could this also be an alternative C-Terminus at lower occupancy? Regards
Kornelius On Fri, Apr 26, 2013 at 10:45 AM, Boaz Shaanan <bshaa...@exchange.bgu.ac.il>wrote: > Hi, it looks like gly-asp not asp-gly in this case, doesn'it? > Cheers, Boaz > > > > -------- הודעה מקורית -------- > מאת: Jonathan Cooper <bogba...@yahoo.co.uk> > תאריך: > אל: CCP4BB@JISCMAIL.AC.UK > נושא: Re: [ccp4bb] Curious electron density associated with Asp sidechain > > > Hello Tony > > > is that Asp-Gly? If so, it could be prone to succinimide formation. > Check out this paper: > > > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323960/ > > > and references therein! > > > Good luck > > > Jon.Cooper > > --- On *Thu, 25/4/13, Antony Oliver <antony.oli...@sussex.ac.uk>* wrote: > > > From: Antony Oliver <antony.oli...@sussex.ac.uk> > Subject: [ccp4bb] Curious electron density associated with Asp sidechain > To: CCP4BB@JISCMAIL.AC.UK > Date: Thursday, 25 April, 2013, 17:10 > > Dear CCP4 colleagues. > > I'm just finishing up a refinement, but am left with one little curio that > I just can't seem to solve. > > One aspartic acid residue is associated with some extra, unexplained > electron density. > > --> please see: http://i.imgur.com/vCYOqam.png > > Where, the Fo-Fc map is contoured at 3.78 rsmd in Coot. > > I have tried a number of different modelling scenarios, but as yet can't > reach a wholly satisfactory conclusion; waters, alternate conformers, > really don't seem to cut it. I though about some radiation-induced > phenomena, but this data set was collected on a home-source, so I guess > this is unlikely. > > So, I would really appreciate some ideas and suggestions. Hopefully it is > blindingly obvious to someone. > > Random Thought: could it be PEGylation of the side-chain? > > Some other hopefully useful background information: > > * I'm sure it is/was an ASP, because the same protein (made from the same > construct) has been used in previous crystallisations, and the resultant > structures have clear, unambiguous electron density for the side chain. > > * the crystallization condition is PEG 200, with some Na/K phosphate at pH > 5.8, and NaCl. The protein itself contains HEPES buffer. > > With many thanks, > > Tony. > > --- > Dr Antony W Oliver > Senior Research Fellow > CR-UK DNA Repair Enzymes Group > Genome Damage and Stability Centre > Science Park Road > University of Sussex > Falmer, Brighton, BN1 9RQ > > email: > antony.oli...@sussex.ac.uk<http://mc/compose?to=antony.oli...@sussex.ac.uk> > tel (office): +44 (0)1273 678349 > tel (lab): +44 (0)1273 677512 > > -- *Kornelius Zeth* *Email: kornelius.z...@gmail.com* *Unidad de Biofisica (CSIC-UPV/EHU) Barrio Sarriena s/n 48940, Leioa, Vizcaya* *SPAIN*
