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 Ec: 4.1.1.7 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
crystal cell	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 Diffraction	resolution	1.60 Å
ligand	CA, MG, TPP	enzyme	Lyase E.C.4.1.1.7 BRENDA
related structures	by homologous chain: 1MCZ, 1PI3
Gene Ontology	Chain Function Process Component A
Primary reference	The 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)

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