Re: [ccp4bb] Dose anyone see this ligand before?
Dear Dale Tronrud, Thanks for your advise. Initially, i focused on the shape of the density. As you suggest, i checked all possible biological molecules and common additives used in purification and crystallization. I found that the structure of bis-tris-propane is similar to the target density. And the environment of crystallization contain this molecular. So, i will try it. Thanks again! Wei At 2013-07-18 02:20:10,Dale Tronrud det...@uoxray.uoregon.edu wrote: Do you have any reason to expect either of these molecules would be in your crystal? The model you build has to fit the density, be consistent with the surrounding environment (which you haven't shared with us) and you have to have some story for how that molecule got in your crystal. Personally I would steer away from industrial compounds and focus more on biological molecules and common additives used in purification and crystallization. The environment is critical to identifying this molecule. What hydrogen bonds does this molecule make? What charges are near by? Certainly the presence or absence of hydrogen bonds will distinguish between these two compounds before you go to the trouble to build a model of either. Dale Tronrud On 7/17/2013 6:35 AM, Wei Feng wrote: Dear all, Thank you for your advices. I had tried to use MPD and pyrophosphate etc to fix the density map but all of them were too small. We guess that the molecular formula should be C8H18O2. So we search this formula in google and find two candidate molecules 1: http://flyingexport.en.ecplaza.net/dhad-99-5--137042-689140.html 2: http://en.m.wikipedia.org/wiki/Di-tert-butyl_peroxide Could you tell me how to get the coordinate of these molecules? Thank you for your time! Wei
Re: [ccp4bb] Dose anyone see this ligand before?
Remember, that MPD is chiral, so you have two possibilities at C4. After putting MPD into your model the FoFc-density should clearly tell you (your resolution looks better than 2 A), if the group on the left in your picture is a phosphate / sulfate or if it only has a carbon in the middle of the tetrahedrally bound atom. Check for hydrogen bonding partners, which help to identify hydroxy groups. greetings Gottfried At Wednesday, 17-07-2013 on 06:14 sonali dhindwal wrote: hi Wei, This looks like MPD, 2-Methyl-2,4-pentanediol. May b u have added it as ur cryo-protectant. Thanks and Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” - From: sonali dhindwal To: ccp4...@hotmail.com Sent: Wednesday, 17 July 2013 9:44 AM Subject: Re: [ccp4bb] Dose anyone see this ligand before? hi Wei, This looks like MPD, 2-Methyl-2,4-pentanediol. May b u have added it as ur cryo-protectant. Thanks and Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” - From: Wei Feng To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, 16 July 2013 9:05 PM Subject: [ccp4bb] Dose anyone see this ligand before? Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei
Re: [ccp4bb] Dose anyone see this ligand before?
Try here: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=8031loc=ec_rcs download the sdf and use the sdf to pdb converter Or I think phenix can read in sdf and convert them Jürgen On Jul 17, 2013, at 9:35 AM, Wei Feng wrote: Dear all, Thank you for your advices. I had tried to use MPD and pyrophosphate etc to fix the density map but all of them were too small. We guess that the molecular formula should be C8H18O2. So we search this formula in google and find two candidate molecules 1: http://flyingexport.en.ecplaza.net/dhad-99-5--137042-689140.html 2: http://en.m.wikipedia.org/wiki/Di-tert-butyl_peroxide Could you tell me how to get the coordinate of these molecules? Thank you for your time! Wei .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Dose anyone see this ligand before?
Do you have any reason to expect either of these molecules would be in your crystal? The model you build has to fit the density, be consistent with the surrounding environment (which you haven't shared with us) and you have to have some story for how that molecule got in your crystal. Personally I would steer away from industrial compounds and focus more on biological molecules and common additives used in purification and crystallization. The environment is critical to identifying this molecule. What hydrogen bonds does this molecule make? What charges are near by? Certainly the presence or absence of hydrogen bonds will distinguish between these two compounds before you go to the trouble to build a model of either. Dale Tronrud On 7/17/2013 6:35 AM, Wei Feng wrote: Dear all, Thank you for your advices. I had tried to use MPD and pyrophosphate etc to fix the density map but all of them were too small. We guess that the molecular formula should be C8H18O2. So we search this formula in google and find two candidate molecules 1: http://flyingexport.en.ecplaza.net/dhad-99-5--137042-689140.html 2: http://en.m.wikipedia.org/wiki/Di-tert-butyl_peroxide Could you tell me how to get the coordinate of these molecules? Thank you for your time! Wei
Re: [ccp4bb] Dose anyone see this ligand before?
