 |
 |
Hi Yamei, Depending on your dataset and collection, if you have collected any anomalous data, you can check for peaks that indicate phosphorus atoms in anomalous maps. It might even be worth feeding into ANoDe ( http://shelx.uni-ac.gwdg.de/SHELX/anode.php) if you have sufficiently high multiplicity on e.g. a Cu source. (Disclaimer: I'm no expert. Others here know how this works much better than I do) Shane Caldwell McGill University On Tue, Dec 9, 2014 at 8:35 AM, R. M. Garavito <[log in to unmask]> wrote: > Yamei, > > This is not unusual, particularly for many proteins that bind nucleotide > derivatives, especially GDP/GTP binding proteins, as Nat said. If it is GDP > that is tightly bound at high occupancy, it should be quite easy to > identify because of the pyrophosphates and the guanine ring. To build > into, pop in a GDP molecule from another GDP/GTP binding protein structure; > there is GDP .cif files in the CCP4 and Phenix libraries. Just be aware > that there are at least two major conformers seen regarding > the guanine ring (syn and anti). While in GDP/GTP binding proteins the > ring conformer I believe is anti (the ring not over the ribose), in > GDP-sugar enzymes, it can be syn (the ring over the ribose). > > 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 <%28517%29%20355-9724> Lab: (517) > 353-9125 <%28517%29%20353-9125>* > *FAX: (517) 353-9334 <%28517%29%20353-9334> > Email: [log in to unmask] <[log in to unmask]>* > ****************************************************************** > > > > > On Dec 8, 2014, at 10:15 PM, Yamei Yu <[log in to unmask]> wrote: > > Hi all, > > We crystallised a small GTPase expressed in E. Coli and found some > densities in GDP/GTP binding site. We didn’t add any GDP/GTP or GDP/GPD > homologues during protein expression, purification and crystallisation. The > resolution is not high, we couldn’t tell what it is. Is there any method to > detect what it is? Thanks! > > Best wishes! > > yamei > > > > > ************************************************ > > Yamei Yu > State Key Laboratory of Biotherapy／Collaborative Innovation > Center of Biotherapy, > West China Hospital, > Sichuan University,Chengdu,610041, P.R.China > Tel: 15882013485 > Email: [log in to unmask] > [log in to unmask] > [log in to unmask] > > >