I am trying to resist answering ccp4bb ... but
> Thanks to all who responded. 180 degrees flip of the problematic NAGs,
> did help. If you have a poor density (which I guess, generally is the
> case for large glycoprotein structures) you have to depend on trial
> and error strategy to get the right NAG conformation. I don't know
> how other refinement programs handle this, but after Phenix.refinement
> run, one has to definitely check the geometry of the NAGs carefully.
There is no such thing as 'trial-and-error'
Look up the polysaccharide you are expecting to find for the species you
are working with
see for example
Varki A et al. Essentials of Glycobiology. Cold Spring Harbor
Laboratory Press; 2nd edition
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=glyco2
Note fundamentally that an Asn-Nag is always beta- so why not check in the
first place that you have NAG attached in a beta conformation if you have
alpha - then you are wrong and the density will flatten the C1 - The
ccp4bb notes about rotating 180deg is misleading as it is not a
conformational change it is a configurational change. It is made by an
enzyme not by a crystallographer - all chemistry in biology is run by
enzymes each species makes particular sugars in a particular order look it
up, you cant get a oligosaccharide that cant be made by a particular
species
You are not going to find an N-linked Glycan unknown to glycobiology so
first of all look up what is expected
e.g. http://www.glycoforum.gr.jp/
http://www.genome.jp/ligand/kcam/
http://www.functionalglycomics.org/static/index.shtml
http://www.glyco.ac.ru/bcsdb3/
http://www.casper.organ.su.se/ECODAB/
http://www.functionalglycomics.org/static/gt/gtdb.shtml
http://akashia.sci.hokudai.ac.jp/
http://hexose.chem.ku.edu/sugar.php
http://www.eurocarbdb.org/
then try
http://www.glycosciences.de/modeling/sweet2/doc/index.php
this will give you a 3D model in PDB format of your maximum glycan - dont
do what has happened in the past in the PDB just try adding sugars at
random connections and configurations
you can also look at
http://www.ebi.ac.uk/eurocarb/gwb/builder.action
There are tools on http://www.glycosciences.de/
e.g.
http://www.glycosciences.de/modeling/glycomapsdb/
to tell you the expected conformational maps of the glycosidic linkage -
you believe in Ramachandran for peptide bonds so why not for glycosidic
bonds)
The PDB has a legacy of wrong connections, wrong conformations, poor
geometry of oligosaccharides especially glycans where the coordinates
respresent unknown molecules
The density may be poor but if you know what say a plant may produce then
fit what you can of that particular saccharide in observable
density the linkages, 1-2, 1-3, 1-4, 1-6 are all specified and people
should stop making them up at random
for example plants have basically these N-glycans
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=glyco2&part=ch22&rendertype=figure&id=ch22.f1
sweet (above) will make the 3d coordinates you can try fitting as much as
is observed knowing the configuration and trying the conformations from
glycomapsdb
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