@Jarva: I was looking for something like your distribution. I would very much like to know how did you get the data? Can you show us (or me)? Please. I would like to play with it. Same to @Mesters, how do you get that list?
PS @Waterman I agree with you, it is a problem. @Everybody: Thanks for taking your time to answer my questions. El sáb., 21 de sep. de 2019 a la(s) 04:27, Michael Jarva ( jarv...@wehi.edu.au) escribió: > Hi Murphy and CCP4BB, > > the question intrigued me so I took the liberty to query the PDB and do > some crude extraction of entries that fit your query. > > Attached is the the list of all PDB IDs corresponding to 42 unique > Protein/Space group combinations, and a neat boxplot chart of the pH > distributions for these. > > In short, I extracted each PDB entry that fit the following criteria: > > 1. X-ray structures with a resolution <2.6Å > 2. Crystals comprising only protein chains corresponding to a single > UniProt Accession ID > 3. Is a WT sequence as compared to the UniProt Accession > 4. Has a crystallisation pH specified in the PDB > > These ~30,000 hits were binned by the unique combination of UniProt > ID/Space Group and further trimmed by only keeping entries that have: > > 1. At least 5 PDB IDs in the bin. > 2. Has a pH crystallisation range corresponding to at least 4 pH units > (i.e 4-7, or 6-10, etc) > > This is by no means an exhaustive list of what you're looking for but > doing a more thorough evaluation would be a significant time investment. I > have also not evaluated these hits by the presence of co-factors or ligands. > > For those interested, but not so interested they want to open the > spreadsheet, here are the top 11 pH ranges: > > Uniprot Acc Space Group PDB entries Min pH Average pH Max pH Range Name > P22629 I 2 2 2 33 1.4 4.1 10.4 9.1 Streptavidin > P18902 P 21 21 21 5 2.0 5.0 9.0 7.0 Retinol-binding protein 4 > P11073 P 21 21 21 13 4.5 8.0 11.2 6.7 Pectate lyase C > Q9U6Y8 P 1 21 1 6 4.2 7.2 10.5 6.3 Red fluorescent protein > P00760 P 31 2 1 59 3.9 7.3 10.0 6.2 Cationic trypsin > P42212 P 1 21 1 7 2.0 5.6 8.0 6.0 Green fluorescent protein > P00918 P 1 21 1 446 5.1 8.0 11.0 5.9 Carbonic anhydrase 2 > P00698 P 21 21 21 28 3.8 5.3 9.6 5.8 Lysozyme C > P43235 P 43 21 2 17 2.9 6.0 8.7 5.8 Cathepsin K > P00698 P 43 21 2 461 3.0 4.6 8.5 5.5 Lysozyme C > P00772 P 21 21 21 33 4.6 5.9 10.0 5.4 Elastase-1 > please let me know if this helps or if there's any questions about what or > how I did it > > best regards > Michael > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of > Murpholino Peligro <murpholi...@gmail.com> > *Sent:* Friday, September 20, 2019 9:03 AM > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject:* [ccp4bb] Are there any proteins capable of crystallizing at a > wide range of pH having the same space group? > > A quick glance at the entries of hen egg white lysozyme in the PDB show > that it can be crystallized at different pH values, but the space group is > not always the same. I still have to refine the analysis but I was > wondering that maybe there are a few proteins that can crystallize at a > wide range (maybe not that wide) of pH values and still have the same space > group? > > To refine the analysis a wee further: By any chance do you know any > proteins overpopulating the PDB (i.e. besides HEWL)? > > Lots of thanks as always. > > Murphy > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > _______________________________________________ > > The information in this email is confidential and intended solely for the > addressee. > You must not disclose, forward, print or use it without the permission of > the sender. > > The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of > the Kulin > Nation as the traditional owners of the land where our campuses are > located and > the continuing connection to country and community. > _______________________________________________ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
