"but another view might help."
I second that. I would specifically like to be assured that it is not sitting
on a special symmetry position.
=======================================================================
All Things Serve the Beam
=======================================================================
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Zachary A. Wood
<0000d585377c7e8a-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, June 5, 2024 12:41 PM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Ligand identification in X-ray density
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
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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.
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