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When USA budget is back :-\ you may give a try to : http://webbook.nist.gov/chemistry/ It helped me several times, very intuitive, I use just a formula for a search, it also accept a wild character for unknown number of atoms. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: [log in to unmask] Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 3, 2013, at 16:33 , Andre Luis Berteli Ambrosio <[log in to unmask]> wrote: > Dear Michael, thank you for the prompt reply. > The host was indeed E. coli. > From what I have been reading I completely agree on the lack of biological support for such a molecule but still the map seems very convincing of the presence of cis bonds at such positions… Could such a conformation arise due to something other than unsaturations? > We are working on isolating the lipid from the purified protein I will sure follow your suggestions on the additional characterization of this molecule, especially adding NMR analysis to it. Thanks also for referencing the literature. > With kind regards, > > -Andre. > > > De: CCP4 bulletin board [mailto:[log in to unmask]] Em nome de R. M. Garavito > Enviada em: quinta-feira, 3 de outubro de 2013 10:16 > Para: [log in to unmask] > Assunto: Re: [ccp4bb] Identity of a Bacterial lipid > > Dear Andre, > > It always impressive to see a near atomic resolution structure with a bound lipid. Congratulations. However, to identify what lipid you have requires a bit more analysis than just looking in databases. First, what is the bacterium you are using as the host? If it is E. coli, then the known lipids are very well characterized. Also, VERY FEW E. coli lipids have sites of unsaturation, and virtually polyunsaturated fatty acids (PUFAs) have one sp3 carbon in between the double bonds (arising from the mechanisms of biosynthesis). So your proposed structure doesn't seem right from a biological sense, which makes looking into databases unproductive. > > However, since you solved the structure, do your produce enough protein to isolate the putative lipid by simple TLC? With the help of a good lipid lab you should be able to tell what it with greater certainty. Try to get a copy of Techniques of Lipidology by Morris Kates from Elsevier. Although it is old school stuff, it will help you isolate enough for mass spec and NMR analysis. > > Good luck, > > Michael > > **************************************************************** > R. Michael Garavito, Ph.D. > Professor of Biochemistry & Molecular Biology > 603 Wilson Rd., Rm. 513 > Michigan State University > East Lansing, MI 48824-1319 > Office: (517) 355-9724 Lab: (517) 353-9125 > FAX: (517) 353-9334 Email: [log in to unmask] > **************************************************************** > > > > > On Oct 3, 2013, at 8:42 AM, Andre Luis Berteli Ambrosio wrote: > > > Dear colleagues, > > We have just determined the crystal structure (at 1.1 A max resolution) of a recombinant protein that crystallized in complex with a leftover bacterial lipid, the full identity of which we are currently struggling to identify. Please see attached (3 views of the molecule). > > The map strongly suggests an 18-carbon long polyunsaturated fatty acid, with 5 conjugated unsaturations (at positions 5, 7, 9, 11 and 13, all cis), covalently bound to some extra chemical group at is polar head. This extra group seems to be comprised of 4 (5?) atoms, though I am afraid cannot tell if it extends further into not-so-well-structured atoms. > > Myself and a student have spent the last two days searching on the web for possible matches for this ligand without any success. For instance, we have generated a SMILES formula for the aliphatic tail comprising the unsaturations and browsed for similar compounds at PubChem with different similarity cutoffs, but nothing seemed to resemble the complete molecule. > > We would appreciate if you could make any comments on the nature of this ligand or perhaps suggest your favorite computational tools. We will perform mass spec on it soon. > > Thank you beforehand. > > Andre LB Ambrosio, DSc > Laboratório Nacional de Biociências - LNBio > CNPEM, Brazil > > <FA-density.png> >