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" <[log in to unmask]>
To: [log in to unmask]
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 <[log in to unmask]> on behalf of Lumbini
> Yadav <[log in to unmask]>
> *Sent:* Wednesday, July 10, 2019 13:12
> *To:* [log in to unmask]
> *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
> <[log in to unmask] <mailto:[log in to unmask]>> 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 <[log in to unmask]
> <mailto:[log in to unmask]>> 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
> <[log in to unmask] <mailto:[log in to unmask]>>
> wrote:
>
> The key word for refmac is ANOM MAPONLY
> Are you using GUI2?
> Eleanor
>
> On Wed, 10 Jul 2019 at 09:32, Lumbini Yadav
> <[log in to unmask] <mailto:[log in to unmask]>> 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
> <[log in to unmask]
> <mailto:[log in to unmask]>> 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:[log in to unmask]
> <mailto:[log in to unmask]>] *On Behalf Of
> *Lumbini Yadav
> *Sent:* Tuesday, July 09, 2019 5:22 AM
> *To:* [log in to unmask]
> <mailto:[log in to unmask]>
> *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____
>
> __ __
>
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