Hi All, To add, on couple of occasions I re-determined the structure of so-called "contaminants". Once, the structure of Secreted Ferritin (PDB 1Z6O) from crystals that were supposedly that of TNF ligand:receptor complex (proteins expressed in Tni cells), and in the second instant re-determined the structure of bacterial carbonic-anhydrase. On both instants, contaminants were identified through cell-constant search (at that time no ContaMiner server available) in PDB, after realizing that standard Molecular Replacement did not work. Luckily, did not spend too much time on these cases.
Best Wishes to All for "contaminant" free crystals on this Thanksgiving Day, Partha On Thu, Nov 23, 2017 at 6:23 PM, Edward A. Berry <ber...@upstate.edu> wrote: > My 2 cents worth: > I think contaminer is an extremely useful service. I may be a sloppy > biochemist, > but I am not the only one. There are multiple structures in the database > of say > bacterioferritin or AcrB that were solved from crystals that were supposed > to > be something else. I remember in a discussion with the organizer of my > session > at a Gordon conference, she excitedly announced that there would be > preliminary > crystallographic data on respiratory Complex I. But by the time of the > conference > the authors discovered they had crystallized something else. And the > beautiful crystals > of Paracoccus Complex II (from Doug Rees's lab?) that graced the catalog of > Hampton Research (And I believe were part of the basis for the first > membrane > protein screen) never saw publication. The authors of > http://www.sciencedirect.com/science/article/pii/S0304416506000894 > certainly feel there is a real problem. Some proteins crystallize readily > even when > present as minor contaminants. And some protein complexes become more > heterogeneous > if over-purified due to partial loss of loosely-bound subunits. > Most of my career I've worked with high-abundance natural-source proteins. > During a recent foray into the realm of overexpressed proteins, my group > has > crystallized (and solved) at least a half dozen wrong proteins from E. > coli. > I spent months on one of these (ATCase in Rhomb sg with low-level > obverse/reverse > twinning that caused it to sometimes index as P3) Then solved the rest > rapidly > by checking the closest several hits with nearest-cell. All of these > E.coli proteins > were already present in the PDB. I wonder how many were from accidental > crystals. > And now bacterioferritin (this time from M. smegmatis) keeps coming back > to haunt us. > > I would say any time with a new crystal when a molecular replacement > unexpectedly fails, > and even before you start to collect heavy atom or selenomet data, it > would be worth > to submit to nearest-cell and contaminer. I would be more likely to > question the > utility of an anisotropy correction server, given that modern > maximum-likelihood > refinement programs can deal with weak data satisfactorily (speaking from > ignorance- I'm sure supporting evidence and examples exist, I just haven't > bothered to look them up. And I know my colleagues here at Upstate have > used > anisotropy correction to good effect with a difficult problem- I hope they > weren't using filled-in maps!) > eab > > On 11/23/2017 03:24 PM, Tristan Croll wrote: > >> Dear Radu, >> >> I think this is a little harsh. Biology is a fabulously messy thing, and >> very prone to doing the unexpected. See the excellent paper by >> Niedzialkowska et al. at https://www.ncbi.nlm.nih.gov/p >> mc/articles/PMC4815408/#!po=13.6905 for some examples. Sometimes >> unexpected things (which just happen to have a similar size to your target) >> carry through all the purification steps - I remember having terrible >> trouble isolating his-tagged IGF-I (not for crystallization) from Sf9 >> lysates due to a cathepsin-like protease that stuck doggedly to the Ni-NTA >> column even under 8M urea, yet co-eluted in imidazole. Even if contaminant >> proteins are barely visible on your SDS-PAGE gel, if they crystallise >> easily and your target doesn’t... all these things and many others have >> happened, and have undoubtedly driven the occasional poor grad student to >> the brink of giving it all up. >> >> I guess in these days of relatively cheap and ubiquitous mass spec it may >> make sense to sacrifice a crystal to trypsin digest and MS/MS sequencing >> just for peace of mind, but in the average case I think that’s likely to be >> overkill. Shooting crystals at a synchrotron is now very routine, so I >> think it makes perfect sense to provide a computational check for the >> (hopefully rare) surprise case. >> >> Best regards, >> >> Tristan >> Tristan Croll >> Research Fellow >> Cambridge Institute for Medical Research >> University of Cambridge CB2 0XY >> >> >> >> On 23 Nov 2017, at 19:35, r...@mrc-lmb.cam.ac.uk <mailto: >> r...