SeMET inconsistency

From: Kayashree M
Date: 21 October 2011 16:53


Dear users,

I had posted this question already but in a different context.

One of the Se-Met derivatised protein that we have solve is a homodimer
(with 4 MET in the chains that crystallised) of which one chain has 3 MSE
residues, while the other chain has only 2 MSE.

Are there any such instances in PDB, where two homodimer (or any mer)
wherein each has different percentage of MSE?
Because when we change the only MET to MSE a negative density would
arise. The tools to analyse anomalous peaks is not giving peaks for the
MSE residues as the data was collected at 1.541Ang wavelength.

Thank you
Kavya

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From: VAN RAAIJ , MARK JOHAN


Dear Kavya,

I don't think it is likely you have five MSE and one MET. Rather, I would guess the side-chain has some disorder, i.e. one or more alternative conformations. If you don't see density for alternative conformations, the best way to model the disorder might be partial occupancy of the MSE that gives negative difference density peaks.

Mark

dangerous content byMAILSCANNER[1], and is
believed to be clean.

Links:
------

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid

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From: Kayashree M

Respected Sir,

Probably that may be the case I will check. Thank you
for the suggestion.

With Regards
Kavya