Oooops, correct, got my reasoning turned around too…. But it could still be a betain if the water is more distant… We need a different view!
Best J. __. Dr. math. et dis. nat. Jeroen R. Mesters Biological Safety Officer (BBS) Deputy, Lecturer, Program Coordinator Infection Biology Visiting Professorship in Biophysics South Bohemian University [attachment.png] University of Lübeck Center for Structural and Cell Biology in Medicine Institute of Biochemistry Ratzeburger Allee 160 23562 Lübeck Tel +49 451 3101 3105 https://orcid.org/0000-0001-8532-6699 Am 05.06.2024 um 19:22 schrieb Zachary A. Wood <z...@uga.edu>: I sent my last response too soon…. The ‘top’ end of the molecule in the image looks more like a carboxylic acid accepting H-bonds from two backbone amides (supporting the betaine assignment, and not MPD), but the ‘bottom’ end of the molecule looks like it is forming an H-bond with a well-ordered water molecule. If it were betaine, then that end would be three methyls there (but MPD would have a hydroxyl there). I am starting to think it is neither…probably one of the organic acids in the crystallization mix. 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: Jeroen Mesters <jeroen.mest...@uni-luebeck.de> Date: Wednesday, June 5, 2024 at 1:17 PM To: Zachary A. Wood <z...@uga.edu> Cc: CCP4BB@jiscmail.ac.uk <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Ligand identification in X-ray density You don't often get email from jeroen.mest...@uni-luebeck.de. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Yes! That is why I excluded MPD as there is the water molecule close-by…. But we need a different view…. Best J. __ Dr. math. et dis. nat. Jeroen R. Mesters Biological Safety Officer (BBS) Deputy, Lecturer, Program Coordinator Infection Biology Visiting Professorship in Biophysics South Bohemian University University of Lübeck Center for Structural and Cell Biology in Medicine Institute of Biochemistry Ratzeburger Allee 160 23562 Lübeck Tel +49 451 3101 3105 https://orcid.org/0000-0001-8532-6699 Am 05.06.2024 um 19:11 schrieb Zachary A. Wood <0000d585377c7e8a-dmarc-requ...@jiscmail.ac.uk>: It is pretty well-ordered, so I would expect the H-bonding pattern to distinguish between betaine and MPD. 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<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Jon Cooper <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:0000488a26d62010-dmarc-requ...@jiscmail.ac.uk>> Date: Wednesday, June 5, 2024 at 1:01 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] Ligand identification in X-ray density [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Or, it could be MPD ;-? Best wishes, Jon Cooper. jon.b.coo...@protonmail.com<mailto:jon.b.coo...@protonmail.com> Sent from Proton Mail Android -------- Original Message -------- On 05/06/2024 17:54, Jeroen Mesters <0000cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:0000cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>> wrote: Thank you for this intriguing information! At the same time, this also implies that not all entities that have been modelled as MPD are actually MDP but could also be a betain, right!?….. Best, Jeroen __ Dr. math. et dis. nat. Jeroen R. Mesters Biological Safety Officer (BBS) Deputy, Lecturer, Program Coordinator Infection Biology Visiting Professorship in Biophysics South Bohemian University University of Lübeck Center for Structural and Cell Biology in Medicine Institute of Biochemistry Ratzeburger Allee 160 23562 Lübeck https://orcid.org/0000-0001-8532-6699 Am 05.06.2024 um 18:41 schrieb Zachary A. Wood <z...@uga.edu<mailto:z...@uga.edu>>: 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<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Jeroen Mesters <0000cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:0000cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>> Date: Wednesday, June 5, 2024 at 12:29 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto: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<mailto: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. 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