At this resolution you should be able to infer differences between C and O based on the map levels at each location. Another dead giveaway is the bond lengths and the asymmetry of the top region - that is not a carboxylic acid to me.
This looks lime MPD to me, very classic shape. Artem On Wed, Jun 5, 2024, 1:37 PM Jeroen Mesters < 0000cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk> wrote: > 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 > > > [image: 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> on behalf of Jon > Cooper <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> > *Date: *Wednesday, June 5, 2024 at 1:01 PM > *To: *CCP4BB@JISCMAIL.AC.UK <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 > > Sent from Proton Mail Android > > > > -------- Original Message -------- > On 05/06/2024 17:54, Jeroen Mesters < > 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>: > > > > 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 > > > ------------------------------ > > 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 > > > > > > ------------------------------ > > 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/
