[phenixbb] O-linked glycosylation refinement in Phenix

Qiang Chen chen at red.dfci.harvard.edu
Tue Apr 12 09:22:43 PDT 2011


Hi,
My protein was expressed in mammalian cells. The EGF domain within this
protein has a consensus sequence for addition of O-fucose to EGF domain.

And, thanks for the template, Nigel! I got your e-mail. But I'm not
familiar with this and don't know how to make the file.

> Minor non-crystallographic question:
>
> Are you sure that the sugar group attached to the Thr is a Fucose, and
> not an N-acetyl Galactosamine?
> I don't know where your protein is from, but vertebrates usually have
> a GalNac as the first sugar.
>
> http://www.ncbi.nlm.nih.gov/books/NBK20721/
>
>
> Dave
> ============================
> David C. Briggs PhD
> Father, Structural Biologist and Sceptic
> ============================
> University of Manchester E-mail:
> david.c.briggs at manchester.ac.uk
> ============================
> http://manchester.academia.edu/DavidBriggs (v.sensible)
> http://xtaldave.wordpress.com/ (sensible)
> http://xtaldave.posterous.com/ (less sensible)
> Twitter: @xtaldave
> Skype: DocDCB
> ============================
>
>
>
> On 12 April 2011 05:41, Pavel Afonine <pafonine at lbl.gov> wrote:
>> Hi Qiang,
>>
>> although apply_cif_link is probably more elegant way of doing this, you
>> can
>> always use custom bonds (if you can't get apply_cif_link to work):
>>
>> http://phenix-online.org/documentation/refinement.htm#anch86
>>
>> Using custom bonds you can define a covalent bond between any two atoms.
>>
>> For example, this
>>
>> refinement.geometry_restraints.edits {
>>    bond {
>>      atom_selection_1 = chain A and resseq 17 and name O
>>      atom_selection_2 = chain B and resseq 18 and name N
>>      distance_ideal = 1.5
>>      sigma = 0.02
>>    }
>> }
>>
>> will define a bond between these two atoms
>>
>> HETATM  115  O   LIG A  17       3.129  18.483   4.947  1.00 44.08
>> O
>> HETATM  116  N   LIG B  18      -2.025   7.355   5.786  1.00 33.96
>> N
>>
>> You can define any number of such bonds by duplicating bond {} scope of
>> parameters. You can define angle as well.
>>
>> Check .geo  file to see if atoms in question are bonded.
>>
>> Pavel.
>>
>>
>> On 4/11/11 2:15 PM, Qiang Chen wrote:
>>>
>>> Dear all,
>>>
>>> I'm refining a structure which has both N-linked and O-linked
>>> glycosylation. I use Phenix to do the refinement. It works well for the
>>> N-linked NAG. I defined the link as the following:
>>>
>>>     apply_cif_link {
>>>       data_link = "NAG-ASN"
>>>       residue_selection_1 = "chain A and resname NAG and resid 701"
>>>       residue_selection_2 = "chain A and resname ASN and resid 518"
>>>     }
>>>
>>> But it doesn't work when I defined the fucose-threonine link as the
>>> similar way:
>>>
>>>     apply_cif_link {
>>>       data_link = "FUC-THR"
>>>       residue_selection_1 = "chain A and resname FUC and resid 801"
>>>       residue_selection_2 = "chain A and resname THR and resid 596"
>>>     }
>>>
>>> The error message is "missing CIF link: data_link_FUC-THR".
>>>
>>> Does anyone have the cif link file of FUC-THR?
>>>
>>> Thanks a lot!
>>>
>>>
>>> Qiang
>>
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>>
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