HI Jiyong, If you still have protein left, you may try to sequence it. In some cases, even N-terminal digestion is very helpful. In my previous, I always got a 90KDa protein, which was very close to my target kinase. Based on the protein sequencing, we identified it was one of those chaperones.
Best, Kevin On Sun, Dec 17, 2017 at 11:39 PM, Jiyong Su <sujy...@nenu.edu.cn> wrote: > Dear Pedro Matias, > > Thanks for you advice. > > After I manually changed the side chain of the residues, I got a > "artificial" primary structure. I did a blast by using this primary > structure. > Finally, I found the amino acid sequence of this protein. The electron > density could perfectly match the sequence. > BTW, this protein is from a lovely weird bacteria which was cultured by a > student. > > Best regards, > > Jiyong > > > > > -- > Yours Sincerely, > > Jiyong Su > > The School of Life Sciences > Northeast Normal University > Changchun 130024, China > Email: sujy...@nenu.edu.cn > Tele: + 0086 13244318851 > > > > > 在 2017-12-14 21:08:57，Pedro Matias <mat...@itqb.unl.pt> 写道： > >Hello, > > > >Welcome to the club of unexpected results! > > > >You don't provide a lot of background, but based on what you wrote you can: > > > >1. Do a BLAST search using a known part of your sequence to find whether > >this sequence has been deposited. > > > >2. Assign the different residues based on the chemical environment and > >electron density and refine the structure. > > > >I'm sure you can submit the refined structure to the PDB even from an > >unknown protein. > > > >Regards, > > > >Pedro Matias > > > > > >Às 12:08 de 14/12/2017, Jiyong Su escreveu: > >> 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 > >> > > > >-- > > > >Industry and Medicine Applied Crystallography > >Macromolecular Crystallography Unit > >___________________________________ > >Phones : (351-21) 446-9100 Ext. 1669 > > (351-21) 446-9669 (direct) > > Fax : (351-21) 441-1277 or 443-3644 > > > >email : mat...@itqb.unl.pt > > > >http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography > >http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit > > > >Mailing address : > >Instituto de Tecnologia Quimica e Biologica António Xavier > >Universidade Nova de Lisboa > >Av. da República > >2780-157 Oeiras > >PORTUGAL > > > >ITQB NOVA, a great choice for your PhD > >https://youtu.be/de6j-aaTWNQ > > > >Master Programme in Biochemistry for Health > >https://youtu.be/UKstDCFjYI8 > > > -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/
