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 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/
