Re: [phenixbb] O-linked glycosylation refinement in Phenix

Send me the model (off line and held in the strictest confidence) and I'll run and few things and check a few things. Nigel On Tue, Apr 12, 2011 at 9:22 AM, Qiang Chen wrote:

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: [email protected] ============================ 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 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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