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
