Probably arginine and tyrosine do like each other a fair bit. They can form both cation-pi interactions and hydrogen bonds. Best wishes James
On 1 Feb 2022, at 16:41, Jon Cooper <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: 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 < misba.ah...@gmail.com> 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<mailto: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<mailto:g...@globalphasing.com>> To: CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto: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<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffebs.onlinelibrary.wiley.com%2Fdoi%2Fpdfdirect%2F10.1016%2F0014-5793(72)80224-2&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=quySIsk%2BnzbHh5o3bYoOGbiXsx1ItJGTt3y6aI2oc5M%3D&reserved=0> > > > > 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<mailto: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<mailto: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<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of > > > > misba.ah...@gmail.com<mailto:misba.ah...@gmail.com> > > > > <misba.ah...@gmail.com<mailto:misba.ah...@gmail.com>> > > > > *Sent:* 29 January 2022 09:45:24 > > > > *To:* CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto: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<mailto:tom.p...@csiro.au> > > > >> > > > >> ------------------------------ > > > >> *From:* CCP4 bulletin board > > > >> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of > > Misba > > > >> Ahmad <misba.ah...@gmail.com<mailto:misba.ah...@gmail.com>> > > > >> *Sent:* Saturday, January 29, 2022 8:12 PM > > > >> *To:* CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> > > > >> <CCP4BB@JISCMAIL.AC.UK<mailto: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<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=En0%2FQm6ab6N1tngcVea7xBP7vJFEzwFQCEVcIZqCbQg%3D&reserved=0> > > > >> > 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