Wei I heartily second Dale's comment. Since you do know what has been in contact with your protein, you should be able to make a list of ALL POSSIBLE compounds your protein has been exposed to. However, don't go off the deep end. You say that "We guess that the molecular formula should be C8H18O2. So we search this formula in google and find two candidate molecules," but how did you determine C8H18O2 when you can't see hydrogen, and guessing the elemental composition of a ligand may be possible at high resolution IF you know your occupancy.
Two observations I have are: 1. Anything you exposed your protein to could bind to it tightly regardless of the number of purification steps the protein went through. But as Dale said, the ligand is most likely biologically derived. 2. As an example of the "exception proves the rule" circumstance, I believe it was the monoamine oxidase B structure that had one of the plasticizers from the plastic trays bound in the active site. Something to think about as we drink from our water bottles and mull about neurochemistry. Nonetheless, it was not a wild, off-the-shelf ligand, but some thing the protein had been in contact with. Cheers, 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: rmgarav...@gmail.com **************************************************************** On Jul 17, 2013, at 2:20 PM, Dale Tronrud wrote: > Do you have any reason to expect either of these molecules would be in > your crystal? The model you build has to fit the density, be consistent with > the surrounding environment (which you haven't shared with us) and you > have to have some story for how that molecule got in your crystal. Personally > I would steer away from industrial compounds and focus more on biological > molecules and common additives used in purification and crystallization. > > The environment is critical to identifying this molecule. What hydrogen > bonds > does this molecule make? What charges are near by? Certainly the presence > or absence of hydrogen bonds will distinguish between these two compounds > before you go to the trouble to build a model of either. > > Dale Tronrud > > On 7/17/2013 6:35 AM, Wei Feng wrote: >> Dear all, >> Thank you for your advices. >> I had tried to use MPD and pyrophosphate etc to fix the density map but all >> of them were too small. >> We guess that the molecular formula should be C8H18O2. So we search this >> formula in google and find two candidate molecules >> 1: http://flyingexport.en.ecplaza.net/dhad-99-5--137042-689140.html >> 2: http://en.m.wikipedia.org/wiki/Di-tert-butyl_peroxide >> Could you tell me how to get the coordinate of these molecules? >> Thank you for your time! >> Wei >> >> >> >>
