Hello Everyone, It does look like trimethylglycine (betaine), but another view might help. If it is, it is also made in ecoli and PEOPLE. It is a pretty common metabolite in the microbial and animal kingdom…useful for balancing osmotic stress and stabilizing protein structure (it is a strong kosmotrope).
Best regards, Z *********************************************** Zachary A. Wood, Ph.D. (He/Him) Professor and Graduate Coordinator Josiah Meigs Distinguished Teaching Professor Associate Director of SER-CAT Department of Biochemistry & Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab: 706-583-0303 FAX: 706-542-1738 *********************************************** From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jeroen Mesters <0000cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk> Date: Wednesday, June 5, 2024 at 12:29 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Ligand identification in X-ray density You don't often get email from 0000cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi, proteins my pick up ligands from the „source" from which they were isolated…. Looks to me like trimethylglycine, an amino-acid derivative found in plants… Regards, Jeroen __ https://orcid.org/0000-0001-8532-6699 Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan <khadijahameenk...@gmail.com>: Dear All, I am a first-year PhD student in a structural biology lab. I am building a model in 1.5 ang X-ray diffraction data. I would appreciate your suggestions for fitting a ligand in an unknown X-ray density (attached image) in the protein binding pocket. The details for protein purification and crystallization buffers are below: Purification: NaCl, Tris-HCl pH 8.5, Glycerol Crystallization: Carboxylic acid mix (Sodium formate, Ammonium acetate, Sodium citrate, Potassium Sodium Tartrate and Sodium Oxamate),Tris, Bicine buffer, Precipitant (PEG3350, MPD) I have tried fitting all the buffer and crystallization components but none of these components are giving the right solution (Either the difference map gets red with increased B-factor or it remains green). I would really appreciate your input on this. I have attached an image showing the density. Thank you. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
