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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).Michael603 Wilson Rd., Rm. 513****************************************************************R. Michael Garavito, Ph.D.Professor of Biochemistry & Molecular BiologyMichigan State UniversityEast Lansing, MI 48824-1319****************************************************************
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 YuState Key Laboratory of Biotherapy／Collaborative InnovationCenter of Biotherapy,West China Hospital,Sichuan University,Chengdu,610041, P.R.ChinaTel: 15882013485Email: [log in to unmask]