Dear CCP4bb thanks so much for the helpful information regarding carbohydrate refinement. Kim's recommendation (see below) for the validation server worked really well and helped me to finally figure out what is going on. Seems as if REFMAC5 (part of ccp4-6.0.2 version) is not handling alpha-L-fucose links correctly - even when I use a correct alpha-linked model (from the server), and define the link and the sugar appropriately (see below), it comes back from the refinement with a beta-linkage.
LINK C1 NAG A 501 ND2 ASN A 105 NAG-ASN LINK O6 NAG A 501 C1 FUC A 506 ALPHA1-6 MODRES NAG A 501 NAG-b-D RENAME MODRES FUC A 506 FUC-a-L RENAME Maybe someone of the hardcore REFMAC refinement guys (who is familiar with the libraries) would be willing to check if there is an issue with the dictionary for alpha-L-fucose or if I am still missing something????? Thanks for your help, cheers, Petra > you can use > http://www.glycosciences.de/modeling/sweet2/doc/index.php > to get a pdb file of your sugar > > and after fitting in density and refinement use > http://www.dkfz-heidelberg.de/spec/glycosciences.de/tools/pdbcare/ > to check the stereochemistry > > this should identify if there is a refmac dictionary problem > > your sugar is a "Core Fucosylated And Bisected N-glycan (N-Link 2)" > [see the sweet doc pages] > > you can make the IUPAC notation in plain ASCII > > a-D-Manp-(1-6)+ > | > | a-L-Fucp-(1-6)+ > | | > | b-D-GlcpNAc-(1-4)-Asn > | | > b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)+ > | > | > | > | > | > a-D-Manp-(1-3)+ > > and drop this into sweet and get an idealised torsion angle(d) pdb > > > an o/p is www.ebi.ac.uk/~henrick/sug.pdb > > unfortunately the original pdb output is not exactly pdb > you have to move the residue name column and the > ASN is labelled as UNK > > the torsion angles are from the database > http://www.glycosciences.de/modeling/glycomapsdb/ > > if you want to check your fitted conformation with what is expected > (a lot more freedom than a ramachandran but basically > the same type of plots) > > > > > > -- > Kim HENRICK [EMAIL PROTECTED] ::telephone: +44 (0) 1223 494629 > -- Petra Verdino, PhD Research Associate The Scripps Research Institute, BCC206 10550 North Torrey Pines Road CA 92037 La Jolla, USA tel:1-858-784-2294 fax:1-858-784-2980
