I do think one has to consider whether there is a sufficient scientific advance to justify publication. After all, peer reviewers are already overworked. From the information given I don't think I would try to publish this but I'd certainly consider depositing in the PDB and contaminant database. What about putting it in BioRxiv?
Bert ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Debanu <deb...@alumni.rutgers.edu> Sent: 05 April 2017 16:23 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Accidental crystallization of E. coli protein I think it is worth reporting/publishing this crystallization and structure in addition to depositing it in the PDB and ContaMiner/ContaBase databases. Items you can consider in reporting it based on the following but can take a better decision if you complete the structure to deposition quality: a) Crystallization conditions are likely different from the crystallized version from the recombinant expression? b) Try to see why the resolution might be higher: crystal size, crystallization conditions, x-ray source, processing and refinement programs/current protocols? Always nice to have a higher resolution and/or better refined current structure for others to use especially if the target also has other potential importance. You never know when someone later can use it for homology modeling or virtual library screening. c) As you complete full structure determination, you may also find additional features in the maps/structure compared to previous reports, i.e., differences around functional sites possibly conformational variations, endogenous or known densities that may have some functional implications, etc. I also think publicly-funded research that involves a complete piece of work that may be useful for others now or in the future should be reported since publications are also record keeping for the future. Everything does not have to have high scientific impact today. Best, Debanu -- Debanu Das On Wed, Apr 5, 2017 at 4:46 AM, Stefan Arold <stefantar...@gmail.com> wrote: > Hi Mohamed, > I don't recall such a case of a crystallized proteolytically cleaved > contaminant (see our recent summary of contamination cases > http://scripts.iucr.org/cgi-bin/paper?ei5009 , and references therein). > I would certainly recommend depositing the data at the PDB - it may help > others address questions that need the higher resolution, or facilitate MR. > We can then also include your protein into our ContaMiner & ContaBase > webserver & database. https://strube.cbrc.kaust.edu.sa/contaminer/ ContaMiner - strube.cbrc.kaust.edu.sa<https://strube.cbrc.kaust.edu.sa/contaminer/> strube.cbrc.kaust.edu.sa ContaMiner What is it ? ContaMiner is a rapid automated large-scale detection of contaminant crystals. Protein contaminants, from the expression host, purification ... > Best wishes > Stefan > > On 5 April 2017 at 00:16, Mohamed Noor <mohamed.n...@staffmail.ul.ie> wrote: >> >> During the crystallization of a totally unrelated protein from a different >> bacterium in E. coli, we managed to somehow crystallize an E. coli protein. >> It turned out to be only the catalytic domain of an enzyme. Two previous >> reports both used recombinant expression of this enzyme followed by limited >> proteolysis in order to crystallize this domain. >> >> Has something like this been reported before? I know the stories of AcrB >> etc., but I am looking specifically for a 'naturally proteolyzed' >> crystallization. >> >> Looking at our structure and the previously published one, there is not >> much difference, with an rmsd of about 0.3 A but our data resolution is a >> bit higher. This is perhaps unsurprising as the unit cells are very similar >> (in fact, I just did a quick RBR). Should we bother depositing and >> publishing this observation? >> >> Thanks. >> Mohamed > >
