2QJM Lyase date Jul 08, 2007
title Crystal Structure Of The K271e Mutant Of Mannonate Dehydrata Novosphingobium Aromaticivorans Complexed With Mg And D-Man
authors A.A.Fedorov, E.V.Fedorov, J.F.Rakus, J.E.Vick, J.A.Gerlt, S.C.Alm
compound source
Molecule: Mandelate Racemasemuconate Lactonizing Enzyme
Chain: A, B, C, D
Engineered: Yes
Mutation: Yes
 Organism_scientific: Novosphingobium Aromaticivorans
Organism_taxid: 48935
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.168 R_Free 0.206
crystal
cell
length a length b length c angle alpha angle beta angle gamma
116.254 165.312 166.853 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand CS2, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceEvolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans., Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA, Biochemistry. 2007 Nov 13;46(45):12896-908. Epub 2007 Oct 18. PMID:17944491
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (260 Kb) [Save to disk]
  • Biological Unit Coordinates (2qjm.pdb1.gz) 129 Kb
  • Biological Unit Coordinates (2qjm.pdb2.gz) 129 Kb
  • Biological Unit Coordinates (2qjm.pdb3.gz) 501 Kb
  • LPC: Ligand-Protein Contacts for 2QJM
  • CSU: Contacts of Structural Units for 2QJM
  • Likely Quarternary Molecular Structure file(s) for 2QJM
  • Structure Factors (1062 Kb)
  • Retrieve 2QJM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2QJM from S2C, [Save to disk]
  • Re-refined 2qjm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2QJM 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 2QJM
  • 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 2QJM, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2qjm_C] [2qjm_B] [2qjm_D] [2qjm] [2qjm_A]
  • SWISS-PROT database: [A4XF23]
  • Domain organization of [A4XF23_NOVAD] by SWISSPFAM
  • Domain found in 2QJM: [MR_MLE ] by SMART
    • Other resources with information on 2QJM
  • Community annotation for 2QJM 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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