1412
Atcc: 700720
Gene: Yfaw, Stm2291
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.202 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.222 122.003 141.350 90.00 108.24 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand MG, MLT enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (529 Kb) [Save to disk]
  • Biological Unit Coordinates (3d47.pdb1.gz) 136 Kb
  • Biological Unit Coordinates (3d47.pdb2.gz) 136 Kb
  • Biological Unit Coordinates (3d47.pdb3.gz) 136 Kb
  • Biological Unit Coordinates (3d47.pdb4.gz) 136 Kb
  • Biological Unit Coordinates (3d47.pdb5.gz) 523 Kb
  • LPC: Ligand-Protein Contacts for 3D47
  • CSU: Contacts of Structural Units for 3D47
  • Likely Quarternary Molecular Structure file(s) for 3D47
  • Structure Factors (2240 Kb)
  • Retrieve 3D47 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D47 from S2C, [Save to disk]
  • Re-refined 3d47 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3D47 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 3D47
  • 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 3D47, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d47_H] [3d47_A] [3d47_F] [3d47_D] [3d47_E] [3d47] [3d47_C] [3d47_B] [3d47_G]
  • SWISS-PROT database: [Q8ZNF9]
  • Domain organization of [RHAMD_SALTY] by SWISSPFAM
  • Domain found in 3D47: [MR_MLE ] by SMART
    • Other resources with information on 3D47
  • Community annotation for 3D47 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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