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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: Kelvin Luther kluther {- at -} IC {- dot -} SUNYSB {- dot -} EDU Date: 2007-06-14 It was not my intent to get involved in a debate like this. I sent a back-channel note to point out that if you are unfamiliar with alpha and beta in sugar bonds, are thinking D sugar, and you actually have an L sugar, you might confuse in a structure whether you have an alpha or beta linkage. Typically, when using opposite and same we are thinking of Haworth projections. Alpha is opposite in a Haworth projection (or anti, thus easy to remember), and the same side in a Fischer (which complicates things, is less intuitively interpretable as a structure, and makes this harder to remember). Perhaps I should have given an in depth description and I'm sure my description could have been much better. I wrote the note quickly in the hopes of helping someone. Draw out Fischer projections for all four forms of glucose, convert them to Haworth diagrams and you have alpha D with axial constituents on C5 and C1, with C6 above the ring, the C1 hydroxyl below. With alpha L, again, two axial constituents, but this time C6 below and the C1 hydroxyl above the ring. With beta-D, two axial constituents, both above the ring, with beta-L, two axial constituents, both below the ring. Hope this helps, Kelvin Luther ps. If you want to show a picture of the sugar model, perhaps we could determine if it really is alpha or beta. On Thu, 14 Jun 2007, Kim Henrick wrote: > 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 CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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