Re: [ccp4bb] Structure with missing density

Hello Rajesh We serendipitously encountered three cases where a contaminating fungus led to proteolysis of the proteins, which was required for their crystallization. We identified the fungus by sequencing a little bit of its genome, and found that it is Penicillium! Here are two of the papers

Re: [ccp4bb] Structure with missing density

Dear Rajesh, We had a similar problem with a yeast glutaminyl-tRNA synthetase. In eukaryotic systems these have an appended N-terminal domain not present in prokaryotes. When the full length protein was crystallized the last ~200 residues were missing from the structure. A packing diagram (high

Re: [ccp4bb] Structure with missing density

Hi, Long crystallization times and irreproducibility together with missing residues points strongly to some slow proteolysis in your crystal drops that eventually generated a crystallizable fragment. A lot of people actually do this on purpose by adding proteases to generate stable fragments. Here

[ccp4bb] Structure with missing density

Dear BB, I apologize for the off topic. But I strongly believe this is the right place to ask my question. We are working on a protein that is 300 amino acids in length. After many efforts, we could solve the structure at 1.60 Å resolution. It took almost 10 months to get this crystal and we

[ccp4bb] Postdoctoral position In Biochemistry / Microbiology at the University of Minnesota

Dear All, A Postdoctoral position is immediately available in the group of Mikael Elias in the Department of Biochemistry, Molecular Biology and Biophysics at the University of Minnesota, USA. The research at our lab combines structural biology, enzymology, bioinformatics, and microbiology (

Re: [ccp4bb] Building carbohydrates in coot using glyco module

Here I was thinking I had the latest version of coot, but I didn't! I downloaded 0.8.9 and everything is working now. Thanks! Erik From: Paul Emsley Sent: Friday, March 9, 2018 12:57:19 PM To: Erik Klontz Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Building

Re: [ccp4bb] Building carbohydrates in coot using glyco module

On 09/03/2018 17:29, Erik Klontz wrote: I have solved a few Fc crystal structures, and am having trouble building the full length glycans onto them. I've been using the coot "glyco" module which I really like, Glad to hear it. but I don't see any options for adding B(1-2) NAG. I'm using th

[ccp4bb] Building carbohydrates in coot using glyco module

Hi All, I have solved a few Fc crystal structures, and am having trouble building the full length glycans onto them. I've been using the coot "glyco" module which I really like, but I don't see any options for adding B(1-2) NAG. I'm using the latest version of coot on windows. I've seen screen

Re: [ccp4bb] cif questions

On 08/03/2018 17:55, Thomas, Leonard M. wrote: Hello All, Hello Thomas, We have run into a problem recently when working with cif files for ligands that have been either soaked or cocrystallized with the proteins we are looking at.  Most of the ligands cif files have been used previously a

Re: [ccp4bb] cif questions

I’ve just discovered that for Coot 0.8.8, when importing the cif file for the ligand, select All under the “Select Mol” pulldown menu to get the restraints imported properly, then all the Chi angles become available. HTH. Jason On Mar 8, 2018, at 11:55 AM, Thomas, Leonard M. mailto:lmtho...@o

[ccp4bb] Postdoc position at University of Wisconsin-Madison

Dear all, You are invited to apply for a postdoctoral position in the structural biology and functional proteomics lab of McArdle Cancer Institute of University of Wisconsin at Madison. We are interested in understanding the structural basis and mechanisms of protein phosphatase 2A (PP2A) holo