Re: [ccp4bb] mysterious density

2022-03-14 Thread Diana Tomchick 
Contour the 2Fo-Fc map at lower sigma than 1.3, and see if the resulting 
density looks like MES. As others have said, if there is no specific pocket or 
interactions for the non-sulfonic acid head group, then I would expect that 
density to be weaker or smeared out due to positional disorder.

Diana

**
Diana R. Tomchick
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Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
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(214) 645-6353 (fax)




On Mar 13, 2022, at 9:19 AM, Amir Khan 
mailto:k...@crystal.harvard.edu>> wrote:


EXTERNAL MAIL

Hi,

I wonder whether anyone can advise on the ‘tadpole’ like density. The head is 
currently a phosphate
and I’ve placed a water in tail, but it obviously looks connected… would 
appreciate any help!

Green density at 5 sigma (Fo-fc), while blue is 2fo-fc at 1.3 sigma.

Crystallization condition is unknown, though it came from sparse matrix 
commercial (either Wizard, Pact Prem, or JCSG+).

Thanks!

Amir



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Re: [ccp4bb] mysterious density

2022-03-13 Thread David Briggs 
MES or HEPES, I reckon.

Both of them can lose definition for the electron density in the 
morpolino/piperazine 6-membered ring due to flexibility between the ring and 
the sulphonic acid group when - leading to the tadpole-like density you 
describe.

HTH,

Dave


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Senior Laboratory Research Scientist

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The Francis Crick Institute

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From: CCP4 bulletin board  on behalf of Xavier 
Brazzolotto 
Sent: 13 March 2022 17:28
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] mysterious density


External Sender: Use caution.


A MES buffer molecule ?

> Le 13 mars 2022 à 18:08, doriano lamba  a écrit :
>
> Glycerol-3-phosphate?
> My 2cents
> DL
> Il 2022-03-13 15:19 Amir Khan ha scritto:
>> Hi,
>> I wonder whether anyone can advise on the ‘tadpole’ like density.
>> The head is currently a phosphate
>> and I’ve placed a water in tail, but it obviously looks connected…
>> would appreciate any help!
>> Green density at 5 sigma (Fo-fc), while blue is 2fo-fc at 1.3 sigma.
>> Crystallization condition is unknown, though it came from sparse
>> matrix commercial (either Wizard, Pact Prem, or JCSG+).
>> Thanks!
>> Amir
>> -
>> To unsubscribe from the CCP4BB list, click the following link:
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> I-34149 Trieste - Italy
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> Skype-name: doriano.lamba
> E-mail: doriano.la...@ic.cnr.it
>
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Re: [ccp4bb] mysterious density

2022-03-13 Thread Xavier Brazzolotto 
A MES buffer molecule ?

> Le 13 mars 2022 à 18:08, doriano lamba  a écrit :
> 
> Glycerol-3-phosphate?
> My 2cents
> DL
> Il 2022-03-13 15:19 Amir Khan ha scritto:
>> Hi,
>> I wonder whether anyone can advise on the ‘tadpole’ like density.
>> The head is currently a phosphate
>> and I’ve placed a water in tail, but it obviously looks connected…
>> would appreciate any help!
>> Green density at 5 sigma (Fo-fc), while blue is 2fo-fc at 1.3 sigma.
>> Crystallization condition is unknown, though it came from sparse
>> matrix commercial (either Wizard, Pact Prem, or JCSG+).
>> Thanks!
>> Amir
>> -
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
> -- 
> Dr. Doriano Lamba
> Scientific Associate - Retired Fellow
> 
> Istituto di Cristallografia - C.N.R.
> Sede Secondaria di Trieste
> Area Science Park - Basovizza
> Building Q1 - Room 106
> Strada Statale 14 - Km. 163.5
> I-34149 Trieste - Italy
> 
> Mobile Phone: ++39 330411796
> Skype-name: doriano.lamba
> E-mail: doriano.la...@ic.cnr.it
> 
> ___
> WoS ResearchID: http://www.researcherid.com/rid/B-2961-2011
> ORCID ID:   http://orcid.org/-0001-6859-7868
> Google Scholar: 
> https://scholar.google.it/citations?hl=en&user=YzLT5gUJ&view_op=list_works
> Research Gate:  https://www.researchgate.net/profile/Doriano_Lamba2
> Scopus ID:  https://www.scopus.com/authid/detail.url?authorId=7003374970
> 
> 
> 
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Re: [ccp4bb] Mysterious density

2010-09-04 Thread Nat Echols 
On Fri, Sep 3, 2010 at 4:53 PM, Jin H. Park wrote:

> I have solved the structure. But, there seems oddly strong density above
> histidine residue.
> What could this density be?
> The protein was in Tris buffer, with NaCl and DTT, and crystallized in
> NaSCN with PEG.
> (electron density in the pictures is at 1.5 sigma)
>

In addition to the other possibilities mentioned, a quick Google search
indicates that thiocyanate can bind to histidine.  If you raise the sigma
cutoff much higher, what does it look like?

-Nat

Re: [ccp4bb] Mysterious density

2010-09-03 Thread Bret Church 
Hi Jin,

The text book might suggest metal ions, or even phosphorylation.these do
require evidence in the form additional structure beyond the metal or
phosphorus though...

