4JD5 Lyase date Feb 23, 2013
title Crystal Structure Of Benzoylformate Decarboxylase Mutant L40
authors W.R.P.Novak, F.H.Andrews, A.R.Tom, P.R.Gunderman, M.J.Mcleish
compound source
Molecule: Benzoylformate Decarboxylase
Chain: A
Synonym: Bfd, Bfdc
Engineered: Yes
Mutation: Yes
Organism_scientific: Pseudomonas Putida
Organism_taxid: 303
Gene: Mdlc
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24
symmetry Space Group: I 2 2 2
R_factor 0.134 R_Free 0.152
length a length b length c angle alpha angle beta angle gamma
81.550 95.790 137.150 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.33 Å
ligand CA, GOL, NA, TZD enzyme Lyase E.C. BRENDA

Primary referenceA bulky hydrophobic residue is not required to maintain the v-conformation of enzyme-bound thiamin diphosphate., Andrews FH, Tom AR, Gunderman PR, Novak WR, McLeish MJ, Biochemistry. 2013 May 7;52(18):3028-30. doi: 10.1021/bi400368j. Epub 2013 Apr, 23. PMID:23607689
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (156 Kb) [Save to disk]
  • Biological Unit Coordinates (4jd5.pdb1.gz) 591 Kb
  • LPC: Ligand-Protein Contacts for 4JD5
  • CSU: Contacts of Structural Units for 4JD5
  • Structure Factors (1675 Kb)
  • Retrieve 4JD5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JD5 from S2C, [Save to disk]
  • Re-refined 4jd5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JD5 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 4JD5
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4JD5, from MSDmotif at EBI
  • Fold representative 4jd5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jd5_A] [4jd5]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4JD5
  • Community annotation for 4JD5 at PDBWiki (http://pdbwiki.org)

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