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.ilwrote:
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.ukhttp://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*
