Dear All,
Thanks for all of the responses so far.. Mark - I don't think it's caused by radiation damage, although this is certainly a concern. Using only a small subset of images from the start of data collection still gives fairly clear density with no positive or negative peaks around the cys and lys. Christian - I haven't used jligand before but that was nice and simple.. I think a simple link record may suffice here though. Matthew - Definitely a weird bond, potentially the cys was oxidised first and the beam caused more weirdness, I really have no idea! Having said that, I don't think this is the cause (see above). David - Thanks for the paper! Focco - Thanks for the publication! Paul - I tried the "Make link via Acedrg" route but had some issues (my model exploded).. I'll send you the details off list later! Cheers! Jonathan ________________________________ From: Jonathan Davies Sent: 17 April 2018 18:03 To: CCP4BB@JISCMAIL.AC.UK Subject: Cys Lys bond? Dear CCP4BB, I've recently solved a structure to 1.15 Angstrom which has extremely clear density for what appears to be a lysine covalently bound to a cysteine (S-N). The distance between the cys-S and lys-N is 1.8 A. I thought initially that there may be a methyl group between the two (based on this paper http://doi.org/10.1002/pro.2958) but there definitely isn't enough space. Some more info: The protein was purified from recombinant E. coli expression, standard buffers (Tris, NaCl). Crystallisation condition contains sodium acetate and PEG. The residues in question are not part of an active-site. I have two questions: Has anyone seen a cys that is involved in a sulfanamide bond with a lys? How would one go about modeling this bond in a way that doesn't upset coot, refmac or PDB validation? Thanks in advance! Jonathan
