refining phosphorylated residues

From: Rajesh kumar
Date: 21 March 2012 23:00

Dear All,

I have a structure of a protein and peptide complex, in which peptide has modified residues ( phosphoserine and phosphothreonine). 

During refinement these both gets disconnected  with adjacent residues and its hard to connect them.

Could you please suggest me some options.

Thanks

Rajesh

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From: Joel Tyndall

Hi Rajesh,

 

If I understand correctly, the phospho groups become disconnected from either the serine or threonine. If this is the case, you can use the SEP monomer for phosphoserine and TPO monomer for phosphothreonine. (replace the amino acid residues with these)

 

These are built into ccp4 and coot

 

Hope this helps

 

Joel

 

_________________________________

Joel Tyndall, PhD

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From: Joel Tyndall

As a follow up question the bulletin board, why is SEP a peptide (L-peptide) and TPO not (non-polymer)?

 

Joel

 

_________________________________

Joel Tyndall, PhD

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From: Rajesh kumar

Hi Joel, thanks for the reply. It's not phospho group but the whole residue get disconnected. In coot if I do refinement they get disconnected. 

Thanks

Rajesh
Sent from my iPhone

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From: Boaz Shaanan

HI,

You could use the LINK command after going through Jligand for your modified residues. There is a very nice tutorial here:

http://www.ysbl.york.ac.uk/mxstat/JLigand/

in case you haven't done this before.

          Boaz

 

 

Boaz Shaanan, Ph.D.

 

 

                

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From: Eleanor Dodson


Have you checked the dictionary cif calls them L-peptide?

Eleanor

The header should look like this..

# data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level ALA ALA 'ALANINE ' L-peptide 10 5 . # On Mar 21 2012, Rajesh kumar wrote:

Dear All, I have a structure of a protein and peptide complex, in which peptide has modified residues ( phosphoserine and phosphothreonine). During refinement these both gets disconnected with adjacent residues and its hard to connect them.Could you please suggest me some options. ThanksRajesh

--
Professor Eleanor Dodson

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From: Garib N Murshudov

In new version (it should be in ccp4 6.2.0, if not then it will come ccp4 6.3, otherwise you can take it from York's web site: ) TPO as well as SEP are peptides.

Break in coot may be due to misinterpretation of SEP or TPO as peptide in coot and it may be because of older version of the dictionary. Do the distances, angles between neighbouring residues make sence? If not then refinement also had problems

regards

Garib

Garib N Murshudov 

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From: Rajesh kumar

Dear All,

Thanks for the suggestions. I will work on them.

I had not worked on the modified residues, so thanks for all the valuable suggestions.

Regards

Rajesh