1BFD Lyase date Apr 30, 1998
title Benzoylformate Decarboxylase From Pseudomonas Putida
authors M.S.Hasson, A.Muscate, M.J.Mcleish, L.S.Polovnikova, J.A.Gerlt, G.L.Kenyon, G.A.Petsko, D.Ringe
compound source
Molecule: Benzoylformate Decarboxylase
Chain: A
Engineered: Yes
Organism_scientific: Pseudomonas Putida
Organism_taxid: 303
Strain: Rf4738
Atcc: Atcc 12633
Collection: Atcc 12633
Gene: Mdlc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm105
Expression_system_plasmid: Pkk233-2
Expression_system_gene: Mdlc
symmetry Space Group: I 2 2 2
R_factor 0.152 R_Free 0.186
length a length b length c angle alpha angle beta angle gamma
82.300 96.600 138.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand CA, MG, TPP enzyme Lyase E.C. BRENDA
related structures by homologous chain: 1MCZ, 1PI3

Primary referenceThe crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes., Hasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt JA, Kenyon GL, Petsko GA, Ringe D, Biochemistry 1998 Jul 14;37(28):9918-30. PMID:9665697
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (1bfd.pdb1.gz) 343 Kb
  • LPC: Ligand-Protein Contacts for 1BFD
  • CSU: Contacts of Structural Units for 1BFD
  • Likely Quarternary Molecular Structure file(s) for 1BFD
  • Structure Factors (462 Kb)
  • Retrieve 1BFD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BFD from S2C, [Save to disk]
  • Re-refined 1bfd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1BFD 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 1BFD
  • 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 1BFD, from MSDmotif at EBI
  • Genome occurence of 1BFD's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bfd_1, region 182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1bfd_2, region 2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1bfd_3, region 342-524 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1bfd_A] [1bfd]
  • SWISS-PROT database: [P20906]
  • Domain organization of [MDLC_PSEPU] by SWISSPFAM
  • Other resources with information on 1BFD
  • Community annotation for 1BFD 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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