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 Lab: (517) 353-9125 FAX: (517) 353-9334 Email: [email protected] **************************************************************** On Dec 8, 2014, at 10:15 PM, Yamei Yu <[email protected]> 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: [email protected] > [email protected] > [email protected] >
