Lipid or PEG from your crystallisation condition? --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ
email: [email protected] tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Oct 3, 2013, at 1:42 PM, 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>
