[ccp4bb] Probable bugs in acedrg

Hi, I have been exploring a PDB model that contains an RNA molecule with a ligand stuck on the 3' phosphate. To perform real-space refinement in Coot I needed to create a standard geometry CIF for the ligand and one for the linkage between the ligand and an Adenine. The CIF for the ligand in

Re: [ccp4bb] Protein fold and the moonlighting function

I think you’re asking if two proteins with the same fold can have different activities. As was previously mentioned, this is quite common. The best characterized example is the TIM barrel fold - such proteins can be isomerases, transferases, hydrolases, lyases, or oxidoreductases, to name a fe

Re: [ccp4bb] Protein fold and the moonlighting function

Hello,  Re: "I think you’re asking about 2 proteins with a similar fold having similar but not exactly the same functions - yes, that does occur." Indeed, I suspect it is very common, if not the norm. OK, so I now gather/remember moonlighting proteins are ones with more than one function - than

[ccp4bb] Post-doctoral position in cryo-EM at IOCB Prague

Job description A fellowship-funded postdoc position is open in Dr Sebastian Zoll’s group at the Institute of Organic Chemistry and Biochemsitry (IOCB) in Prague. Dr Zoll’s group is using a combination of biochemical, biophysical, immunological and structural biology techniques to understand th

Re: [ccp4bb] Mixed oligomeric states in crystallo

5FRT We got scooped on this one a long time ago - but back in 2015 it was very gratifying to see that the academic group who published this structure have also obtained an ASU with two dimers and one monomer - same exact story as what we saw. The difference can be attributed to the movement of a s

Re: [ccp4bb] Mixed oligomeric states in crystallo

Here's a few examples: https://www.rcsb.org/structure/1A2K The crystal has an A3B2 stoichiometry. The paper describes how they find A2B2 in solution, concluding the extra A molecule comes from "fortuitous packing" in the crystal https://www.rcsb.org/structure/2RBL A design protein, but with very

Re: [ccp4bb] Protein fold and the moonlighting function

Hi Rajnandani, I’m happy to help you with questions about moonlighting proteins. My lab created the MoonProt Database (moonlightingproteins.org). I think you’re asking about 2 proteins with a similar fold having similar but not exactly the same functions - yes

Re: [ccp4bb] AW: [ccp4bb] Urea vs. Guanidinium/HCl

Thank you for the clarification! First of all, many proteins will exhibit this sort of behavior when stored in liquid form at moderately low temperature. One solution is to store in glycerol (35 percent and up) at -20C. Or in deep freeze at -80C or in LN2. The one remaining question that would b

Re: [ccp4bb] Protein fold and the moonlighting function

Can you possibly expand a bit on exactly what you are asking?Jon CooperOn 2 Feb 2020 09:28, Rajnandani Kashyap wrote:Dear AllI am curious to know about the promiscuous activity of a protein based on their fold. Can a protein having same fold also have same function (say not 100% but some activity)

Re: [ccp4bb] AW: [ccp4bb] Urea vs. Guanidinium/HCl

Hello, have you tried eluting from nickel-NTA straight into glycerol buffer so the protein has absolutely minimal time on it's own? Also, 10 mg/ml is quite a high concentration in my book. What is in your purification buffer? Just interested. Hope your competitors aren't reading all this! Best wish

[ccp4bb] Post-doctoral position in cryo-EM at IOCB Prague

Job description A fellowship-funded postdoc position is open in Dr Sebastian Zoll’s group at the Institute of Organic Chemistry and Biochemsitry (IOCB) in Prague. Dr Zoll’s group is using a combination of biochemical, biophysical, immunological and structural biology techniques to understand t

Re: [ccp4bb] AW: [ccp4bb] Urea vs. Guanidinium/HCl

Have you tried maintaining the protein in a solution with a low concentration of excess cofactor? Light vs dark? Excess reducing agent or different reducing agent or oxygen-depleted and under argon? John > On Feb 2, 2020, at 4:22 AM, Jon Hughes > wrote: > >  > Thanks for you interest. Ok, h

[ccp4bb] Protein fold and the moonlighting function

Dear All I am curious to know about the promiscuous activity of a protein based on their fold. Can a protein having same fold also have same function (say not 100% but some activity) as the homologous structure. Please also let me know few relevant PDB structures where such kind of activity is sh

[ccp4bb] AW: [ccp4bb] Urea vs. Guanidinium/HCl

Thanks for you interest. Ok, here are some more details. The protein is Cph1 (uniprot Q55168) as a full-length (ca. 80 kDa) holophytochrome, produced with a C-terminal His6 tag together with its co-factor in E. coli, purified via NiNTA and SEC. It is red/far-red photochromic (that is, photoact