Hello,Thank you for your kind reply.Do I need to link them together in the
structure? Is there a method for that?
>From the other replies I thought I should mention how I purified the protein
>complex.The protein is secreted in HighFive cells, to purify it by its 6xHis
>tag, I used Ni sepharose excel beads, eluted with Imidazole and then further
>purified with size exclusion. To get rid of the tags and leucine zipper I used
>to mimic the transmembrane domain, I subjected the protein to V8
>edndoproteinase in 0.1M Tris pH8.5 (cuts after an exposed Glutamate). Then
>purified again with Ni sepharose excel and size exclusion prior to
>crystallisation. It crystallised in 0.2M Zinc acetate, 0.1M Imidazole pH 6.5,
>10% PEG 8K.I have worked on three other crystals of the similar molecule,
>which crsytalized in different conditions, and this is the only one I see such
>blobs.Thank you gain.Best regards,Samer
On Monday, July 20, 2020, 05:27:18 PM GMT+1, EchelonIV
<[email protected]> wrote:
Hello,
what immediately comes into mind is phosphohistidine, especially since the
density looks rather large, but the geometry seems a bit off for that but I
cannot judge only from one angle. You could of course try to fit it in and see
how it looks.
Cheers,Arne
On Mon, Jul 20, 2020 at 6:17 PM samer halabi
<[email protected]> wrote:
Hello all,
I have few blobs in an MHC II structure I am working on, especially opposite to
Histidine as in the accompanying screenshot, that I am confused about.
In the crystal conditions, I have Tris, Imidazole, Acetate, PEG and Glycerol.
Whatever ligand I am fitting in I am getting a clash (overlap -1.029), which
makes me think whether there is a covalent bond forming between Histidine and
other molecule. Perhaps by oxidation.
I would greatly appreciate if you can advice me about it, whether there is some
kind of ligand I can try to fit and if this is something that occurs in some
structures.
Thank you.
Best regards,
Samer
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--
--Arne RaasakkaPhD BiochemistryDepartment of Biomedicine, University of
BergenNorway
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