Hi Shijun, Unfortunately, it happens very often that a ligand (in your case Chloramphenicol) does not bind to the protein in the crystal. If you look into the twilight gallery, there is a large number of crystal structures where people desperately tried to fit their precious ligand in what turned out to be solvent or buffer molecules. So it is perfectly common that you don’t see your Chlorampenicol.
Concerning the AcCOA, here it is very well possible that the part which is covalently linked via the disulfide bond, is well defined in the electron density, but that parts of the molecule, farther away from the link are not visible because they are disordered. You should also look at your protein: is it an enzyme? What kind of reaction does it catalyze? What kind of reaction products do you expect? If you are uncertain what happened, you could try to identify the bound molecule with mass spec. Cheers, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von ??? Gesendet: Donnerstag, 5. Juli 2018 11:33 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] disulfate bond ? Hi Thanks for all your suggestions . It is out of our hope even though it is disulfide bond, so I wondering what's the biological meaning for this kind of disulfide bond. I used AcCOA and Chloramphenicol when I screen crystal, but I could only put a COA in the election density even that the election density is not good enough.Any good suggestion or experience? Best Regards shijun -----原始邮件----- 发件人:"Artem Evdokimov" <artem.evdoki...@gmail.com> 发送时间:2018-07-04 20:01:47 (星期三) 收件人: CCP4BB@JISCMAIL.AC.UK 抄送: 主题: Re: [ccp4bb] disulfate bond ? It seems that your CoA is one carbon out of reference. You have spotty difference density over the ligand. Shift it left by one carbon bond and redune to see if density fits better. Artem On Wed, Jul 4, 2018, 02:26 张士军 <21620150150...@stu.xmu.edu.cn<mailto:21620150150...@stu.xmu.edu.cn>> wrote: Hi all I got a structure which has COA in it, and the SH in the tail of COA is very close to the SH side chain of Cys in the structure. I don't know whether it is disulfate bond or not? I remember they should link together if they are disulfate bond,am I right? so what could this be? Thanks a lot!!! best regards shijun ________________________________ 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=DwMGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=xhrVRgV5xKX3fils0hFzokp23q1R7XKLP-344hBuuqE&s=Gn_aZWoVj7sHfatIGGi411OHLBAbP_u7dwsFOOmKYMg&e=> ________________________________ 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=DwMGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=xhrVRgV5xKX3fils0hFzokp23q1R7XKLP-344hBuuqE&s=Gn_aZWoVj7sHfatIGGi411OHLBAbP_u7dwsFOOmKYMg&e=> ________________________________ 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=DwMGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=xhrVRgV5xKX3fils0hFzokp23q1R7XKLP-344hBuuqE&s=Gn_aZWoVj7sHfatIGGi411OHLBAbP_u7dwsFOOmKYMg&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
