27-May-2019 Dear Jonathan A good example to see the actual 'breaking of an S-S bond' can be found in:
Weik, Ravelli, Kryger, McSweeney, Raves, Harel, Gros, Silman, Kroon, & Sussman "Specific chemical and structural damage to proteins produced by synchrotron radiation” PNAS 97, 623-628 (2000). See cover illustration of the breaking of one S-S bond as a function of time at: http://www.weizmann.ac.il/Structural_Biology/Sussman/cover-pages/pnasb & http://www.weizmann.ac.il/Structural_Biology/Sussman/radiation-damage-0 best regards, Joel -------------------------------------------------------------------------------- Prof. Joel L. Sussman joel.suss...@weizmann.ac.il<mailto:joel.suss...@weizmann.ac.il> www.weizmann.ac.il/~joel<http://www.weizmann.ac.il/~joel> Dept. of Structural Biology tel: +972 (8) 934 6309 proteopedia.org<http://www.weizmann.ac.il/~joel> Weizmann Institute of Science fax: +972 (8) 934 6312 Rehovot 76100 ISRAEL mob: +972 (50) 510 9600 --------------------------------------------------------------------------------- On 27May, 2019, at 9:53, herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com> <herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>> wrote: Dear Jonathan, In these cases, I usually see positive difference density nearby, indicating an alternative position for one of the sulfurs, i.e. the disulfide bridge was partly broken. I am too lazy to fit these, but if you want to do a perfect job, you might want to fit an alternative conformation for this sulfur. You may have to create an alternative conformation for the other sulfur as well to have one bonded disulfide bridge and one open one. Considering deposition: you are the depositor. If you believe that the model you made is the most faithful representation of the “true” structure, you should deposit it and the pdb will have to accept. In the worst case they will add some warnings. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jonathan Cooper Gesendet: Montag, 27. Mai 2019 00:20 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: [EXTERNAL] [ccp4bb] Disulphide occupancies. EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk> When you refine structures with disulphide bridges you often get negative difference density for the sulphurs, presumably due to the well-known radiation damage effects. The negative difference density often won't disappear with usual B-factor refinement. However, it seems to go away if you refine the occupancy of the affected sulphur atoms e.g. to 0.9 or thereabouts. Would it be acceptable to publish/deposit structures where the sulphur occupancy is less than one, given a suitable REMARK in the pdb file? Thank you. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMCaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=0j--BHSa9riffnsR93Mocor_5HE2Pf8s8CKWzlFXYXs&s=ZBlTcvbvqNmi2UiuIKmPof8P_HPBYN76iHzpjcU9_ro&e=> ________________________________ 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
