Re: [ccp4bb] Help with interpreting Tyrosine modification
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" 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 > 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 > > > 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 CollegeEmail: > > > > 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 on behalf of > > > > 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 on behalf of > > Misba > > > >> Ahmad > > > >> *Sent:* Saturday, January 29, 2022 8:12 PM > > > >> *To:* 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: > > > >>
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 > 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 > > > 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 CollegeEmail: > > > > 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 on behalf of > > > > 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 on behalf of > > Misba > > > >> Ahmad > > > >> *Sent:* Saturday, January 29, 2022 8:12 PM > > > >> *To:* 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=1 > > > >> > > > > > > > > -- > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > > > > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > >
Re: [ccp4bb] Updating Ubuntu 18 LTS to 20?
Dear Jim and Jon Thanks very much for your information and thoughts! Cheers, Domen On Fri, Jan 14, 2022 at 10:09 PM Jim Fairman wrote: > Hi Domen, > > I have been running 20.04 for quite some time now without any issues. In > my experience, performing in-place upgrades from a previous version (eg: > 14.04 to 16.04, 16.04 to 18.04) caused some issues and I usually ended up > having to wipe the system and perform fresh installs, but your mileage may > vary. My standard operating procedure is to backup your home directory and > any important files and perform a fresh install. > > The rolling release distributions like Arch and Manjaro avoid the issues > of having to perform upgrades across major versions, but always running the > "latest" packages may sometimes cause issues. However, I haven't found > this in my usage of them over the past 4 or 5 years. > > Cheers, Jim > -- > Jim Fairman > C: 1-240-479-6575 > > > On Fri, Jan 14, 2022 at 1:00 PM Domen Zafred > wrote: > >> Hi all, >> >> has anyone updated the Ubuntu 18.04 LTS Bionic Beaver to the never 20.04? >> That means with programs we usually have installed (java, phython, xds, >> ccp4 & coot, phenix, R, data warrior, pymol, nomacine, etc)? Any troubles, >> recommendations? >> 22 LTS is coming out this year, I'm not sure if jumping from 18 to 22 >> would be a good idea, but 18 is getting old. >> >> Thanks for any hints >> >> Domen >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Help with interpreting Tyrosine modification
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 > 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 CollegeEmail: > > 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 on behalf of > > 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 on behalf of Misba > >> Ahmad > >> *Sent:* Saturday, January 29, 2022 8:12 PM > >> *To:* 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=1 > >> > > > > -- > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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=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/
