Re: [ccp4bb]: Side Chain Assignement

[Bart Hazes <bhazes@ualberta.ca>]

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At 1.9A you should be able to distinguish Leu from Asp/Asn. However, Asp/Asn,
Glu/Gln, Thr/Val will be difficult. In addition, you may have assigned the odd
alanine to a residue with a disordered sidechain. You can use hydrogen bonding
patterns to make some of the distinctions though.

I also suggest, if you didn't already do so, to throw your pseudo sequence
through a BLAST search. If there are some close homologs then you can use that
tentatively as "prior information" until you determine the real sequence
experimentally.

Bart

On Mon, 10 Jun 2002 nagem@lnls.br wrote:

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>
> Dear CCP4 users,
>
> I am refining a structure at 1.9 A resolution, spacegroup P212121, one molecule
> per assymetric unit. Unfortunatelly the primary structure for this protein is
> unkonw (purified protein), but its tertiary structure was solved (main chain and
> pseudo-side chains). This "pseudo-model" is refined and the R-factor and R-free
> are around 19%. Initial MIRAS phases are reliable and initial map is practically
> continuous in all its extension. My question is: Is there any program that uses
> this pseudo-model and the initial MIRAS map (or an omit-map) to validate the
> side chain and/or to guess the most probably side-chain? I am not sure if at 1.9
> A I will be able to distinguish between Leu, Asn and Asp (as an example) solely
> by the electron density... Cysteine, Methione residues can be identified by the
> anomalous signal and the peak in the 2Fo-Fc map. Other residues are easily
> identified (Proline, Arginine, Tyrosine ...) but what can I do distinguish
> between Leu/Asn/Asp, Gln/Glu, Val/Thr...?
> Amino acid sequence analysis is under way, but it may take a while since this is
> a big protein.
>
> Any help is welcome!
>
> All the best
>
> Ronaldo Nagem.
>

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