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Re: [ccp4bb] ISSUE RESOLVED - REFMAC converts alpha-L-fucose into beta-L-fucose] |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: ISSUE RESOLVED - REFMAC converts alpha-L-fucose into beta-L-fucose] From: verdino {- at -} SCRIPPS {- dot -} EDU verdino {- at -} SCRIPPS {- dot -} EDU Date: 2007-06-13 Sorry guys, my previous message obviously reflected that I am not very familiar with sugars. Kelvin's email clarified what was going on: the REFMAC dictionary for a-L-fucose is perfectly correct, my mistake was that I was not aware of the reverse relation of alpha and beta-linkages in L and D-sugars! Thanks again for the clarification, and sorry for bugging you all, the sugar-greenhorn Petra ---------------------------- Original Message ---------------------------- Subject: Re: [ccp4bb] REFMAC converts alpha-L-fucose into beta-L-fucose From: "Kelvin Luther" Date: Wed, June 13, 2007 5:00 pm To: verdino@scripps.edu -------------------------------------------------------------------------- I just wanted to mention something in case you're not familiar with sugars. Alpha and Beta for an L sugar will be reverse of alpha and beta for a D sugar. Alpha for a D-sugar is when the c6 constituent and the anomeric carbon constituent are in opposite orientations. With fucose, an L sugar, such a configuration would be beta. Hope this is the problem, in which case, there isn't one. Cheers,this Kelvin Luther On Wed, 13 Jun 2007, verdino@SCRIPPS.EDU wrote: > 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 henrick@ebi.ac.uk ::telephone: +44 (0) 1223 494629 >> > > > ***************************************************** Kelvin Luther Program in Molecular and Cellular Biology Stony Brook University Stony Brook, New York 11794 USA mailto:kluther@ic.sunysb.edu ***************************************************** -- 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 CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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