Re: [ccp4bb] Extra density on Cysteine
Dear Tina, my guess would be minor oxidation of the cysteine. The green positive difference density suggests a bound atom in three different positions; this could however just be the first atom of something bigger like beta-mercaptoethanol, with the rest of that molecule too disordered to see. By eye-balling, the blue electron density does not look much bigger than expected for sulfur, so whatever it is, I would think it's very minor and probably not even worth modelling. I am also guessing this map is after refinement is almost complete and the overall difference map quite flat, so three sigmas of difference density (if that is what is contoured) may correspond to quite few electrons, i.e. low occupancy of the adduct. Another explanation might be "anomalous behaviour" of the sulfur, similar to residual difference densities often observed near metal ions. A physicist will likely have a better idea about this than me. Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. +34 91 585 4616 (internal 432092) > On 21 Jun 2024, at 11:02, hsyu11gmail wrote: > > Dear all, > > We recently solved a structure to 2.1 A, and found an additional Fo-Fc > density on the side chain of a cysteine residue. The structure has been > reported previously, and no modification found at this site. The distances > between the cysteine and other residues also does not appear to be long > enough for any modifications. > > Does anyone has an idea about this map? > > Thanks. > > Kind regards, > Tina > > > > > hsyu11gmail > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] extra density on Cysteine
2cystein.jpeg looks just like oxidation of cysteine to S-hydroxy-cysteine (a.k.a. cysteine sulfenic acid). I have seen this repeatedly in one of my structures (E. coli aminopeptidase P, see 1WL9 for an example). We discuss this a bit in Graham et al (2005) Biochemistry 44: 13820-36 - see Figure 2 and surrounding text. Cheers, Stephen On 8/14/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > > Dear all, > > I am refining a 2.0A structure. I found that there were some extra density > on two cysteines, even though I have added 5mM BME in the protein buffer. > > I am wondering whether the first one (Cys292) is a bme and the second one is > an oxidized cysteine. Any suggestion? > > I attached the images for your reference. thanks > > Regards > _ > Xu Ting ,Ph.D > 10 Biopolis Road > Singapore 138670 > Fax: +65 6722 2916 > Phone: +65 6722 2980 > -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
Re: [ccp4bb] extra density on Cysteine
Rather difficult to decide. It depends on whether BME was present during all protein purification steps. Also, BME is somewhat short lived. You have to add new BME every few days or so. At least one looks like it could be oxidized, a process that cannot be reversed by BME J. Artem Evdokimov wrote: Hi, They’re likely both BME adducts, just in the first case the CH2CH2OH portion is way more disordered. Artem *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of [EMAIL PROTECTED] *Sent:* Monday, August 13, 2007 9:59 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] extra density on Cysteine Dear all, I am refining a 2.0A structure. I found that there were some extra density on two cysteines, even though I have added 5mM BME in the protein buffer. I am wondering whether the first one (Cys292) is a bme and the second one is an oxidized cysteine. Any suggestion? I attached the images for your reference. thanks Regards _ Xu Ting ,Ph.D 10 Biopolis Road Singapore 138670 Fax: +65 6722 2916 Phone: +65 6722 2980 -- Jeroen Raymundus Mesters, Ph.D. Institut fuer Biochemie, Universitaet zu Luebeck Zentrum fuer Medizinische Struktur und Zellbiologie Ratzeburger Allee 160, D-23538 Luebeck Tel: +49-451-5004070, Fax: +49-451-5004068 E-mail: [EMAIL PROTECTED] Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
Re: [ccp4bb] extra density on Cysteine
Hi, They're likely both BME adducts, just in the first case the CH2CH2OH portion is way more disordered. Artem _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Monday, August 13, 2007 9:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] extra density on Cysteine Dear all, I am refining a 2.0A structure. I found that there were some extra density on two cysteines, even though I have added 5mM BME in the protein buffer. I am wondering whether the first one (Cys292) is a bme and the second one is an oxidized cysteine. Any suggestion? I attached the images for your reference. thanks Regards _ Xu Ting ,Ph.D 10 Biopolis Road Singapore 138670 Fax: +65 6722 2916 Phone: +65 6722 2980
