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" <[email protected]>
To: [email protected]
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 <[email protected]> on behalf of Lumbini
Yadav <[email protected]>
*Sent:* Wednesday, July 10, 2019 13:12
*To:* [email protected]
*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
<[email protected] <mailto:[email protected]>> 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 <[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>>
wrote:
The key word for refmac is ANOM MAPONLY
Are you using GUI2?
Eleanor
On Wed, 10 Jul 2019 at 09:32, Lumbini Yadav
<[email protected] <mailto:[email protected]>> 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
<[email protected]
<mailto:[email protected]>> 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:[email protected]
<mailto:[email protected]>] *On Behalf Of
*Lumbini Yadav
*Sent:* Tuesday, July 09, 2019 5:22 AM
*To:* [email protected]
<mailto:[email protected]>
*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 [email protected]
----------------------------------------------------
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
