2DW7 Lyase date Aug 07, 2006
title Crystal Structure Of D-Tartrate Dehydratase From Bradyrhizob Japonicum Complexed With Mg++ And Meso-Tartrate
authors A.A.Fedorov, E.V.Fedorov, W.S.Yew, B.M.Wood, J.A.Gerlt, S.C.Almo
compound source
Molecule: Bll6730 Protein
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Synonym: D-Tartrate Dehydratase
Ec: 4.2.1.81
Engineered: Yes
Organism_scientific: Bradyrhizobium Japonicum
Organism_taxid: 375
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15b
symmetry Space Group: P 1
R_factor 0.241 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.837 162.542 168.181 117.76 90.03 90.67
method X-Ray Diffractionresolution 2.50 Å
ligand MG, SRT enzyme Lyase E.C.4.2.1.81 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, N, K, E, M, C, L, A, J, O, P, B, H, D, I, G


Primary referenceEvolution of Enzymatic Activities in the Enolase Superfamily: d-Tartrate Dehydratase from Bradyrhizobium japonicum(,)., Yew WS, Fedorov AA, Fedorov EV, Wood BM, Almo SC, Gerlt JA, Biochemistry. 2006 Dec 12;45(49):14598-14608. PMID:17144653
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (970 Kb) [Save to disk]
  • Biological Unit Coordinates (2dw7.pdb1.gz) 130 Kb
  • Biological Unit Coordinates (2dw7.pdb2.gz) 132 Kb
  • Biological Unit Coordinates (2dw7.pdb3.gz) 131 Kb
  • Biological Unit Coordinates (2dw7.pdb4.gz) 130 Kb
  • Biological Unit Coordinates (2dw7.pdb5.gz) 130 Kb
  • Biological Unit Coordinates (2dw7.pdb6.gz) 131 Kb
  • Biological Unit Coordinates (2dw7.pdb7.gz) 130 Kb
  • Biological Unit Coordinates (2dw7.pdb8.gz) 130 Kb
  • LPC: Ligand-Protein Contacts for 2DW7
  • CSU: Contacts of Structural Units for 2DW7
  • Likely Quarternary Molecular Structure file(s) for 2DW7
  • Structure Factors (3212 Kb)
  • Retrieve 2DW7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DW7 from S2C, [Save to disk]
  • Re-refined 2dw7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DW7 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 2DW7
  • 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 2DW7, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dw7_J] [2dw7_B] [2dw7_E] [2dw7_M] [2dw7_C] [2dw7_D] [2dw7_P] [2dw7_L] [2dw7_K] [2dw7_N] [2dw7_H] [2dw7_I] [2dw7_G] [2dw7_A] [2dw7_O] [2dw7] [2dw7_F]
  • SWISS-PROT database: [Q89FH0]
  • Domain organization of [Q89FH0_BRAJA] by SWISSPFAM
  • Domain found in 2DW7: [MR_MLE ] by SMART
  • Other resources with information on 2DW7
  • Community annotation for 2DW7 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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