[ccp4bb] AW: [ccp4bb] Unknown Ligand Density
Dear Nick, I would contact some MassSpec people and ask if they could find out the mass of your mystery ligand. I would also carefully look at the neighboring protein. It might be an alternate conformation of a partially disordered loop. Finally, I would check literature to see if a natural ligand/cofactor of your protein would fit. However, your ligand seems to be bound in a crystal contact so it may be an artifact. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Nick Thomas Gesendet: Mittwoch, 14. Juni 2017 18:40 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Unknown Ligand Density Dear CCP4bb, I am refining a structure and have come across strong electron density for an unknown ligand (image attached). Would someone be able to identify this unknown ligand that somehow was co-purified with the protein. The electron density shape does not match anything included in the crystallization conditions. The crystallization condition is 0.1M MES monohydrate, pH 6.5, 1.6 M Magnesium sulphate heptahydrate
Re: [ccp4bb] Unknown Ligand Density
Flying spaghetti monster. Ramen! Sorry. Could not resist. Artem www.harkerbio.com "...touched by His Noodly Appendage" On Jun 14, 2017 12:51 PM, "Nick Thomas" wrote: Dear CCP4bb, I am refining a structure and have come across strong electron density for an unknown ligand (image attached). Would someone be able to identify this unknown ligand that somehow was co-purified with the protein. The electron density shape does not match anything included in the crystallization conditions. The crystallization condition is 0.1M MES monohydrate, pH 6.5, 1.6 M Magnesium sulphate heptahydrate
Re: [ccp4bb] Unknown Ligand Density
First thing to check - is there any anomalous scatterer peak in the density? Easy to do an anom diff map from GUI2 - choose REFMAC and add - do anom diff fourier, then follow with a diff peak search in COOT . Eleanor On 14 June 2017 at 18:04, Sanishvili, Ruslan wrote: > Difficult to guess from what is visible of the protein but is this density > on a two-fold axis? > > Or, it could be Slimer the ghost... > > Cheers, > > Nukri > > > Ruslan Sanishvili (Nukri), Ph.D. > Macromolecular Crystallographer > GM/CA@APS > X-ray Science Division, ANL > 9700 S. Cass Ave. > Lemont, IL 60439 > > Tel: (630)252-0665 <(630)%20252-0665> > Fax: (630)252-0667 <(630)%20252-0667> > rsanishv...@anl.gov > > > > -- > *From:* CCP4 bulletin board on behalf of Nick > Thomas > *Sent:* Wednesday, June 14, 2017 11:39 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Unknown Ligand Density > > Dear CCP4bb, > > I am refining a structure and have come across strong electron density for > an unknown ligand (image attached). Would someone be able to identify > this unknown ligand that somehow was co-purified with the protein. > > > The electron density shape does not match anything included in the > crystallization conditions. > > > The crystallization condition is > 0.1M MES monohydrate, pH 6.5, 1.6 M Magnesium sulphate heptahydrate >
Re: [ccp4bb] Unknown Ligand Density
Difficult to guess from what is visible of the protein but is this density on a two-fold axis? Or, it could be Slimer the ghost... Cheers, Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: CCP4 bulletin board on behalf of Nick Thomas Sent: Wednesday, June 14, 2017 11:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unknown Ligand Density Dear CCP4bb, I am refining a structure and have come across strong electron density for an unknown ligand (image attached). Would someone be able to identify this unknown ligand that somehow was co-purified with the protein. The electron density shape does not match anything included in the crystallization conditions. The crystallization condition is 0.1M MES monohydrate, pH 6.5, 1.6 M Magnesium sulphate heptahydrate
Re: [ccp4bb] unknown ligand density
Hi It helps to see the environment of the blob, and to know what the resolution is - this *looks* like mid-range resolution (like maybe 2.4A) but because there is no reference in the image the size can be very misleading. Also, contour levels are good to know. Basically, more information. Artem www.harkerbio.com "from blobs to ligands, Gungam-style" - Cosmic Cats approve of this message On Tue, Mar 14, 2017 at 2:03 PM, Dr A.A. Jalan wrote: > Dear all, > > Could anyone suggest possible ligands to explain the density in attached > images. The crystals were grown in NaNO3, PEG 3350 and cryoprotected with > Glycerol. > > Thank you > > Abhishek > >
[ccp4bb] unknown ligand density
Hello all, I have a structure of my protein at 1.3 Ang. There is a clear density in the binding site but I can't seem to figure out what the ligand is. The crystalization conditions contain PEG, sulfate, TMAO and acetate buffer. The protein was purified by a Ni-NTA column and went into phosphate buffer after that. The ligand appears is interacting with a histidine and a water atom and is most likely acetate. Pictures can be viewed at www.xtalmerski.tumblr.com. However, there seems to be an additional atom on the acetate, which would be the easy answer but the buffer was of the 99+% purity (admittedly from Sigma) so I doubt that enough proprionic acid would make it through to account for 100% ligand occupancy. I also looked at TMAO decomposition by NMR under the same conditions for twice as long as the time it took to grow crystals and there was no apparent decomposition (which is 95% by NMR of course). A possible precendent in the literature for TMAO rearrangement requires a homolytic decomposition to formaldehyde and then formation of the new product to get oxygen migration which may be a bit of a stretch to suggest as a new enzyme catalyzed reaction Plus, refinement with that product isn't perfect either as the nitrogen has too many electrons to be in the tertiary center to fit this density. So, has anyone seen or heard or can imagine a way to get an extra atom on acetate? Thanks for any help you can give. Matthew Merski Post-doc Shoichet Group UCSF
