Re: [ccp4bb] Mystery blob

[Diana Tomchick]

It’s the Easter Bunny!

But seriously, it looks like more than one compound, perhaps hydrogen bonded to 
each other.

Diana Tomchick

Sent from my iPhone

On Mar 7, 2024, at 7:32 AM, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:


EXTERNAL MAIL

Anyone ANY idea what this could be?? Beautiful density but...

I am told:
The possible/likely components of the protein solution/cryo/crystallisation 
buffer are:
NaCl, MES, a tiny bit of HEPES possibly, ligand ( GR8.027 = the pentasaccharide 
near catalytic residues Glu276 and Glu165), Et3N which is monomer TEA (a 
possible counterion for the ligand - see diagram below), glycerol (cryo)
There may also be carbonate ions present from the ligand.  Any thoughts 
appreciated!!



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Re: [ccp4bb] mystery-blob-itis

[Isabel Garcia-Saez]

Thank you very much for your suggestions. The truth is that I am  
following more or less the usual pathways for ligand identification as  
you Boaz suggested but I was just wondering if there was something to  
identify ligands in a bit less intuitive/classical manner (some sort  
of pattern recognition, etc...).


Well, I will continue with the trial/error stuff... you cannot  
escape ... :-).


Cheers

Isabel


Le 18 déc. 09 à 12:03, Boaz Shaanan a écrit :


Hi Isabel,

I don't have a direct answer about ways to find potential ligands  
(by the way, Arp/wArp and coot have a tool for that, and probably  
phenix too, which you may have already tried) beyond what you've  
already tried. But what has worked for me many times is to start by  
putting waters into those blobs and refine them. If these blobs hide  
some ligands, or components of crystallization buffer,  these waters  
will cluster and give you better hints, in most cases. On different  
occasions I located this way peg molecules (waters arranged in a  
circle), Mg+2 with the coordination sheel, phosphates, sulfates  
which weren't obvious to begin with. I think it's worth trying.


Cheers,

 Boaz



- Original Message -
From: Isabel Garcia-Saez isabel.gar...@ibs.fr
Date: Friday, December 18, 2009 11:20
Subject: [ccp4bb] mystery-blob-itis
To: CCP4BB@JISCMAIL.AC.UK

 Dear all,
 Curiously, I think I am just suffering an acute attack of
 mystery-
 blob-itis as well. I try to finish up the refinement of two
 structures
 and I am puzzled about a few blobs I found (from waters than
 could be
 ions to density that could be PEG). I have been digging out
 ligands
 from PDBSum, HICup, try to find ions with WASP, etc, but does
 anyone
 know a better way to identified misterious blobs densities (sort
 of
 database of ligand densities, pattern recognition...)?.

 Thanks a lot,

 Isabel





 Isabel Garcia-Saez PhD
 Institut de Biologie Structurale Jean-Pierre Ebel
 Laboratoire des Protéines du Cytosquelette
 41, rue Jules Horowitz
 F-38027 Grenoble CEDEX 1
 France
 tel.: 00-33-438 789615
 FAX:  00-33-438 785494
 e-mail: isabel.gar...@ibs.fr
 http://www.ibs.fr






Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan

‎




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