You could run your sequence through this web server first: http://ffas.burnham.org/XtalPred-cgi/xtal.pl
Then regarding your loops you could use MUSTANG (or any other 3D alignment tool which generates a superimposed ensemble of structures) http://www.ncbi.nlm.nih.gov/pubmed/16736488 to identify with your other homologs which regions should be trimmed off. Then you turn to your favorite site directed mutagenesis kit and chop off the loops. How big is your protein ? Have you tried different expression systems ? Good luck ! Jürgen On Jul 18, 2011, at 9:01 PM, Obayed Ullah wrote: Hi all I wrote last time but got only one feedback. I know some of you guys must have this experience that how to delete loops from the protein. Please help me with suggestions. I am working with a human protein which have around 20% sequence identity with the other proteins of the same family. Structure of some of the proteins from this family have been solved. All the solved structures have around 20% identity with my protein. I am trying to crystallize the protein but it looks like very hard to get crystal. I have tried different N and C terminally truncated constructs for crystallization but no crystal. My feeling is that probably there is some flexible loops with in the protein which limiting the crystallization. So I want to delete the loops with in the protein (not to truncate in the terminal, I already have done this). I am not asking suggestion about how to delete the loop rather how to decide where the loop is. I am not sure how much it will be helpful to get a homology model of such a protein having low sequence identity. Is there any strategy to decide where the loop could be? Does anybody know any established/ rational method to do that. Waiting for your suggestions Obayed Ullah ...................... Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