Wei I heartily second Dale's comment. Since you do know what has been in contact with your protein, you should be able to make a list of ALL POSSIBLE compounds your protein has been exposed to. However, don't go off the deep end. You say that We guess that the molecular formula should be C8H18O2. So we search this formula in google and find two candidate molecules, but how did you determine C8H18O2 when you can't see hydrogen, and guessing the elemental composition of a ligand may be possible at high resolution IF you know your occupancy. Two observations I have are: 1. Anything you exposed your protein to could bind to it tightly regardless of the number of purification steps the protein went through. But as Dale said, the ligand is most likely biologically derived. 2. As an example of the exception proves the rule circumstance, I believe it was the monoamine oxidase B structure that had one of the plasticizers from the plastic trays bound in the active site. Something to think about as we drink from our water bottles and mull about neurochemistry. Nonetheless, it was not a wild, off-the-shelf ligand, but some thing the protein had been in contact with. Cheers, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On Jul 17, 2013, at 2:20 PM, Dale Tronrud wrote: Do you have any reason to expect either of these molecules would be in your crystal? The model you build has to fit the density, be consistent with the surrounding environment (which you haven't shared with us) and you have to have some story for how that molecule got in your crystal. Personally I would steer away from industrial compounds and focus more on biological molecules and common additives used in purification and crystallization. The environment is critical to identifying this molecule. What hydrogen bonds does this molecule make? What charges are near by? Certainly the presence or absence of hydrogen bonds will distinguish between these two compounds before you go to the trouble to build a model of either. Dale Tronrud On 7/17/2013 6:35 AM, Wei Feng wrote: Dear all, Thank you for your advices. I had tried to use MPD and pyrophosphate etc to fix the density map but all of them were too small. We guess that the molecular formula should be C8H18O2. So we search this formula in google and find two candidate molecules 1: http://flyingexport.en.ecplaza.net/dhad-99-5--137042-689140.html 2: http://en.m.wikipedia.org/wiki/Di-tert-butyl_peroxide Could you tell me how to get the coordinate of these molecules? Thank you for your time! Wei
Re: [ccp4bb] Dose anyone see this ligand before?
Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei picture1.jpgpicture2.jpg .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Dose anyone see this ligand before?
It actually looks much like pyrophosphate! If your protein is phosphatase and the extra density is in vicinity of the active site it might be the remaining product of reaction. Vaheh From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bosch, Juergen Sent: Tuesday, July 16, 2013 11:53 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Dose anyone see this ligand before? Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei picture1.jpgpicture2.jpg .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Re: [ccp4bb] Dose anyone see this ligand before?
Dear wei, i think you have to keep in mind what do you have in your cristal growing condition, and in you protein buffer. Because maybe you can find which molecules this ligand could be. It's difficult to help more, because we don't know you level of sigma for the map and the resolution of your dataset. But in all case, if you have an idea of what it could be, and you don't find restraint and molecules in existing library, you can use monomer library sketcher in ccp4 to sketch manually your molecule, and generate library of restraints. Hope to help you. Nicolas Le 16/07/13 17:56, Oganesyan, Vaheh a écrit : It actually looks much like pyrophosphate! If your protein is phosphatase and the extra density is in vicinity of the active site it might be the remaining product of reaction. /*/Vaheh/*/ *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Bosch, Juergen *Sent:* Tuesday, July 16, 2013 11:53 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Dose anyone see this ligand before? Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei ** picture1.jpgpicture2.jpg .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Re: [ccp4bb] Dose anyone see this ligand before?
Yes that was what I was thinking as well, that's why the size-comparisson. Jürgen On Jul 16, 2013, at 11:56 AM, Oganesyan, Vaheh wrote: It actually looks much like pyrophosphate! If your protein is phosphatase and the extra density is in vicinity of the active site it might be the remaining product of reaction. Vaheh From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bosch, Juergen Sent: Tuesday, July 16, 2013 11:53 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Dose anyone see this ligand before? Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei picture1.jpgpicture2.jpg .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Dose anyone see this ligand before?
Its look like pyrophosphate to me . wts you protein's nature is this phosphatase or ATPase ?? vandna On Tue, Jul 16, 2013 at 11:19 AM, Bosch, Juergen jubo...@jhsph.edu wrote: Yes that was what I was thinking as well, that's why the size-comparisson. Jürgen On Jul 16, 2013, at 11:56 AM, Oganesyan, Vaheh wrote: It actually looks much like pyrophosphate! If your protein is phosphatase and the extra density is in vicinity of the active site it might be the remaining product of reaction. * Vaheh* -- *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Bosch, Juergen *Sent:* Tuesday, July 16, 2013 11:53 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Dose anyone see this ligand before? Special position ? sulfate-size ? Jürgen On Jul 16, 2013, at 11:35 AM, Wei Feng wrote: Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei * * picture1.jpgpicture2.jpg .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu -- Vandna Kukshal Postdoctral Research Associate Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110
Re: [ccp4bb] Dose anyone see this ligand before?
hi Wei, This looks like MPD, 2-Methyl-2,4-pentanediol. May b u have added it as ur cryo-protectant. Thanks and Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” From: sonali dhindwal sonali11dhind...@yahoo.co.in To: ccp4...@hotmail.com ccp4...@hotmail.com Sent: Wednesday, 17 July 2013 9:44 AM Subject: Re: [ccp4bb] Dose anyone see this ligand before? hi Wei, This looks like MPD, 2-Methyl-2,4-pentanediol. May b u have added it as ur cryo-protectant. Thanks and Regards -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” From: Wei Feng ccp4...@hotmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, 16 July 2013 9:05 PM Subject: [ccp4bb] Dose anyone see this ligand before? Dear all, I found some redundant density in my structure beween two molecule. (see picture 1 and 2) But I am not sure which ligand will be. Dose everyone see this ligand before? If so, can you tell the PDB code or send me the struture file? Thank you for your time! Wei
