[phenixbb] O-linked glycosylation refinement in Phenix

David Briggs drdavidcbriggs at gmail.com
Mon Apr 11 22:17:26 PDT 2011


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
============================
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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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