Dear Uma
1. The protein sequence given in the databases, do from time to time
have errors, particularly if you are working with "old" proteins (when
the sequencing was done a long time ago). What you observe could also be
a threonine or even a valine. You should check whether homologous
protein also have a serine on that position. I Normally do not assign
double conformation unless you have fairly high resolution data, it is a
bit hard to judge what the resolution is here. Often a double
conformation is accompanied with negative difference density on top of
the assigned atom, if you lower the sigma level a little, you often see it.
2. It is also common to have local frameshift errors in loop regions,
even in reasonable high resolution data. I think you should double check
the region to make sure you are not facing this problem, it is
surprisingly difficult to detect sometimes, but you will know when you
got the right.
Cheers
Preben
On 5/21/12 10:57 PM, Uma Ratu wrote:
Dear All:
Some of serine residues in my model have extra positive Fo-Fc density
at the edge of side chain. Some don't have. It is not like from
phosphates.
I am wondered what is the cause for these extra density. Could these
serines be post-translational modified?
I have the images attached. P289ser-0512-1 does not have the extra
green, where P140ser-0512-1 has.
Thank you for you advice and comment
Uma
--
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Group
Nordic EMBL Partnership
Centre for Molecular Medicine Norway (NCMM)
University of Oslo
P.O.Box 1137 Blindern
0318 Oslo, Norway
Email: j.p.mo...@ncmm.uio.no
Tel: +47 2284 0794
http://www.jpmorth.dk
