Hello, I have a membrane protein complex made up of 8 different polypeptides present in two copies each (16mer). The asymmetric unit is the octamer, as determined from previous crystallographic studies. To carry out molecular replacement with the phases from the published structure in AutoMR, should I specify the coordinates of the search model and its overall sequence identity as one file or should I break it down for each subunit ? Also, for the asymmetric unit contents, should I specify the sequence or mass of each subunit separately (as component 1, 2 and so on) keeping the number of copies fixed at 1 ? There is no NCS. Thanks. -- S. Saif Hasan Graduate Student Department of Biological Sciences Hockmeyer Hall of Structural Biology Purdue University 240 S. Martin Jischke Drive West Lafayette, IN 47907
On Mon, Jun 21, 2010 at 12:49 PM, S. Saif Hasan
I have a membrane protein complex made up of 8 different polypeptides present in two copies each (16mer). The asymmetric unit is the octamer, as determined from previous crystallographic studies. To carry out molecular replacement with the phases from the published structure in AutoMR, should I specify the coordinates of the search model and its overall sequence identity as one file or should I break it down for each subunit ?
If it doesn't have any large conformational changes, using the entire octamer might work. It will certainly be much faster than placing each chain separately, so it's worth trying first anyway. You should run rigid-body refinement afterwards with a rigid group for each chain. If you can't place the octamer, try searching for smaller sub-assemblies before you break it down into individual chains. Also, for the asymmetric unit contents, should
I specify the sequence or mass of each subunit separately (as component 1, 2 and so on) keeping the number of copies fixed at 1 ? There is no NCS.
I think you can just specify the overall mass - regardless of whether you're searching for the entire complex or one chain at a time. -Nat
Hi Saif, If I understand you correctly, you can specify the search model with 8 polypeptides as one PDB file and all 8 sequences (separated by blank lines or lines starting with ">" in one sequence file. Also component 1 can be all 8 polypeptides and copies=1. All the best, Tom T
Hello,
I have a membrane protein complex made up of 8 different polypeptides present in two copies each (16mer). The asymmetric unit is the octamer, as determined from previous crystallographic studies. To carry out molecular replacement with the phases from the published structure in AutoMR, should I specify the coordinates of the search model and its overall sequence identity as one file or should I break it down for each subunit ? Also, for the asymmetric unit contents, should I specify the sequence or mass of each subunit separately (as component 1, 2 and so on) keeping the number of copies fixed at 1 ? There is no NCS.
Thanks. -- S. Saif Hasan
Graduate Student Department of Biological Sciences Hockmeyer Hall of Structural Biology Purdue University 240 S. Martin Jischke Drive West Lafayette, IN 47907
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participants (3)
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Nathaniel Echols -
S. Saif Hasan -
Thomas C. Terwilliger