Hello, I did wonder if it might be an alternative conformation for the quanidinium group of that nearby arginine. Being such high resolution, quite low occupancy groups would show up, I think, but it may just be too far away and I don't know how much tyrosine and arginine like each other!
Sent from ProtonMail mobile -------- Original Message -------- On 1 Feb 2022, 09:28, Misba Ahmad wrote: > Thank you for your suggestions. > As this is a high resolution structure (1.1Å) I have been refining it with > anisotropic B-factors. > Placing a propionate or modelling a phosphate at this position blows up > during the refinement. > I will inform you if I am successful in figuring this out. > > Best > Misbha > > On Sat, Jan 29, 2022 at 7:01 PM SHEPARD William > <william.shep...@synchrotron-soleil.fr> wrote: > >> Dear Misba, >> >> Perhaps it's a silly question, but have you tried to model in propionate? >> The carboxylate group could make H-bonds to both the Arginine sidechain and >> the the tyrosine OH group. Propionate should show no anomalous signal. >> >> Just my 2-bits worth. >> >> Cheers, >> Bill >> >> ----- Original Message ----- >> From: "Gerard Bricogne" <g...@globalphasing.com> >> To: CCP4BB@JISCMAIL.AC.UK >> Sent: Saturday, 29 January, 2022 18:34:26 >> Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification >> >> Dear Misba, >> >> Thank you for your reply and for the very clear picture. I hope you >> will be able to share the result once the mystery is solved. >> >> With best wishes, >> >> Gerard. >> >> -- >> On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote: >>> Dear Gerard, >>> The data were collected at 0.966Å and I can see the anomalous peaks for As >>> at Cysteines which are modified and I have correctly modelled those (see >>> image below). However, at this Tyr, I don't see an anomalous signal. >>> >>> [image: 4.png] >>> >>> On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne <g...@globalphasing.com> >>> wrote: >>> >>> > Dear Misba, >>> > >>> > A wild guess: have you considered the possibility that this extra >>> > density could be a cacodylate adduct? Cacodylate is well known to react >>> > with >>> > thiols - see >>> > >>> > >>> > https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2 >>> > >>> > Here the chemistry is different but you never know. If your data are >>> > redundant enough that you have good anomalous completeness, and were >>> > collected above the As K-edge (11.8667 keV), it might be a good idea to >>> > compute an anomalous difference Fourier and check for the presence of a >>> > peak >>> > at the same location as the highest one in your ordinary difference map. >>> > >>> > Only a wild guess, though ... . >>> > >>> > >>> > With best wishes, >>> > >>> > Gerard. >>> > >>> > -- >>> > On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote: >>> > > Placing a water molecule satisfies most of the density and forms nice >>> > > H-bonds but there is still some residual density left (8.6 and 5.6 >>> > > rmsd). >>> > > >>> > > Best >>> > > Misbha >>> > > [image: 3.png] >>> > > >>> > > >>> > > On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer <k.futte...@bham.ac.uk> >>> > > wrote: >>> > > >>> > > > Looks more like water molecules. Phosphorylation would give a much >>> > bigger >>> > > > peak, and shape of density does not fit either. I don't think this is >>> > > > a >>> > > > covalent modification. Model some water molecules and see what the >>> > > > distances are and what difference density is left. >>> > > > >>> > > > >>> > > > Klaus >>> > > > >>> > > > >>> > > > ======================================================= >>> > > > Klaus Fütterer, PhD >>> > > > Reader in Structural Biology >>> > > > >>> > > > >>> > > > School of Biosciences >>> > > > LES College Email: >>> > > > k.futte...@bham.ac.uk >>> > > > University of Birmingham Phone: +44 - 121 - 414 >>> > > > 5895 >>> > > > Birmingham, B15 2TT, UK (voice mail messages >>> > > > will forward to my email inbox) >>> > > > >>> > > > My normal working hours are Mon - Fri 8.30 - 5.30 pm. >>> > > > >>> > > > >>> > > > ======================================================= >>> > > > ------------------------------ >>> > > > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of >>> > > > misba.ah...@gmail.com <misba.ah...@gmail.com> >>> > > > *Sent:* 29 January 2022 09:45:24 >>> > > > *To:* CCP4BB@JISCMAIL.AC.UK >>> > > > *Subject:* Re: [ccp4bb] Help with interpreting Tyrosine modification >>> > > > >>> > > > Hi Tom, >>> > > > The protein was expressed in E Coli. >>> > > > >>> > > > Best >>> > > > Misbha >>> > > > >>> > > > On Sat, 29 Jan 2022, 10:18 Peat, Tom (Manufacturing, Clayton) < >>> > > > tom.p...@csiro.au> wrote: >>> > > > >>> > > >> Hello Misba, >>> > > >> >>> > > >> Doesn't quite look like a phosphate, maybe O-sulfation? >>> > > >> Maybe just as important as the buffer and crystallisation conditions >>> > > >> would be how it was expressed? Insect cells? >>> > > >> >>> > > >> Best of luck, tom >>> > > >> >>> > > >> Tom Peat, PhD >>> > > >> >>> > > >> Biomedical Program, CSIRO >>> > > >> tom.p...@csiro.au >>> > > >> >>> > > >> ------------------------------ >>> > > >> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of >>> > Misba >>> > > >> Ahmad <misba.ah...@gmail.com> >>> > > >> *Sent:* Saturday, January 29, 2022 8:12 PM >>> > > >> *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >>> > > >> *Subject:* [ccp4bb] Help with interpreting Tyrosine modification >>> > > >> >>> > > >> Hi all, >>> > > >> I am trying to interpret this strong difference density peak (11.33 >>> > rmsd) >>> > > >> that shows up on the tyrosine residue. Any help would be greatly >>> > > >> appreciated. >>> > > >> >>> > > >> Purification buffer: 20mM HEPES pH 7.5, 250mM NaCl, 1mM TCEP, 5mM DTT >>> > > >> Crystallisation condition: Sodium propionate, Sodium cacodylate, >>> > BIS-TRIS >>> > > >> propane, PEG 1500 >>> > > >> >>> > > >> Best >>> > > >> Misbha >>> > > >> [image: Picture1.png] >>> > > >> [image: Picture2.png] >>> > > >> >>> > > >> ------------------------------ >>> > > >> >>> > > >> To unsubscribe from the CCP4BB list, click the following link: >>> > > >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> > > >> >>> > > > >>> > > > ------------------------------ >>> > > > >>> > > > To unsubscribe from the CCP4BB list, click the following link: >>> > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> > > > >>> > > >>> > > ######################################################################## >>> > > >>> > > To unsubscribe from the CCP4BB list, click the following link: >>> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> > > >>> > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a >>> > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are >>> > available at https://www.jiscmail.ac.uk/policyandsecurity/ >>> > >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >> list hosted by www.jiscmail.ac.uk, terms & conditions are available at >> https://www.jiscmail.ac.uk/policyandsecurity/ > > --------------------------------------------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
