Re: [ccp4bb] refining phosphorylated residues
HI, You could use the LINK command after going through Jligand for your modified residues. There is a very nice tutorial here: http://www.ysbl.york.ac.uk/mxstat/JLigand/ in case you haven't done this before. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Rajesh kumar [ccp4...@hotmail.com] Sent: Thursday, March 22, 2012 3:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refining phosphorylated residues Hi Joel, thanks for the reply. It's not phospho group but the whole residue get disconnected. In coot if I do refinement they get disconnected. Thanks Rajesh Sent from my iPhone On Mar 21, 2012, at 7:38 PM, Joel Tyndall joel.tynd...@otago.ac.nz wrote: Hi Rajesh, If I understand correctly, the phospho groups become disconnected from either the serine or threonine. If this is the case, you can use the SEP monomer for phosphoserine and TPO monomer for phosphothreonine. (replace the amino acid residues with these) These are built into ccp4 and coot Hope this helps Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta56 Otepoti 9054 Aotearoa Ph / Waea 64 3 4797293 Fax / Waeawhakaahua 64 3 4797034 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Thursday, 22 March 2012 12:00 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] refining phosphorylated residues Dear All, I have a structure of a protein and peptide complex, in which peptide has modified residues ( phosphoserine and phosphothreonine). During refinement these both gets disconnected withadjacentresidues and its hard to connect them. Could you please suggest me some options. Thanks Rajesh
Re: [ccp4bb] refining phosphorylated residues
Have you checked the dictionary cif calls them L-peptide? Eleanor The header should look like this.. # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level ALA ALA 'ALANINE ' L-peptide 10 5 . # On Mar 21 2012, Rajesh kumar wrote: Dear All, I have a structure of a protein and peptide complex, in which peptide has modified residues ( phosphoserine and phosphothreonine). During refinement these both gets disconnected with adjacent residues and its hard to connect them.Could you please suggest me some options. ThanksRajesh -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] refining phosphorylated residues
In new version (it should be in ccp4 6.2.0, if not then it will come ccp4 6.3, otherwise you can take it from York's web site: ) TPO as well as SEP are peptides. Break in coot may be due to misinterpretation of SEP or TPO as peptide in coot and it may be because of older version of the dictionary. Do the distances, angles between neighbouring residues make sence? If not then refinement also had problems regards Garib On 22 Mar 2012, at 00:39, Joel Tyndall wrote: As a follow up question the bulletin board, why is SEP a peptide (L-peptide) and TPO not (non-polymer)? Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Thursday, 22 March 2012 12:00 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] refining phosphorylated residues Dear All, I have a structure of a protein and peptide complex, in which peptide has modified residues ( phosphoserine and phosphothreonine). During refinement these both gets disconnected with adjacent residues and its hard to connect them. Could you please suggest me some options. Thanks Rajesh Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] refining phosphorylated residues
Dear All, Thanks for the suggestions. I will work on them.I had not worked on the modified residues, so thanks for all the valuable suggestions. RegardsRajesh Date: Thu, 22 Mar 2012 10:15:55 + From: ga...@mrc-lmb.cam.ac.uk Subject: Re: [ccp4bb] refining phosphorylated residues To: CCP4BB@JISCMAIL.AC.UK In new version (it should be in ccp4 6.2.0, if not then it will come ccp4 6.3, otherwise you can take it from York's web site: ) TPO as well as SEP are peptides. Break in coot may be due to misinterpretation of SEP or TPO as peptide in coot and it may be because of older version of the dictionary. Do the distances, angles between neighbouring residues make sence? If not then refinement also had problems regardsGarib On 22 Mar 2012, at 00:39, Joel Tyndall wrote:As a follow up question the bulletin board, why is SEP a peptide (L-peptide) and TPO not (non-polymer)? Joel _Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Thursday, 22 March 2012 12:00 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] refining phosphorylated residues Dear All, I have a structure of a protein and peptide complex, in which peptide has modified residues ( phosphoserine and phosphothreonine). During refinement these both gets disconnected with adjacent residues and its hard to connect them.Could you please suggest me some options. ThanksRajesh Garib N Murshudov Structural Studies DivisionMRC Laboratory of Molecular BiologyHills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
[ccp4bb] refining phosphorylated residues
Dear All, I have a structure of a protein and peptide complex, in which peptide has modified residues ( phosphoserine and phosphothreonine). During refinement these both gets disconnected with adjacent residues and its hard to connect them.Could you please suggest me some options. ThanksRajesh
Re: [ccp4bb] refining phosphorylated residues
As a follow up question the bulletin board, why is SEP a peptide (L-peptide) and TPO not (non-polymer)? Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Thursday, 22 March 2012 12:00 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] refining phosphorylated residues Dear All, I have a structure of a protein and peptide complex, in which peptide has modified residues ( phosphoserine and phosphothreonine). During refinement these both gets disconnected with adjacent residues and its hard to connect them. Could you please suggest me some options. Thanks Rajesh
Re: [ccp4bb] refining phosphorylated residues
Hi Joel, thanks for the reply. It's not phospho group but the whole residue get disconnected. In coot if I do refinement they get disconnected. Thanks Rajesh Sent from my iPhone On Mar 21, 2012, at 7:38 PM, Joel Tyndall joel.tynd...@otago.ac.nz wrote: Hi Rajesh, If I understand correctly, the phospho groups become disconnected from either the serine or threonine. If this is the case, you can use the SEP monomer for phosphoserine and TPO monomer for phosphothreonine. (replace the amino acid residues with these) These are built into ccp4 and coot Hope this helps Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Thursday, 22 March 2012 12:00 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] refining phosphorylated residues Dear All, I have a structure of a protein and peptide complex, in which peptide has modified residues ( phosphoserine and phosphothreonine). During refinement these both gets disconnected with adjacent residues and its hard to connect them. Could you please suggest me some options. Thanks Rajesh
