Re: [ccp4bb] insertion of a chemical
On 30/06/2020 10:51, Daniele Veggi wrote: Dear CCP4bb, I'm trying to insert an Acetone molecule between two cysteine residues in coot or modifying the pdb. I'm working on this modified molecule where the disulfide bridge was chemichally opened and inserted an acetone molecule between the two cysteine. MS data confirm this modification (98% of molecules modified) but I can not insert the acetone covalently linked to the S of both cysteine (S-ACN-S). Maybe what I think and what I am doing is not the right solution (the disulfide bridge is still alive?) anyway i would like to know how to link the acetone to the two cysteine Here's how to make a link between a ligand and the protein using Coot and Acedrg: https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html Making a link from a ligand to two protein residues is tricky (I wouldn't know how to do it off the top of my head). Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] insertion of a chemical
To verify the presence of a non protein ligand, you need to come at this from an unbiased perspective. 1. Remove what you think is not there (e.g. disulfide bond) by truncating the Cys residues 2. Examine the difference density map to see if it conforms to your expectations of what is proposed to be there (or does not) 3. If appropriate, build and attach ligand and re-refine. I am assuming that you are proposing a thioketal adduct, which is not the same as inserting an acetone molecule in the structure. You can find generic instructions for these types of tasks on my XRD-protocols site, https://sites.google.com/colgate.edu/xrd-protocols. Roger Rowlett On Tue, Jun 30, 2020, 7:25 AM Daniele Veggi wrote: > Hi Yadav, > yes, this is only a representation of what I would like to do. If during > the refinement will continue to appear density, probably I'm on the good > track..but currently my big issue is inserting the ACN > covalently linked to both cys. > > many thanks > > Daniele Veggi > GSK Vaccines Siena Italy > > > > > > Il giorno mar 30 giu 2020 alle ore 12:52 Lumbini Yadav < > lumbin...@gmail.com> ha scritto: > >> Hi Daniele, >> Do you see Fo-Fc density near disuphide bond where you are trying to fit >> acetone? >> >> On Tue, Jun 30, 2020 at 3:28 PM Daniele Veggi >> wrote: >> >>> Dear CCP4bb, >>> >>> I'm trying to insert an Acetone molecule between two cysteine residues >>> in coot or modifying the pdb. I'm working on this modified molecule where >>> the disulfide bridge was chemichally opened and inserted an acetone >>> molecule between the two cysteine. >>> >>> MS data confirm this modification (98% of molecules modified) but I can >>> not insert the acetone covalently linked to the S of both cysteine >>> (S-ACN-S). >>> Maybe what I think and what I am doing is not the right solution (the >>> disulfide bridge is still alive?) anyway i would like to know how to link >>> the acetone to the two cysteine >>> To better understand what I mean in attach you find a screenshot >>> >>> I thank in advance all those who will have the courtesy to make a >>> suggestion >>> >>> Daniele Veggi >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >>> >> > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] insertion of a chemical
As also suggested by Dr. Roger you should first see the density then the next step of molecule addition is suggested. Omit is also a good idea for further confirmation. On Tue, Jun 30, 2020 at 4:55 PM Daniele Veggi wrote: > Hi Yadav, > yes, this is only a representation of what I would like to do. If during > the refinement will continue to appear density, probably I'm on the good > track..but currently my big issue is inserting the ACN > covalently linked to both cys. > > many thanks > > Daniele Veggi > GSK Vaccines Siena Italy > > > > > > Il giorno mar 30 giu 2020 alle ore 12:52 Lumbini Yadav < > lumbin...@gmail.com> ha scritto: > >> Hi Daniele, >> Do you see Fo-Fc density near disuphide bond where you are trying to fit >> acetone? >> >> On Tue, Jun 30, 2020 at 3:28 PM Daniele Veggi >> wrote: >> >>> Dear CCP4bb, >>> >>> I'm trying to insert an Acetone molecule between two cysteine residues >>> in coot or modifying the pdb. I'm working on this modified molecule where >>> the disulfide bridge was chemichally opened and inserted an acetone >>> molecule between the two cysteine. >>> >>> MS data confirm this modification (98% of molecules modified) but I can >>> not insert the acetone covalently linked to the S of both cysteine >>> (S-ACN-S). >>> Maybe what I think and what I am doing is not the right solution (the >>> disulfide bridge is still alive?) anyway i would like to know how to link >>> the acetone to the two cysteine >>> To better understand what I mean in attach you find a screenshot >>> >>> I thank in advance all those who will have the courtesy to make a >>> suggestion >>> >>> Daniele Veggi >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >>> >> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] insertion of a chemical
