I think this is very wise. It can be better to say that you don't know then to guess if people will take your answer for granted.
Cheers, Robbie On 11 Jul 2019 11:09, Raz Zarivach <000033371661b7b1-dmarc-requ...@jiscmail.ac.uk> wrote: Hi All With so many alternative suggestions, wouldn't be better to leave it without guessing the wrong molecule? Raz On 11/07/2019 10:55, Anthony Addlagatta wrote: > For some reason if your sulfur on cysteine becomes sulfide anion, you can > model sodium/potassium. Distance seems to be optimum for S...Na contact. > Since you do not see any anomalous signal, this is one possibility. I also > see small blobs around which may resolve to be water molecules. > > Anthony > > ----- Original Message ----- > From: "hideaki niwa" <hideaki.n...@riken.jp> > To: CCP4BB@JISCMAIL.AC.UK > Sent: Thursday, July 11, 2019 12:22:39 PM > Subject: Re: [ccp4bb] Fo-Fc density close to cysteine residue > > Hi Sergei, > > At a first glance I thought so too, but if it is an arsenic atom there > should be a strong anomalous signal. Also the distance 2.5A seems a bit > long. > > Hideaki Niwa > > RIKEN Center for Biosystems Dynamics Research > Yokohama, 230-0045 JAPAN > > On 2019/07/10 23:45, Sergei Strelkov wrote: >> Dear Lumbini, >> >> >> Certainly not a proof but your density looks like >> (di)methyl-arsinoyl-cysteine (PDB residue type CAF). This modification >> can happen when the protein has been exposed to cacodylate buffer. You >> can find such residues (and maps) in the PDB entries 3LPT or 5MDI. >> >> >> Best wishes, >> >> Sergei >> >> >> Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of >> Pharmaceutical Sciences, KU Leuven O&N2, Campus Gasthuisberg, Herestraat >> 49 bus 822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 >> 29 41 32 Lab pages: http://pharm.kuleuven.be/Biocrystallography >> >> ------------------------------------------------------------------------ >> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Lumbini >> Yadav <lumbin...@gmail.com> >> *Sent:* Wednesday, July 10, 2019 13:12 >> *To:* CCP4BB@JISCMAIL.AC.UK >> *Subject:* Re: [ccp4bb] Fo-Fc density close to cysteine residue >> Thank you for the valuable input >> >> On Wed, Jul 10, 2019 at 4:25 PM Eleanor Dodson >> <eleanor.dod...@york.ac.uk <mailto:eleanor.dod...@york.ac.uk>> wrote: >> >> Well - that more or less proves the residue is a CYS - there is a >> peak in the PHAN map right on the S. >> And that the extra density does not contain an anomalous scatterer >> so is probably not a metal or a sulphate or... >> >> But that still doesnt explain WHAT it is . Sorry not to be more help.. >> >> Eleanor >> >> On Wed, 10 Jul 2019 at 11:32, Lumbini Yadav <lumbin...@gmail.com >> <mailto:lumbin...@gmail.com>> wrote: >> >> No I am using ccp4i. I tried doing SAD refinement in refmac and >> the output image is attached below . >> I do not seen density near cysteine that was visible in Fo-Fc map >> >> On Wed, Jul 10, 2019 at 3:40 PM Eleanor Dodson >> <eleanor.dod...@york.ac.uk <mailto:eleanor.dod...@york.ac.uk>> >> wrote: >> >> The key word for refmac is ANOM MAPONLY >> Are you using GUI2? >> Eleanor >> >> On Wed, 10 Jul 2019 at 09:32, Lumbini Yadav >> <lumbin...@gmail.com <mailto:lumbin...@gmail.com>> wrote: >> >> I have soaked my crystals in?? sodium dithionite a >> reducing agent. I have not done mass spec but sequence >> is confirmed >> >> On Tue, Jul 9, 2019 at 9:26 PM Bonsor, Daniel >> <dbon...@som.umaryland.edu >> <mailto:dbon...@som.umaryland.edu>> wrote: >> >> Have you mass-speced the protein before >> crystallization to make sure it wasn???t derivatized >> during expression and/or purification, or compared >> the mass spec of the crystals verses purified >> protein? Any fancy reagents or other reductants used >> during purification?____ >> >> ____ >> >> What about S-Acetyl-cysteine (3-letter code: SCY). ____ >> >> __ __ >> >> Best,____ >> >> __ __ >> >> Dan____ >> >> __ __ >> >> Daniel A Bonsor PhD.____ >> >> Sundberg Lab____ >> >> Institute of Human Virology____ >> >> University of Maryland, Baltimore____ >> >> 725 W Lombard Street N370____ >> >> Baltimore____ >> >> Maryland____ >> >> MD 21201____ >> >> Tel: (410) 706-7457____ >> >> __ __ >> >> __ __ >> >> *From:*CCP4 bulletin board >> [mailto:CCP4BB@JISCMAIL.AC.UK >> <mailto:CCP4BB@JISCMAIL.AC.UK>] *On Behalf Of >> *Lumbini Yadav >> *Sent:* Tuesday, July 09, 2019 5:22 AM >> *To:* CCP4BB@JISCMAIL.AC.UK >> <mailto:CCP4BB@JISCMAIL.AC.UK> >> *Subject:* [ccp4bb] Fo-Fc density close to cysteine >> residue____ >> >> __ __ >> >> Dear all,____ >> >> ____ >> >> We have found a huge Fo-Fc density close to cysteine >> residue (see attached image) in the structure with >> resolution of 1.2A. In the crystallization >> condition, we have PEG 3350, Potassium phosphate >> monobasic, glycerol and protein was in Tris and >> NaCl. Before freezing the crystals were soaked in >> mother liquor containing sodium dithionite.____ >> >> ____ >> >> I have tried different modified cysteine (CSX, CSO, >> OCS, CME, CSS, SNC,CSD, CXM,SCH,CSU) from the >> library and also SO_3 , SO_2 ??and peroxide. But in >> all the screenings we do see some part of Fo-Fc >> density unaddressed at 3 sigma.____ >> >> ____ >> >> Does anyone have an idea about what this density >> could be? Covalent modification?____ >> >> ____ >> >> Thanks.____ >> >> ____ >> >> >> >> ____ >> >> Kind regards,____ >> >> Lumbini____ >> >> __ __ >> >> >> ------------------------------------------------------------------------ >> >> 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 >> > ######################################################################## > > 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 > -- ---------------------------------------------------- Raz Zarivach, Ph.D. Department of Life Sciences and the NIBN Ben-Gurion University of the Negev POB 653, 84105, Beer-Sheva, Israel Home page: https://lifewp.bgu.ac.il/wp/zarivach/ tel: +972-8-6461999 fax: +972-8-6472970 skype: zarivach zariv...@bgu.ac.il ---------------------------------------------------- ######################################################################## 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
