Re: [ccp4bb] Ligand identification in X-ray density

[Artem Evdokimov]

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 <
cf8d8aa45b08-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/-0001-8532-6699
>
> Am 05.06.2024 um 19:22 schrieb Zachary A. Wood :
>
> 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 
> *Date: *Wednesday, June 5, 2024 at 1:17 PM
> *To: *Zachary A. Wood 
> *Cc: *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/-0001-8532-6699
>
>
>
> Am 05.06.2024 um 19:11 schrieb Zachary A. Wood <
> d585377c7e8a-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  on behalf of Jon
> Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
> *Date: *Wednesday, June 5, 2024 at 1:01 PM
> *To: *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 <
> cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Thank you for this intriguing information!
>
>
>
> At the same time, this also implies that 

Re: [ccp4bb] Ligand identification in X-ray density

[Jeroen Mesters]

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/-0001-8532-6699

Am 05.06.2024 um 19:22 schrieb Zachary A. Wood :

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 
Date: Wednesday, June 5, 2024 at 1:17 PM
To: Zachary A. Wood 
Cc: 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/-0001-8532-6699


Am 05.06.2024 um 19:11 schrieb Zachary A. Wood 
<d585377c7e8a-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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday, June 5, 2024 at 1:01 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto: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 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-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/-0001-8532-6699

Am 05.06.2024 um 18:41 schrieb Zachary A. Wood 
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


***
Zach

Re: [ccp4bb] Ligand identification in X-ray density

[Zachary A. Wood]

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 
Date: Wednesday, June 5, 2024 at 1:17 PM
To: Zachary A. Wood 
Cc: 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/-0001-8532-6699


Am 05.06.2024 um 19:11 schrieb Zachary A. Wood 
<d585377c7e8a-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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday, June 5, 2024 at 1:01 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto: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 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-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/-0001-8532-6699

Am 05.06.2024 um 18:41 schrieb Zachary A. Wood 
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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>>
Date: Wedne

Re: [ccp4bb] Ligand identification in X-ray density

[Jeroen Mesters]

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/-0001-8532-6699

Am 05.06.2024 um 19:11 schrieb Zachary A. Wood 
<d585377c7e8a-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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday, June 5, 2024 at 1:01 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto: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 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-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/-0001-8532-6699


Am 05.06.2024 um 18:41 schrieb Zachary A. Wood 
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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday, June 5, 2024 at 12:29 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto: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 
cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-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/-0001-8532-6699

Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
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 t

Re: [ccp4bb] Ligand identification in X-ray density

[Zachary A. Wood]

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  on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Date: Wednesday, June 5, 2024 at 1:01 PM
To: 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 
<cf8d8aa45b08-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/-0001-8532-6699


Am 05.06.2024 um 18:41 schrieb Zachary A. Wood :

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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday, June 5, 2024 at 12:29 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto: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 
cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-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/-0001-8532-6699

Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
:

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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Re: [ccp4bb] Ligand identification in X-ray density

[Jon Cooper]

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 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/-0001-8532-6699
>
>> Am 05.06.2024 um 18:41 schrieb Zachary A. Wood :
>>
>> 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  on behalf of Jeroen Mesters 
>> <cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>
>> Date:Wednesday, June 5, 2024 at 12:29 PM
>> To:CCP4BB@JISCMAIL.AC.UK
>> Subject:Re: [ccp4bb] Ligand identification in X-ray density
>>
>> You don't often get email 
>> fromcf8d8aa45b08-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/-0001-8532-6699
>>
>>> Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
>>> :
>>>
>>> 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:
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>
> ---
>
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Re: [ccp4bb] Ligand identification in X-ray density

[Jeroen Mesters]

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/-0001-8532-6699

Am 05.06.2024 um 18:41 schrieb Zachary A. Wood :

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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday, June 5, 2024 at 12:29 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto: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 
cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-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/-0001-8532-6699


Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
:

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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Re: [ccp4bb] Ligand identification in X-ray density

[David J. Schuller]

"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  on behalf of Zachary A. Wood 
<d585377c7e8a-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, June 5, 2024 12:41 PM
To: 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  on behalf of Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>
Date: Wednesday, June 5, 2024 at 12:29 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Ligand identification in X-ray density

