Finding a search model:TOXD

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Tutorial authored by Nick Keep

Models for molecular replacement are found by database searching. When solving a new structure, you would need to search with your sequence(s) against the protein databank to find a model structure. This can be done in a number of places. The toxd sequence is


  1. Go to the search page on the RCSB website
  2. Find the option to search by sequence in the pull-dowm menu and paste the sequence into the query window, and run the search
  3. The top hit will be the structure of toxd itself. In real life you would be disappointed to find your target structure at the top of the list! Download the three lower homology models 1DEN, 1BF0 and 1TFX onto your computer. There are a number of different ways to do this:
    • Click on the text icon and then when the text window opens, use the right mouse to save page to disk, or
    • Click on the icon with the pale blue download arrow, which will give you a gzipped pdb file. You will need to unzip this file before using it.
  4. Take note of the homology and the chain(s) to which the homology applies
  5. View the structures in a graphics program (e.g. rasmol, xtalview, coot)
  6. For one of the PDB files you will need to select the chains you want for your model. You can just edit the PDB file in a text editor or you can use the Edit PDB File utility in ccp4i under Coordinate Utilities. Select pdbset as the program to perform a selection for output as a pdb file. You need to check select by chain name and enter the chain of choice.
  7. It is a good idea to remove waters from a PDB file before using it as a model, as these are unlikely to be structurally conserved between model and target. Phaser removes these automatically, but other molecular replacment programs do not. Run pdbset on all three files as above but this time to Exclude water molecules.
  8. View the edited structures in a graphics program (e.g. rasmol, xtalview, coot) to double check that you have the model you intended to get
  9. Retry the molecular replacement with the above search models
    • How does Phaser handle the multiple models given for an NMR structure?
  10. Is the success of molecular replacement related to sequence identity?
    • Consider the structure solution method. Why do NMR models make poor molecular replacement models?