Re: [ccp4bb] Different conformation of chains
Dear Shine.star1609, Your structural observation may be really different from the original one. There are several things to do now: 1. Check whether the same interpretation could be possible in the original structure. Are there maps or the original diffraction data? You could also reprocess them. 2. Read the published methods carefully and compare your protocol to the published one. The different structure could be interpreted based on the differences. 3. Have you used the same ligand? If not, both the observations are valid and possible. Analyze the interactions. This would definitely be an additional information for your paper. 4. Different conformations in “the same but opposite” chains are possible and observed also in other structures. Are there more structures of this protein? 5. Is there a possibility to contact the original authors? I am sure that there will be more comments soon. Best regards, Petr Od: CCP4 bulletin board za uživatele S Odesláno: Thursday, October 21, 2021 2:52 AM Komu: CCP4BB@JISCMAIL.AC.UK Předmět: [ccp4bb] Different conformation of chains Dear All, I am working with a protein, the structure of which is already published in the PDB (2 chains in asu) The published structure has a break of around 20 residues. I have crystallized the same protein and saw some density near the gap (20 residues break). I could build 3-4 residues in ChainA and 8 residues in ChainB (in the 20 residue break region). After refinement these showed good density and b factor. But the issue is that in ChainA, it goes straight. While in ChainB, the 8 residues converge into a loop and goes to the other side. The protein is a monomer in solution, is it possible to have different conformation in different chains that is completely opposite. Also the 8 residues (ChainB) that is build now occupies the site where ligand was placed in the published structure. I am not sure how to interpret this (since in ChainA that site is unoccupied as contrast to ChainB). Any thoughts/suggestions will be really helpful. Thanks you To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Different conformation of chains
Hi, if I understood your question correctly, then one of 13 scenarios described here: http://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12 fits your situation and you should be able to handle it in refinement all right. For more specific advice please feel free to contact me directly (off list) with relevant files. Good luck! Pavel On Wed, Oct 20, 2021 at 5:53 PM S wrote: > Dear All, > > I am working with a protein, the structure of which is already published > in the PDB (2 chains in asu) The published structure has a break of around > 20 residues. > > I have crystallized the same protein and saw some density near the gap (20 > residues break). > I could build 3-4 residues in ChainA and 8 residues in ChainB (in the 20 > residue break region). After refinement these showed good density and b > factor. > But the issue is that in ChainA, it goes straight. While in ChainB, the 8 > residues converge into a loop and goes to the other side. > > The protein is a monomer in solution, is it possible to have different > conformation in different chains that is completely opposite. > Also the 8 residues (ChainB) that is build now occupies the site where > ligand was placed in the published structure. I am not sure how to > interpret this (since in ChainA that site is unoccupied as contrast to > ChainB). > > Any thoughts/suggestions will be really helpful. > > Thanks you > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Different conformation of chains
Dear All, I am working with a protein, the structure of which is already published in the PDB (2 chains in asu) The published structure has a break of around 20 residues. I have crystallized the same protein and saw some density near the gap (20 residues break). I could build 3-4 residues in ChainA and 8 residues in ChainB (in the 20 residue break region). After refinement these showed good density and b factor. But the issue is that in ChainA, it goes straight. While in ChainB, the 8 residues converge into a loop and goes to the other side. The protein is a monomer in solution, is it possible to have different conformation in different chains that is completely opposite. Also the 8 residues (ChainB) that is build now occupies the site where ligand was placed in the published structure. I am not sure how to interpret this (since in ChainA that site is unoccupied as contrast to ChainB). Any thoughts/suggestions will be really helpful. Thanks you To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
