Hello Wei, There is a simple way of assessing the Biphenyl in your condition is as follows: 1) You can take you concentrated mother liquor (given: if you are sure no aromatic compound is available in ML) and take a absorption spectra at wavelength range of 200-300, if you get a maxima at near about 240-250 means possibility of having biphenyl compound in the ML will be high many folds. You can give a quick trial by using this method.
2) or As Marc suggestion is very good to go for mass spectroscopy for the identification. Good Luck On Tue, Nov 29, 2016 at 2:13 PM, Marc Graille < [email protected]> wrote: > Dear Wei, > > to get more information on this putative “butterfly-like” ligand, you can > perform non-denaturing and denaturing mass spectrometry. This should give > you the molecular weight of this compound, which most probably comes from > E. coli and co-purifies with your protein of interest. In parallel, you > could imagine to purify this compound by HPLC purification. Based on the > shape and the details on the density, it might be rich in aromatic rings > and then reversed-phase column might be useful. If you end up with enough > material, you could try NMR to get info on this ligand. > Before performing such experiments, you should definitely check whether > this ligand binds to a conserved region of your protein such as a putative > active site. If this molecule binds to a region formed by poorly conserved > residues, you have to consider whether this is important or not to know > precisely the identity of this compound. I mean biologically important. > Ideally, this would of course be important to model the correct ligand in > the electron density but I am sure it will not be the first structure > deposited at the PDB with unattributed density or an unknown ligand. > > HTH, > > Best wishes, > Marc > > Le 29 nov. 2016 à 09:26, Wei Liu <[email protected]> a écrit : > > Hi all, > > Thanks for all answers and suggestions to my question regarding the > density for an unknown ligand. Many people raised a possibility that the > density corresponding molecule might locate at a two-fold symmetry axis, > but I am quite sure to rule out this possibility. I tried to placed a > molecule of biphenyl sulfide, which can roughly fit into one half of the > density in question, and performed one round of refinement. As shown in the > attached picture, strong residual density still exist in the rest half, > where no symmetry atoms can be seen. So apparently a real molecule rather > than an artifact lied in this structure, but I am still wondering from > where such a molecule comes and strongly binds to our protein, E. coli or > impurities in the crystallization conditions, as Prem suggested, and if > there is any experimental methods to identify this compound. > > Looking forward to more suggestions. > > Best > Wei > > <Snapshot20161128.png> > > > Marc GRAILLE, PhD > Directeur de recherche CNRS > > Laboratoire de Biochimie > ECOLE POLYTECHNIQUE - UMR7654 CNRS > 91128 PALAISEAU CEDEX > > > > > Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09 > Email: [email protected] > > Team: Translation and degradation of eukaryotic mRNAs > https://portail.polytechnique.edu/bioc/recherche/couplage- > entre-la-traduction-et-la-degradation-des-arnm-chez-les-eucaryotes > Team supported by the ATIP-Avenir CNRS program > > > > >
