I just want add that the redundant PDB got a new site http://pdbflex.org/ (It's pretty cool actually) Thanks to Robyn for pointing that out.
El dom., 22 de sep. de 2019 a la(s) 10:18, Robyn Stanfield ( [email protected]) escribió: > Hi, > > The Burnham changed names sometime back, that may be why that link > disappeared. Check the Adam Godzik lab page( http://godziklab.org/pages/ > ) else if this info is not there just e-mail Adam and I’ll bet he can fix > you up with the database in question. He is very helpful. > > Good luck, > > Robyn > > > > *From:* CCP4 bulletin board <[email protected]> * On Behalf Of *David > Waterman > *Sent:* Friday, September 20, 2019 4:09 PM > *To:* [email protected] > *Subject:* Re: [ccp4bb] Are there any proteins capable of crystallizing > at a wide range of pH having the same space group? > > > > archive.org suggests the database existed up to December 2018, but > appears to be no more. > > > > What to do when scientific resources associated with published papers > disappear like this? It seems to be a problem that is not very well > addressed. > > > > Cheers > > David > > > > On Fri, 20 Sep 2019, 04:26 Murpholino Peligro, <[email protected]> > wrote: > > Following my last question I was searching for a redundant PDB and found > this paper https://doi.org/10.1016/j.str.2007.07.012. I went to the > methods section and found out that the link to the database of redundant > protein structures is now gone (http://dper.burnham.org/). Anyone knows > of a similar database? Or anyone knows how to make one? > > > > Thanks again for your help. > > > > > > Murph > > > > El jue., 19 de sep. de 2019 a la(s) 19:04, Dale Tronrud ( > [email protected]) escribió: > > > My recollection is that gamma-chymotrypsin crystals will persist in > pHs all the way from 3 to 9. I don't know if the crystals will grow > over that range. > > There are a fair number of phage T4 lysozymes variants in the PDB. I > don't think this is considered "overpopulation" but a valuable > contribution to humanity. ;-) > > Dale Tronrud > > On 9/19/2019 4:03 PM, Murpholino Peligro wrote: > > 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 > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
