[phenixbb] O-linked glycosylation refinement in Phenix

Nigel Moriarty nwmoriarty at lbl.gov
Tue Apr 12 09:29:42 PDT 2011


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 <chen at red.dfci.harvard.edu> 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:
>> 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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-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


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