Bret 




On 4/09/10 9:53 AM, "Jin H. Park"  wrote:

> 
> 
> Dear CCP4 community,
> 
> 
> 
> I have solved the structure. But, there seems oddly strong density above
> histidine residue.
> What could this density be?
> The protein was in Tris buffer, with NaCl and DTT, and crystallized in NaSCN
> with PEG. 
> (electron density in the pictures is at 1.5 sigma)
> 
> Thanks.

Re: [ccp4bb] Mysterious density

2010-09-03 Thread Janet Newman 
Hi Jin,

Could it be the wrong amino acid in the sequence?   Have you sequenced the gene 
construct that you used?  The codon usage for HIS is CAC or CAU, and for TYR is 
UAC or UAU. - 

Cheers, Janet



From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Jin H. Park 
[jinhp...@mail.med.upenn.edu]
Sent: 04 September 2010 09:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Mysterious density

Dear CCP4 community,



I have solved the structure. But, there seems oddly strong density above 
histidine residue.
What could this density be?
The protein was in Tris buffer, with NaCl and DTT, and crystallized in NaSCN 
with PEG.
(electron density in the pictures is at 1.5 sigma)

Thanks.

Re: [ccp4bb] Mysterious density

2010-07-09 Thread Dale Tronrud 
   Cyclized DTT can look similar to this blob.  Of course the sulfur
atoms would make one end of the blob more dense than the other.

Dale Tronrud

On 07/09/10 05:12, Nick Quade wrote:
> Dear CCP4 community,
> 
> I have solved the structure of a protein in complex with DNA. But,
> inside the protein there seems to be a ligand binding pocket with some
> strong density
> (*http://picasaweb.google.de/113264696790316881054/Desktop#). *The
> protein was in Tris buffer, with some NaCl, MgCl2 and DTT and
> crystallized in Li2SO4 with MES. What could this density be? I can
> exclude MES as crystals grown with citrate buffer have the same density.
> So I guess it might be something I co-purified or perhaps some
> degradation product of the DNA? The electron density in the pictures is
> at 1.5sigma.
> 
> Thanks in advance.
> 
> Nick

Re: [ccp4bb] Mysterious density

2010-07-09 Thread Paula Lario 
Another thing to consider is alternate ligand conformation. The water density 
(elongated) and the pocket composition (aromatic) could result in two 
alternative binding orientations (of the buffer? I need 3D). I would play 
around with models to see if it fits the density.

Paula Lario 

#778-828-3701


On Jul 9, 2010, at 5:12 AM, Nick Quade  wrote:

> Dear CCP4 community,
> 
> I have solved the structure of a protein in complex with DNA. But, inside the 
> protein there seems to be a ligand binding pocket with some strong density 
> (*http://picasaweb.google.de/113264696790316881054/Desktop#). *The protein 
> was in Tris buffer, with some NaCl, MgCl2 and DTT and crystallized in Li2SO4 
> with MES. What could this density be? I can exclude MES as crystals grown 
> with citrate buffer have the same density. So I guess it might be something I 
> co-purified or perhaps some degradation product of the DNA? The electron 
> density in the pictures is at 1.5sigma.
> 
> Thanks in advance.
> 
> Nick

Re: [ccp4bb] Mysterious density

2010-07-09 Thread Vellieux Frederic 

Blobology (a branch of macromolecular crystallography).

You could maybe place benzoate in there (the 6 membered ring on "top" in 
the pictures), refine, compute a new map and see if you can make 
something out of it. Why benzoate: because the ring would find its place 
nicely in the "hydrophobic" environment, especially the TYR and TRP side 
chains. If it does not make sense (difficult to say from pictures, I 
tried rotating by to no avail...) then place a few waters, refine and 
see if the new density makes sense after refinement.


Fred.

Nick Quade wrote:

Dear CCP4 community,

I have solved the structure of a protein in complex with DNA. But, 
inside the protein there seems to be a ligand binding pocket with some 
strong density 
(*http://picasaweb.google.de/113264696790316881054/Desktop#). *The 
protein was in Tris buffer, with some NaCl, MgCl2 and DTT and 
crystallized in Li2SO4 with MES. What could this density be? I can 
exclude MES as crystals grown with citrate buffer have the same 
density. So I guess it might be something I co-purified or perhaps 
some degradation product of the DNA? The electron density in the 
pictures is at 1.5sigma.


Thanks in advance.

Nick

[ccp4bb] Mysterious density

2010-07-09 Thread Nick Quade 

Dear CCP4 community,

I have solved the structure of a protein in complex with DNA. But, 
inside the protein there seems to be a ligand binding pocket with some 
strong density 
(*http://picasaweb.google.de/113264696790316881054/Desktop#). *The 
protein was in Tris buffer, with some NaCl, MgCl2 and DTT and 
crystallized in Li2SO4 with MES. What could this density be? I can 
exclude MES as crystals grown with citrate buffer have the same density. 
So I guess it might be something I co-purified or perhaps some 
degradation product of the DNA? The electron density in the pictures is 
at 1.5sigma.


Thanks in advance.

Nick