Hi Yadav, yes, this is only a representation of what I would like to do. If during the refinement will continue to appear density, probably I'm on the good track..but currently my big issue is inserting the ACN covalently linked to both cys. many thanks Daniele Veggi GSK Vaccines Siena Italy Il giorno mar 30 giu 2020 alle ore 12:52 Lumbini Yadav ha scritto: > Hi Daniele, > Do you see Fo-Fc density near disuphide bond where you are trying to fit > acetone? > > On Tue, Jun 30, 2020 at 3:28 PM Daniele Veggi > wrote: > >> Dear CCP4bb, >> >> I'm trying to insert an Acetone molecule between two cysteine residues in >> coot or modifying the pdb. I'm working on this modified molecule where the >> disulfide bridge was chemichally opened and inserted an acetone molecule >> between the two cysteine. >> >> MS data confirm this modification (98% of molecules modified) but I can >> not insert the acetone covalently linked to the S of both cysteine >> (S-ACN-S). >> Maybe what I think and what I am doing is not the right solution (the >> disulfide bridge is still alive?) anyway i would like to know how to link >> the acetone to the two cysteine >> To better understand what I mean in attach you find a screenshot >> >> I thank in advance all those who will have the courtesy to make a >> suggestion >> >> Daniele Veggi >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] insertion of a chemical
The first step would be to verify consistent, convincing electron density for the proposed thioketal adduct. A good way to start might be an "omit" map of the region by mutating the Cys residues to Ala, truncating them to the beta-carbon. The resulting difference density may be suggestive of a thioketal adduct or a simple disulfide bridge. Building the thioketal, if actually present, will require addition skill with ligand building and Coot. You are essentially attaching an isopropyl group to the two Cys sulfur atoms. Roger Rowlett Gordon & Dorothy Kline Professor, Emeritus Dept. Of Chemisty Colgate University On Tue, Jun 30, 2020, 5:58 AM Daniele Veggi wrote: > Dear CCP4bb, > > I'm trying to insert an Acetone molecule between two cysteine residues in > coot or modifying the pdb. I'm working on this modified molecule where the > disulfide bridge was chemichally opened and inserted an acetone molecule > between the two cysteine. > > MS data confirm this modification (98% of molecules modified) but I can > not insert the acetone covalently linked to the S of both cysteine > (S-ACN-S). > Maybe what I think and what I am doing is not the right solution (the > disulfide bridge is still alive?) anyway i would like to know how to link > the acetone to the two cysteine > To better understand what I mean in attach you find a screenshot > > I thank in advance all those who will have the courtesy to make a > suggestion > > Daniele Veggi > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] insertion of a chemical
Hi Daniele, Do you see Fo-Fc density near disuphide bond where you are trying to fit acetone? On Tue, Jun 30, 2020 at 3:28 PM Daniele Veggi wrote: > Dear CCP4bb, > > I'm trying to insert an Acetone molecule between two cysteine residues in > coot or modifying the pdb. I'm working on this modified molecule where the > disulfide bridge was chemichally opened and inserted an acetone molecule > between the two cysteine. > > MS data confirm this modification (98% of molecules modified) but I can > not insert the acetone covalently linked to the S of both cysteine > (S-ACN-S). > Maybe what I think and what I am doing is not the right solution (the > disulfide bridge is still alive?) anyway i would like to know how to link > the acetone to the two cysteine > To better understand what I mean in attach you find a screenshot > > I thank in advance all those who will have the courtesy to make a > suggestion > > Daniele Veggi > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] insertion of a chemical
Dear CCP4bb, I'm trying to insert an Acetone molecule between two cysteine residues in coot or modifying the pdb. I'm working on this modified molecule where the disulfide bridge was chemichally opened and inserted an acetone molecule between the two cysteine. MS data confirm this modification (98% of molecules modified) but I can not insert the acetone covalently linked to the S of both cysteine (S-ACN-S). Maybe what I think and what I am doing is not the right solution (the disulfide bridge is still alive?) anyway i would like to know how to link the acetone to the two cysteine To better understand what I mean in attach you find a screenshot I thank in advance all those who will have the courtesy to make a suggestion Daniele Veggi To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
