Re: [ccp4bb] Crystal structure of an unknown protein
To keep this thread on topic - there is no Blue Stone on the Galveston island. Lots of white sand beaches, lots of black birds, lots of new BMW cars in the port (they unload the ship here), a few oil rigs, an occasional cruise ship, but no Blue Stone… Petr Petr Leiman University of Texas Medical Branch Department of BMB Basic Sciences Building 6.600D 301 University Blvd Galveston, TX 77555-0647 Cell: 832 908 6635 Office: 409 747 2078 https://scsb.utmb.edu/faculty/Leiman.asp > On Dec 16, 2017, at 4:42 PM, Anastassis Perrakis wrote: > > > I wonder why you assume know there are "about 20 point mutation sites” if > "this protein is an unknown protein”. > It looks like you are comparing the sequence of a protein you do not know > what it is to the sequence of a protein you dont really know what it is (1). > > I would consider it more likely, it is the E. coli protein and the electron > density is ambigious so some side chains might have been erronously assigned > to a false identity. > > A. > > (1) > Percy: You know, they do say that the Infanta's eyes are more beautiful than > the famous Stone of Galveston. > Edmund: Mm! ... What? > Percy: The famous Stone of Galveston, My Lord. > Edmund: And what's that, exactly? > Percy: Well, it's a famous blue stone, and it comes ... from Galveston. > Edmund: I see. And what about it? > Percy: Well, My Lord, the Infanta's eyes are bluer than it, for a start. > Edmund: I see. And have you ever seen this stone? > Percy: (nods) No, not as such, My Lord, but I know a couple of people who > have, and they say it's very very blue indeed. > Edmund: And have these people seen the Infanta's eyes? > Percy: No, I shouldn't think so, My Lord. > Edmund: And neither have you, presumably. > Percy: No, My Lord. > Edmund: So, what you're telling me, Percy, is that something you have never > seen is slightly less blue than something else you have never seen. > > >>> Dear CCP4bb, >>> In 2014, I collected a high quality data set from a crystal. But I could >>> not solve the structure of that crystal because this protein is a >>> contaminate. >>> Recently, I used StruBE's Contaminer and fortunately got the solution. >>> Thanks ContaMiner!!! This protein is a contaminate protein. >>> However, I found this protein is an unknown protein (about 180 residues) >>> whose amino acid sequence is not totally same as E.coli. There are about 20 >>> point mutation sites comparing to the E.coli protein. This means this >>> protein may be from an unknown bacteria. >>> The space group of this crystal is new. There is also a new ligand in this >>> protein. >>> My question is how could I found the primary structure of this protein and >>> how to deposit this protein in PDB. >>> Best regards, >>> Jiyong >> >> >
Re: [ccp4bb] Crystal structure of an unknown protein
I wonder why you assume know there are "about 20 point mutation sites” if "this protein is an unknown protein”. It looks like you are comparing the sequence of a protein you do not know what it is to the sequence of a protein you dont really know what it is (1). I would consider it more likely, it is the E. coli protein and the electron density is ambigious so some side chains might have been erronously assigned to a false identity. A. (1) Percy: You know, they do say that the Infanta's eyes are more beautiful than the famous Stone of Galveston. Edmund: Mm! ... What? Percy: The famous Stone of Galveston, My Lord. Edmund: And what's that, exactly? Percy: Well, it's a famous blue stone, and it comes ... from Galveston. Edmund: I see. And what about it? Percy: Well, My Lord, the Infanta's eyes are bluer than it, for a start. Edmund: I see. And have you ever seen this stone? Percy: (nods) No, not as such, My Lord, but I know a couple of people who have, and they say it's very very blue indeed. Edmund: And have these people seen the Infanta's eyes? Percy: No, I shouldn't think so, My Lord. Edmund: And neither have you, presumably. Percy: No, My Lord. Edmund: So, what you're telling me, Percy, is that something you have never seen is slightly less blue than something else you have never seen. >> Dear CCP4bb, >> In 2014, I collected a high quality data set from a crystal. But I could not >> solve the structure of that crystal because this protein is a contaminate. >> Recently, I used StruBE's Contaminer and fortunately got the solution. >> Thanks ContaMiner!!! This protein is a contaminate protein. >> However, I found this protein is an unknown protein (about 180 residues) >> whose amino acid sequence is not totally same as E.coli. There are about 20 >> point mutation sites comparing to the E.coli protein. This means this >> protein may be from an unknown bacteria. >> The space group of this crystal is new. There is also a new ligand in this >> protein. >> My question is how could I found the primary structure of this protein and >> how to deposit this protein in PDB. >> Best regards, >> Jiyong > >
Re: [ccp4bb] Crystal structure of an unknown protein
Hi Jiyong, Try running the FITMUNK server in the sequencing mode: http://witold.med.virginia.edu/fitmunk/server/ More information on using FITMUNK to identify your protein: https://www.ncbi.nlm.nih.gov/pubmed/26894674 And here: https://www.ncbi.nlm.nih.gov/pubmed/26660914 Ivan With best regards, Ivan Shabalin, Ph.D. Research Scientist, Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Pinn Hall,Room 4223, Charlottesville, VA 22908 On 12/14/2017 07:08 AM, Jiyong Su wrote: Dear CCP4bb, In 2014, I collected a high quality data set from a crystal. But I could not solve the structure of that crystal because this protein is a contaminate. Recently, I used StruBE's Contaminer and fortunately got the solution. Thanks ContaMiner!!! This protein is a contaminate protein. However, I found this protein is an unknown protein (about 180 residues) whose amino acid sequence is not totally same as E.coli. There are about 20 point mutation sites comparing to the E.coli protein. This means this protein may be from an unknown bacteria. The space group of this crystal is new. There is also a new ligand in this protein. My question is how could I found the primary structure of this protein and how to deposit this protein in PDB. Best regards, Jiyong
[ccp4bb] Electrostatic Potential: Poisson-Boltzmann criteria
Hi I am just calculating the Electrostatic Potential, and I wanted to know your opinion which force field is better.What is criteria to choose and not to choose the pKA... best Jiri
