Re: [ccp4bb] Off-topic: unidentified density for N-terminal Thr modification

2009-06-23 Thread Partha Chakrabarti
Hi Jonathan, This is purely a chemistry guess, but if you have a PEG400 derived compound like: (HO)-CH2-CH2-O-CH2-CHO, i.e, part oxidised, then the CHO might form a N,O acetal ring with the free amine and side chain. Five membered ring formation is kinetically favourable, though the chemistry mi

[ccp4bb] Off-topic: unidentified density for N-terminal Thr modification

2009-06-23 Thread Jonathan Elegheert
Dear bb, I have a high resolution dataset showing that the N-terminal threonine of my protein has been modified and cyclized, with the main chain N and side chain OG1 now involved in a non-planar 5 membered ring sugar-like structure. The molecule seems to be 5-6 atoms long with some 'head grou