@mrc-lmb.cam.ac.uk> wrote: >> >> Dear Stefan, >>> >>> Just a couple of thoughts: >>> >>> - first of all I think that Gerard is absolutely right, it would have >>> been >>> nice to raise such issues first with the developers. In my experience, >>> Staraniso does a fantastic job if used correctly. >>> >>> - but if you're OK with public trials, may I ask: why on Earth would >>> anybody >>> need ContaMiner? Are you trying to offer some sort of computational cure >>> for >>> sloppy biochemistry? There is zero point in crystallizing crap samples, >>> sorry >>> to say this. In my 17 or so years in Strubi I've never heard of anybody >>> crystallizing a "contaminant", being it a purification tag or whatever. >>> >>> I suppose this might have happened to somebody you know, hence the >>> motivation >>> to spend time on the bizarre ContaMiner. Which is a pity, a silly outcome >>> would only teach people to do their job (or train their robots) properly. >>> >>> Best wishes, >>> >>> Radu >>> >>> -- >>> Radu Aricescu >>> MRC Laboratory of Molecular Biology >>> Francis Crick Avenue >>> Cambridge Biomedical Campus >>> Cambridge CB2 0QH, U.K. >>> tel: +44-(0)1223-267049 >>> fax: +44-(0)1223-268305 >>> www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu >>> >>> Dear Stefan, >>>> >>>> Regarding your final paragraph: your server carries a warning >>>> with the exact wording: >>>> >>>> "Submitting StarAniso files can give you suspicious results. Use >>>> with care!" >>>> >>>> It seems rather regrettable that you are posting such a public >>>> warning without ever having contacted the STARANISO developers about >>>> your observations, nor giving any information about what you call >>>> "suspicious" or what the "care" you recommend would consist of. >>>> >>>> We have taken a great deal of care ourselves in developing the >>>> program and offering it to the community through a server, and the >>>> least we would have expected is that any pattern of "suspicious" >>>> results would be referred to us so that we could investigate them. >>>> There may be some assumptions made in MoRDa that we are not aware of, >>>> that might be incompatible with assumptions made in STARANISO - who >>>> knows? Or it could be that some particularly badly collected datasets >>>> are made to look worse after their anisotropy analysis. >>>> >>>> Could we discuss your observations, and what it is exactly that >>>> you call "suspicious", before they end up being referred to in such an >>>> uninformative manner as some sort of "Government Health Warning"? >>>> >>>> I think that would be nice :-) and we would be only too keen to >>>> take whatever extra "care" is needed ourselves. We would all learn >>>> something. >>>> >>>> >>>> With best wishes, >>>> >>>> Gerard. >>>> >>>> (on behalf of the STARANISO developers) >>>> >>>> -- >>>> On Thu, Nov 23, 2017 at 05:02:39PM +0100, Stefan Arold wrote: >>>> >>>>> Dear Community, >>>>> >>>>> A quick message to announce the following two new features on our >>>>> ContaMiner web server for the automated detection of unwantedly >>>>> crystallised contaminants ( >>>>> https://strube.cbrc.kaust.edu.sa/contaminer/submit) >>>>> >>>>> 1) online visualisation of 2FoFc and FoFc maps. In cases of positive >>>>> results, the ‘UglyMol’ tab allows to inspect 2FoFc and FoFc maps >>>>> directly >>>>> in the web browser. Thi >>>>> >>>>> 2) life-update. Previously, results were sent to you once all ~2000 MR >>>>> jobs >>>>> were finished. Now, the individual results for each potential >>>>> contaminant >>>>> will appear as soon as they are finished. This feature should >>>>> substantially >>>>> shorten the time for identifying positive results (i.e. contaminant >>>>> detected), which are terminated faster than negative ones. >>>>> >>>>> 3) custom contaminants. In the ‘Advanced’ tab, users can upload own PDB >>>>> files (more than one is possible) to be included as search models. This >>>>> feature can be used to include PDB files from your lab bench >>>>> neighbour’s >>>>> project to test for potential lab internal contaminations (through >>>>> bacterial contamination or through mix-up of plasmids or glycerol >>>>> stocks). >>>>> This feature could also be ‘abused’ as a means to use the MoRDa >>>>> pipeline >>>>> to >>>>> run molecular replacements with template structures that are not yet >>>>> deposited in the PDB; for example to run molecular replacement and >>>>> initial >>>>> refinement for liganded or complexed versions of an unpublished >>>>> structure. >>>>> This might be particularly interesting for crystallographers away from >>>>> their usual home software environment (e.g. at the beamline). >>>>> >>>>> Finally, a word of warning – Staraniso files might give false >>>>> positives if >>>>> they have large anisotropic cuts. >>>>> >>>>> Keep your crystals clean! >>>>> >>>>> With best wishes >>>>> >>>>> The ContaMiner Team >>>>> >>>> >>>> -- >>>> >>>> =============================================================== >>>> * * >>>> * Gerard Bricogne g...@globalphasing.com <mailto: >>>> g...@globalphasing.com> * >>>> * * >>>> * Global Phasing Ltd. * >>>> * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * >>>> * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * >>>> * * >>>> =============================================================== >>>> >>>>
