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CCP4BB  July 2018

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Subject:

Re: AW: COOT: adding xylose to a plant glycosylation chain

From:

Bärbel Blaum <[log in to unmask]>

Reply-To:

Bärbel Blaum <[log in to unmask]>

Date:

Thu, 5 Jul 2018 16:55:14 +0200

Content-Type:

text/plain

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text/plain (123 lines)

Hi Marilyn,

if 'some luck' happens not to be the case you may be able to create a  
good cif file for the covalent protein-sugar bond with the JLigand  
tool (CCP4 suite). that tool allowed me to connect an isoaspartate  
residue at both ends with my protein chain so that neither coot nor  
refmac blew it up, so I guess it should be able to do the trick for  
you, too. if you do not get it to work you can contact me off-list and  
I'll send my how-to notes for JLigand.

Bärbel


Zitat von [log in to unmask]:

> Hi Marilyn,
>
> I have been struggling with carbohydrates in the pre Glyco module  
> era, which was *not nice*. However, the following strategy works  
> reasonably well:
>
> 1)      Get the XYP monomer with the "get monomer" command.
>
> 2)      Move the XYP manually in its electron density. This can be  
> very approximate
>
> 3)      Do a real space refinement of the XYP monomer alone. This  
> should work should give a decent fit of the monomer
>
> 4)      Delete one of the oxygens of the future linkage and use the  
> "make link" command (extensions-modeling-make link) to link your  
> monomer to the carbohydrate tree.
>
> For buster, I had some restraints files to link carbohydrates, I do  
> not have any experience with phenix refine. With some luck, just a  
> covalent link with reasonably well-defined sugars would be  
> sufficient. Changing the stereochemistry of a standard carbohydrate  
> link file may also do the trick.
>
> Good luck!
> Herman
>
>
> Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag  
> von Yoder, Marilyn
> Gesendet: Donnerstag, 5. Juli 2018 16:01
> An: [log in to unmask]
> Betreff: [EXTERNAL] [ccp4bb] COOT: adding xylose to a plant  
> glycosylation chain
>
> Hello,
>
> I'm having problems adding XYP (beta-xylose) to my glycosylation  
> chain in a plant protein.
>
> I have a 1.87 Angstrom map, 4 molecules in the asymmetric unit.  I  
> have two primary N-glycosylation sites, per protein. I am not using  
> NCS for refinement or model building.
>
> The density for the NAG-(FUC)-NAG is very clear at both sites of all  
> molecules in the a.u. The BMA (beta mannose after the 2nd NAG) is  
> clear at one of the glycosylation sites.  At this glycosylation  
> site, I see good density for a MAN at the C3 and C6 sites of BMA.  I  
> can see good density for a xylose at the C2 - it is really quite  
> clear.
>
> Using COOT, and the Glyco module, set to Hybrid (Plant), I have been  
> able to add all the NAGs, MANs, and FUCs with a press of a mouse  
> button.  It is a *very nice* function of COOT.
>
> But.....  I can't get the XYP added correctly.  I select the "add an  
> XYP-BMA XYP", and it pops the XYP where I want it, but then it  
> rapidly wiggles away.  It is as if it is actively finding an area of  
> no density (I am not exaggerating).  Selecting 'Refine Tree' does  
> not resolve the problem.  I've tried manually moving the xylose  
> close enough, but this is not working well.  It just refines away in  
> Phenix Refine.
>
> For refinement, I used ReadySet to generate the restraints  
> (apparently the XYP-BMA XYP does not have restraints in the standard  
> library - is that correct?)
>
> This is a big enough problem, I am hoping I am just doing something  
> 'big' that is wrong.  I'm assuming (perhaps) it is a library  
> problem. I would appreciate any suggestions.
>
> Software details:
>                On Windows, WinCoot 0.8.9
>                On Mac, Phenix version 1.13-29998-000  (Coot is version 0.8.9)
>                I model build in WinCoot, refine with Phenix on the Mac
>
> Regards,
> Marilyn
>
> ___________________________________________________________
> Marilyn Yoder  |  816-235-1986   |  SCB 526 | Division of Cell  
> Biology & Biophysics, University of Missouri-Kansas City
>
>
> ________________________________
>
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-- 
Bärbel Blaum, Ph.D.
Interfakultäres Institut für Biochemie (IFIB)
Hoppe-Seyler-Strasse 4
D-72076 Tübingen
Germany
+49 70 71 29 733 48
Raum 311

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