I am forwarding an answer I sent previously in response to a similar question. We used refmac5 to refine a number of acyl-enzyme structures: Radisky ES, Lee JM, Lu CJ, Koshland DE Jr. Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates. Proc Natl Acad Sci U S A. 2006 May 2;103(18):6835-40. We kept distance restraints loose and did not use angle restraints on the acyl-enzyme linkage, in order that it should refine with heavier weight on the experimental data. Cheers, Evette
Evette S. Radisky, Ph.D. Assistant Professor and Associate Consultant II Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 (office) (904) 953-3109 (lab) ________________________________ From: Radisky, Evette S. Ph.D. Sent: Wednesday, December 06, 2006 10:40 AM To: CCP4BB Subject: RE: [ccp4bb]: [ccp4bb] Esterification specification in Refmac5 I just checked some of my files where I created an acyl link like that - as I recall, it took some fiddling (and help from others at the ccp4bb) to get the formatting right. Here is what worked in my pdb: LINK C ARG A 5 OG SER X 195 ARG-SER Plus, you then have to define the link in a .cif library file that is also supplied to refmac; mine looked like this: [note, I was purposefully using a very loose restraint on the bond length; a more typical restraint (if you really think you know what the distance is supposed to be) would be 0.02 instead of 0.2] global_ _lib_name ? _lib_version ? _lib_update ? # ------------------------------------------------ # --- LIST OF LINKS --- # data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name ARG-SER ARG . . SER . . bond_ARG-C_=_SER-OG # ------------------------------------------------------ # # --- DESCRIPTION OF LINKS --- # data_link_ARG-SER # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd ARG-SER 1 C 2 OG coval 1.330 0.200 # ------------------------------------------------------ Good luck! Evette Evette S. Radisky, Ph.D. Assistant Professor and Associate Consultant II Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 (office) (904) 953-2857 (lab) ________________________________ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Leo Chavas Sent: Wednesday, December 06, 2006 4:21 AM To: CCP4BB Cc: Leo Chavas Subject: [ccp4bb]: [ccp4bb] Esterification specification in Refmac5 Dear all, I encountered some difficulties to define a link between the C-terminal residue of a protein with an other covalently-bound protein for refinement under Refmac. I tried to define it as a LINK command in the header of the PDB, but it seems that it is not refined at all... Here is what is present in my header: LINK OG SER A 85 1.330 C GLY B 276 SER-GLY What did I do wrong? Could any body help me? Should I specify something more in the script file? Thanks a lot in advance. Leo PS: sorry if the question has already been answered... ========================== Chavas Leonard M.G., Ph.D. Structural Research Center KEK,PF. 1-1 Oho Tuskuba, Ibaraki - Japan --------------------------------------------- PHS: +81(0)29-864-5200 (ext: 2682) e-mail: [EMAIL PROTECTED] URL: http://pfweis.kek.jp/~leo ==========================
