[ccp4bb] Unexplainable Density
While building our crystal structure model we encountered density which we weren't able to assign. The unknown molecule/molecules seems to coordinate a Ni^2+ -ion. This ion is also coordinated by a histidin and probably one H_2 O-molecule. The crystals have been grown from a protein-complex including the carotinoid peridinin, the lipid DGDG and Chlorophyll. Besides this the solution in which they have been grown contains Tris pH 8.5, NiCl_2 and PEG 2000 MME. The linked images show a rotation around the density in 90°-steps (1.1A, 1.2sigma contour level). The above mentioned H_2 O-molecule has been removed. It is supposed to fill the density that is below the Ni^2+ -Ion in the first picture. Images: http://www.bioxtal.rub.de/myst.html.en Any hints are welcome =) Mario
Re: [ccp4bb] Unexplainable Density
You might be interested in some work done on NikA, which binds a nickel complex with a small organic ligand. They tentatively identified the ligand as butane-1,2,4-tricarboxylate. http://www.rcsb.org/pdb/explore.do?structureId=3e3k Good luck, Arthur On Aug 8, 2012, at 4:56 AM, Mario Sniady wrote: While building our crystal structure model we encountered density which we weren't able to assign. The unknown molecule/molecules seems to coordinate a Ni2+-ion. This ion is also coordinated by a histidin and probably one H2O-molecule. The crystals have been grown from a protein-complex including the carotinoid peridinin, the lipid DGDG and Chlorophyll. Besides this the solution in which they have been grown contains Tris pH 8.5, NiCl2 and PEG 2000 MME. The linked images show a rotation around the density in 90°-steps (1.1A, 1.2sigma contour level). The above mentioned H2O-molecule has been removed. It is supposed to fill the density that is below the Ni2+-Ion in the first picture. Images: http://www.bioxtal.rub.de/myst.html.en Any hints are welcome =) Mario
Re: [ccp4bb] Unexplainable Density
From: Mario Sniady [mailto:mario.sni...@bph.rub.de] Sent: Wednesday, August 08, 2012 7:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unexplainable Density It looks like it could be citrate. Is there any possibility of that? John Andersen While building our crystal structure model we encountered density which we weren't able to assign. The unknown molecule/molecules seems to coordinate a Ni2+-ion. This ion is also coordinated by a histidin and probably one H2O-molecule. The crystals have been grown from a protein-complex including the carotinoid peridinin, the lipid DGDG and Chlorophyll. Besides this the solution in which they have been grown contains Tris pH 8.5, NiCl2 and PEG 2000 MME. The linked images show a rotation around the density in 90°-steps (1.1A, 1.2sigma contour level). The above mentioned H2O-molecule has been removed. It is supposed to fill the density that is below the Ni2+-Ion in the first picture. Images: http://www.bioxtal.rub.de/myst.html.en Any hints are welcome =) Mario
Re: [ccp4bb] Unexplainable Density
It is hard for me to visualize density with just screenshots - I like to rotate the image to see the 3d. This is really clear density, however, and you should be able to figure out what it is. As far as I can tell from your images it looks like half of an EDTA with the other half trailing off into the space above. Was your protein exposed to that compound somewhere along the way? Dale Tronrud On 08/08/12 04:56, Mario Sniady wrote: While building our crystal structure model we encountered density which we weren't able to assign. The unknown molecule/molecules seems to coordinate a Ni^2+ -ion. This ion is also coordinated by a histidin and probably one H_2 O-molecule. The crystals have been grown from a protein-complex including the carotinoid peridinin, the lipid DGDG and Chlorophyll. Besides this the solution in which they have been grown contains Tris pH 8.5, NiCl_2 and PEG 2000 MME. The linked images show a rotation around the density in 90°-steps (1.1A, 1.2sigma contour level). The above mentioned H_2 O-molecule has been removed. It is supposed to fill the density that is below the Ni^2+ -Ion in the first picture. Images: http://www.bioxtal.rub.de/myst.html.en Any hints are welcome =) Mario
