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
