3F6B	Lyase	date	Nov 05, 2008
title	Crystal Structure Of Benzoylformate Decarboxylase In Complex Pyridyl Inhibitor Paa
authors	G.S.Brandt, M.J.Mcleish, G.L.Kenyon, G.A.Petsko, D.Ringe, F.Jorda
compound		source
Molecule: Benzoylformate Decarboxylase Chain: X Synonym: Bfd, Bfdc Ec: 4.1.1.7 Engineered: Yes		Organism_scientific: Pseudomonas Putida Organism_taxid: 303 Strain: Dsm 291 Ncib 9494 Nctc 10936 Stanier 90 Atcc: 12633 Gene: Mdlc Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid
symmetry	Space Group: I 2 2 2	R_factor 0.162 R_Free 0.182
crystal cell	length a length b length c angle alpha angle beta angle gamma 81.540 96.070 137.354 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.34 Å
ligand	8PA, MG	enzyme	Lyase E.C.4.1.1.7 BRENDA
Gene Ontology	Chain Function Process Component X
Primary reference	Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase., Chakraborty S, Nemeria NS, Balakrishnan A, Brandt GS, Kneen MM, Yep A, McLeish MJ, Kenyon GL, Petsko GA, Ringe D, Jordan F, Biochemistry. 2009 Feb 10;48(5):981-94. PMID:19140682

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (94 Kb) [Save to disk] Biological Unit Coordinates (3f6b.pdb1.gz) 345 Kb LPC: Ligand-Protein Contacts for 3F6B CSU: Contacts of Structural Units for 3F6B Likely Quarternary Molecular Structure file(s) for 3F6B Structure Factors (2596 Kb) Retrieve 3F6B in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3F6B from S2C, [Save to disk] Re-refined 3f6b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3F6B 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 3F6B

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 3F6B, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3f6b_X] [3f6b] SWISS-PROT database: [P20906] Domain organization of [MDLC_PSEPU] by SWISSPFAM

Other resources with information on 3F6B

Community annotation for 3F6B at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---