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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: Kim Henrick henrick {- at -} EBI {- dot -} AC {- dot -} UK Date: 2007-06-14 perhaps there still is a problem with refmac from the iupac carbohydrate pages http://www.chem.qmul.ac.uk/iupac/2carb/06n07.html see section 2-Carb-7.4. Enantiomers if a sugar has a configuration in a chair form for a trans 1--6 then it will be trans-like in both alpha-L and alpha-D 1C4 to 4C1 but both are axial -O1 see the example above url á-D-glucopyranose-4C1 and á-L-glucopyranose-1C4 the 1,2-torsion changes stays cis or trans depending on the actual sugar changing a 1,6, a five bond connectivity is not possible the orientations stay the same in plane project for alpha-fucose L has O1 O2 up O3 O4 C5 down D has O1 O2 down O3 O4 C5 up no change in any cis or trans torsions in the PDB a-D-FUC is 3-letter code FCA a-L-FUC is 3-letter code FUC you can get the ideal coordinates fro FUC and FCA from either the http://www.ebi.ac.uk/msd-srv/msdchem/ or the wwpdb http://remediation.wwpdb.org/downloads.html and the dictionaries from G.K. http://alpha2.bmc.uu.se/hicup/ alpha and beta change torsion angles from cis/trans > 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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