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<http://pharm.kuleuven.be/anafar> ________________________________ 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 SO3, SO2 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
