5O5C Lyase date Jun 01, 2017
title The Crystal Structure Of Dfoj, The Desferrioxamine Biosynthe Pathway Lysine Decarboxylase From The Fire Blight Disease P Erwinia Amylovora
authors M.Salomone-Stagni, J.D.Bartho, I.Polsinelli, D.Bellini, M.A.Wals N.Demitri, S.Benini
compound source
Molecule: Putative Decarboxylase Involved In Desferrioxamin Biosynthesis;
Chain: A, B, C, D, E, F
Ec: 4.1.1.-
Engineered: Yes
 Organism_scientific: Erwinia Amylovora (Strain Cfbp1430)
Organism_taxid: 665029
Strain: Cfbp1430
Gene: Dfoj, Eamy_3238
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 32
R_factor 0.165 R_Free 0.187
crystal
cell
length a length b length c angle alpha angle beta angle gamma
269.791 269.791 56.194 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand PLP enzyme Lyase E.C.4.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceA complete structural characterization of the desferrioxamine E biosynthetic pathway from the fire blight pathogen Erwinia amylovora., Salomone-Stagni M, Bartho JD, Polsinelli I, Bellini D, Walsh MA, Demitri N, Benini S, J Struct Biol. 2018 Feb 8. pii: S1047-8477(18)30029-7. doi:, 10.1016/j.jsb.2018.02.002. PMID:29428557
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (441 Kb) [Save to disk]
  • Biological Unit Coordinates (5o5c.pdb1.gz) 149 Kb
  • Biological Unit Coordinates (5o5c.pdb2.gz) 149 Kb
  • Biological Unit Coordinates (5o5c.pdb3.gz) 147 Kb
  • LPC: Ligand-Protein Contacts for 5O5C
  • CSU: Contacts of Structural Units for 5O5C
  • Structure Factors (7817 Kb)
  • Retrieve 5O5C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5O5C from S2C, [Save to disk]
    • View 5O5C 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 5O5C
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5o5c_B] [5o5c_D] [5o5c_C] [5o5c_A] [5o5c_E] [5o5c_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5O5C
  • Community annotation for 5O5C at PDBWiki (http://pdbwiki.org)

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