Re: [ccp4bb] unknown density in 1.6 A structure

[Peer Mittl]

Dear Nick,

I like your idea and your comments on this substance. 1,2-hexandiol 
supposed to be chiral but probably it is used as a racemic mixture in 
cosmetics. There is even a crystal structure in the PDB (4EUS) and an 
associated 3 letter code. I´ll give it a try because it seems to fit 
nicely the ED map. I just have to find out how to handle racemics in 
buster refinement. Thank you all for your helpful comments.


Have a nice day.
-Peer

Am 03.06.2021 um 13:00 schrieb Nicholas Keep:
How about an overlay of the structure you have with a second ligand 
conformation where the OH and CH2OH are swapped? ie two alternative 
conformations of the ligand.  That might remove the last green density


1,2-hexanediol is apparently widely used in cosmetics and 
moisturisers.  Did someone somehow touch the protein or 
crystallisation tray with recently moisturised hands?  Even so it must 
have very high affinity for your protein


Best wishes

Nick





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Re: [ccp4bb] unknown density in 1.6 A structure

[Sevvana, Madhumati]

Hi Peer,
Reminds me of a lipocalin structure I solved which co-purified fatty acid with 
it. I could model fatty acids and we along with our collaborators used several 
complementary biophysical methods followed by functional assays to identify the 
ligand.
https://www.sciencedirect.com/science/article/abs/pii/S002228360901078X
[https://ars.els-cdn.com/content/image/1-s2.0-S0022283609X00422-cov150h.gif]
Serendipitous Fatty Acid Binding Reveals the Structural Determinants for Ligand 
Recognition in Apolipoprotein 
M
Apolipoprotein M (ApoM) is a 25-kDa HDL-associated apolipoprotein and a member 
of the lipocalin family of proteins. Mature apoM retains its signal pep…
www.sciencedirect.com
Thank you.
All the best,
Madhu


Madhumati Sevvana, Ph.D.
Assistant Research Scientist
Structural Virology lab of Prof. Richard Kuhn
Hockmeyer Hall of Structural Biology
Department of Biological Sciences
Purdue University, West Lafayette IN




From: CCP4 bulletin board  on behalf of Peer Mittl 

Sent: Thursday, June 3, 2021 06:50
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] unknown density in 1.6 A structure

I'm struggling with the electron density shown in the attachment. The
substance does not seem to come from the crystallization condition nor
from the mounting buffer. The 1.6 A maps are rather clear, because the
compound binds into the hydrophobic core, which seems to be loosely packed.

-Peer





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Re: [ccp4bb] unknown density in 1.6 A structure

[Andrew Mesecar]

Dear Peer,

This reminds me of my colleague Michael Rossmann's discovery of a Pocket
Factor which is a fatty acid-like molecule residing in a hydrophobic pocket
underneath the "canyon" in enteroviruses. See
https://link.springer.com/article/10.1007/s13238-014-0092-6.  You likely
have an endogenous ligand that binds and stays bound during purification.
You may want to do some MS on your purified protein to see if you can
identify it.  Your density should provide enough information on a mass
range to look for.

Andy Mesecar

On Thu, Jun 3, 2021 at 6:50 AM Peer Mittl  wrote:

> I'm struggling with the electron density shown in the attachment. The
> substance does not seem to come from the crystallization condition nor
> from the mounting buffer. The 1.6 A maps are rather clear, because the
> compound binds into the hydrophobic core, which seems to be loosely packed.
>
> -Peer
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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-- 
*Andrew D. Me**secar*
Head, Department of Biochemistry
Walther Professor of Cancer Structural Biology
Deputy Director, Purdue Center for Cancer Research
E-Mail: amese...@purdue.edu
_
*Department of Biochemistry Contact Information:*
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--
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Re: [ccp4bb] unknown density in 1.6 A structure

[Dom Bellini - MRC LMB]

Hi Peer,

If I understand you correctly you are saying that you do not know what 
substance may be in the density; then perhaps you only need to extend by 
an extra atom to create a new kind of symmetrical molecule that will fit 
the density?


BW,

D

On 03/06/2021 11:55, SHEPARD William wrote:

Hi Peer,

Have you tried to model the hydroxyl O1 disordered at the carbonyl
position? Check the H-bonding pattern to the end groups, this might give
some clues.

Cheers,
Bill


Le 03/06/21 12:50, « Peer Mittl »  a écrit :


I'm struggling with the electron density shown in the attachment. The
substance does not seem to come from the crystallization condition nor

>from the mounting buffer. The 1.6 A maps are rather clear, because the

compound binds into the hydrophobic core, which seems to be loosely
packed.

-Peer





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--
Dom Bellini, Xray Crystallography Facility (1S205)
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH
Phone 01223 267839



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Re: [ccp4bb] unknown density in 1.6 A structure

[SHEPARD William]

Hi Peer, 

Have you tried to model the hydroxyl O1 disordered at the carbonyl
position? Check the H-bonding pattern to the end groups, this might give
some clues. 

Cheers, 
Bill


Le 03/06/21 12:50, « Peer Mittl »  a écrit :

>I'm struggling with the electron density shown in the attachment. The
>substance does not seem to come from the crystallization condition nor
>from the mounting buffer. The 1.6 A maps are rather clear, because the
>compound binds into the hydrophobic core, which seems to be loosely
>packed.
>
>-Peer
>
>
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/



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