You don't often get email from cf8d8aa45b08-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/-0001-8532-6699



Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
:



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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Re: [ccp4bb] Ligand identification in X-ray density

[Zachary A. Wood]

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  on behalf of Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>
Date: Wednesday, June 5, 2024 at 12:29 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Ligand identification in X-ray density
You don't often get email from cf8d8aa45b08-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/-0001-8532-6699


Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
:

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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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Ligand identification in X-ray density

[Jeroen Mesters]

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/-0001-8532-6699

Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
:

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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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

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Re: [ccp4bb] Ligand identification

[CRAIG A BINGMAN]

My only comment is that you should consider not only what is in reservoir, but 
also anything present in your sample buffer.

On Jul 18, 2019, at 3:02 PM, Nicola Evans 
<251ca3b4615e-dmarc-requ...@jiscmail.ac.uk>
 wrote:

(well conditions: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 5.5, 
25% PEG 3,350). As this is an the crystal contact region the molecule isn't 
likely to be biologically significant. The data have been solved to 1.9Å. I 
have attached a screenshot of the mysterious density.




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Re: [ccp4bb] Ligand identification

[Ethan Merritt (UW)]

On Thursday, July 18, 2019 1:02:25 PM PDT Nicola Evans wrote:
> > I have an unidentfied blob of density at a crystal contact region. I
> > tried inputting a magnesium ion there, it was clearly incorrect but it
> > improved the R-factors by 3, so I would really like to identify the
> > correct molecule! Is there a tool to identify ligands in structures? I
> > have tried the Phenix ligand identification tool to no avail (although
> > it did find some nice horseshoe shaped PEG ions). I used glycerol and
> > PEG400 as a cryo protectant, and identified a few glycerol and PEG
> > molecules in other parts of the structure but not in this spot (well
> > conditions: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH
> > 5.5, 25% PEG 3,350). As this is an the crystal contact region the
> > molecule isn't likely to be biologically significant. The data have
> > been solved to 1.9Å. I have attached a screenshot of the mysterious
> > density. I would appreciate any suggestions! In addition, I am adding
> > water molecules to this protein, and often there are what appear to be
> > long chains. Are these likely to be long chains of ordered waters, or
> > more PEG molecules? Thanks in advance for your help! Nicola


You might enjoy reading the recent paper by Kowiel et al (2018)
"Automatic recognition of ligands in electron density by machine learning"
https://doi.org/10.1093/bioinformatics/bty626

One of the more convincing examples they give (Fig 6D) is identification of a 
TRIS
molecule.  By coincidence the density in the this figure looks a lot like yours.

cheers,

Ethan

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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[ccp4bb] Assunto: [ccp4bb] Ligand identification

[Andre Godoy]

Hi Nicola,
Try TRIS ir bis-tris,

Chers 
 
  Em qui, 18 18e jul 18e 2019 às 17:03, Nicola 
Evans<251ca3b4615e-dmarc-requ...@jiscmail.ac.uk> escreveu: 
  I have an unidentfied blob of density at a crystal contact region. I tried 
inputting a magnesium ion there, it was clearly incorrect but it improved the 
R-factors by 3, so I would really like to identify the correct molecule! Is 
there a tool to identify ligands in structures? I have tried the Phenix ligand 
identification tool to no avail (although it did find some nice horseshoe 
shaped PEG ions). I used glycerol and PEG400 as a cryo protectant, and 
identified a few glycerol and PEG molecules in other parts of the structure but 
not in this spot (well conditions: 0.2 M Magnesium chloride hexahydrate, 0.1 M 
BIS-TRIS pH 5.5, 25% PEG 3,350). As this is an the crystal contact region the 
molecule isn't likely to be biologically significant. The data have been solved 
to 1.9Å. I have attached a screenshot of the mysterious density. I would 
appreciate any suggestions!In addition, I am adding water molecules to this 
protein, and often there are what appear to be long chains. Are these likely to 
be long chains of ordered waters, or more PEG molecules? Thanks in advance for 
your help!Nicola

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