---------- Forwarded message --------- From: Daniel M. Himmel, Ph. D. <danielmhim...@gmail.com> Date: Mon, Aug 5, 2019 at 12:45 PM Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+ To: <herman.schreu...@sanofi.com>
Pentagonal phosphate geometry would be a transition state, except that three oxygens would be more or less co-planar. Would anything approaching a transition state show up in the electron density of a crystal structure? In myosin ATPase structures, there are phosphate analogs with geometry that approximates a transition state. -Daniel On Mon, Aug 5, 2019 at 11:55 AM <herman.schreu...@sanofi.com> wrote: > 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> 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> > 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> 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
