PS, you also have to define an alternative conformation, but that you probably already did.
Von: Schreuder, Herman /DE Gesendet: Montag, 5. August 2019 17:55 An: 'Maria Håkansson'; CCP4BB@JISCMAIL.AC.UK Betreff: AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+ Hi Maria, Did you rotate the phosphate, or invert it? If you invert the phosphate, you may get into trouble with the parameters. Although a phosphate is symmetric, its oxygens have different names and inverting it leads to all kind of problems, especially in a high resolution map which does not allow the phosphate to flip it back in an “allowed” conformation. If you did rotate the phosphate, I take my words back and you may have to look for ions. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Maria Håkansson Gesendet: Montag, 5. August 2019 17:32 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+ EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk Hi, Thanks for your suggestions but I have tried to invert the phosphate and it is not fitting the map. The geometry is not correct that way and it is too good data to ignore and to my knowledge a pentacoordinated phosphate is a non existent species. That leaves me with ions. Best regards, Maria Maria Håkansson, PhD, Crystallization Facility Manager Principal Scientist SARomics Biostructures AB Medicon Village SE-223 81 Lund, Sweden Mobile: +46 (0)76 8585706 Web: www.saromics.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.saromics.com&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=n8AawGvnjHilw4Yoh7AjCCk8wfameakvWM7OvpbvCJI&s=q-G0klB2rvoNDw6bKWKr8ASbOLmfrjWlRry1Hsms-54&e=> On 5 Aug 2019, at 16:32, Jan Abendroth <jan.abendr...@gmail.com<mailto:jan.abendr...@gmail.com>> wrote: Hi Maria, apart from the suggestions that were already made, take a look at the P-O bond on the right side of the P. Maybe it is just the perspective, this appears to be rather long. So, instead of the alternate conformation, maybe just a flip of the phosphate and a water off to the right? Cheers, Jan On Mon, Aug 5, 2019 at 7:16 AM Nukri Sanishvili <sannu...@gmail.com<mailto:sannu...@gmail.com>> wrote: Hi Maria, Let's not ignore the "missing" density - the red one. If the question is only P vs S, a sulfur would add to the negative density, i.e. make matters worse. It also appears that modeling a phosphate in alternative conformations, as suggested by Wim and Roger, would take care of the issue of negative density as well. Cheers, Nukri On Mon, Aug 5, 2019 at 8:05 AM Maria Håkansson <maria.hakans...@saromics.com<mailto:maria.hakans...@saromics.com>> wrote: Dear CCP4 bulletin board, I am working with some lytic enzymes called endolysines, which bind Zn2+ in the active site. I have three homologues protein determined to 1.2 Å each where the Zn2+ is bound to a cystein, two histidines and one phosphate ion added (1.9-2.3 Å binding distances) in the crystallization experiment. Now to my question. Close to the phosphate (B-factor=20Å2) ion a 8 sigma peak is present in all three endolysines, see below. I have modeled it to a Na+ (B-factor= 30 Å2) or a Li+ (B factor = 13Å2) ion. Sodium has benn added in the crystallization experiments since sodium potassium phosphate salt has been used. The only reason for including Li+ is that I think the binding distances (1.7-2.0 Å) are too short for Na+. I have also tried to make a model with the phosphate in two different conformations but it does not fit. Have anyone seen something similar before? What is the most correct way of dealing with unknown densities? It is difficult to disregard +8 sigma difference density close to the active site. Thanks in advance for any help! Best regards, Maria <Endolysine-Zn2+-site-extra-density.png><Endolysine-Zn2+-site-extra ion.png><Endolysine-Zn2+-site-extra-ion2.png> Maria Håkansson, PhD, Crystallization Facility Manager Principal Scientist SARomics Biostructures AB Medicon Village SE-223 81 Lund, Sweden Mobile: +46 (0)76 8585706 Web: www.saromics.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.saromics.com_&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=n8AawGvnjHilw4Yoh7AjCCk8wfameakvWM7OvpbvCJI&s=iDeElvjjAtCzkGvlyWvkljE9fucoGgiM-zXxXE2PnL0&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=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=n8AawGvnjHilw4Yoh7AjCCk8wfameakvWM7OvpbvCJI&s=PqSMqPoSgx3DQJoW80_1F_4nlxMgJYW_mYsfuYsuwME&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=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=n8AawGvnjHilw4Yoh7AjCCk8wfameakvWM7OvpbvCJI&s=PqSMqPoSgx3DQJoW80_1F_4nlxMgJYW_mYsfuYsuwME&e=> -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__jan.abendroth-5Fat-5Fgmail.com_&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=n8AawGvnjHilw4Yoh7AjCCk8wfameakvWM7OvpbvCJI&s=RR39G-wu5nPYP9UZQtYVll0c-lZ6lKKlu11KENbq1IE&e=> work: JAbendroth_at_embios.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__jabendroth-5Fat-5Fembios.com&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=n8AawGvnjHilw4Yoh7AjCCk8wfameakvWM7OvpbvCJI&s=5hToEb98GNDqgLA_u8gxwZpe8t_uDHUn6j9dGbT4WLY&e=> http://www.emeraldbiostructures.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.emeraldbiostructures.com_&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=n8AawGvnjHilw4Yoh7AjCCk8wfameakvWM7OvpbvCJI&s=Swa9M19Y5vcQmQqYkGbcget2SZ7PUcJGUOSIQ4xgOCo&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=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=n8AawGvnjHilw4Yoh7AjCCk8wfameakvWM7OvpbvCJI&s=PqSMqPoSgx3DQJoW80_1F_4nlxMgJYW_mYsfuYsuwME&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
