Bringing Structure to Biology
Structure validation practical (1)
Welcome to this practical about structure validation using publicly available resources. The emphasis in this practical is on validation of crystal structures of proteins, but some of the lessons extend to structures determined by other methods, and to structures of biomacromolecules other than proteins.
Assessing the quality of a model is called validation. Validation is something that needs to be done both by producers (crystallographers, NMR spectroscopists, electron microscopists, etc.) and users (biologists, enzymologists, medicinal chemists, etc.) of models. Note that we talk of models rather than structures, since a model is just a simplified representation of a human being's hypothesis of what a molecule looks like (a collection of point atoms, often even ignoring hydrogen atoms).
This practical and the resources it covers should help you to:
- Read papers about protein crystal structures (errr, models) and understand the discussion of the model's quality (and ask relevant questions on this subject after hearing a protein crystallographer give a talk on a particular structure, or after reading a manuscript that you are asked to referee).
- Find or generate quality-related information on a given protein model using web-based databases and servers.
- Use this information to form a general opinion as to the overall quality of the model, as well as of certain aspects of it (e.g., the extent to which the presence or conformation of a bound ligand is supported by the crystallographic data).
- Select the better of a set of related models (assuming there are noticeable differences in the quality of these models), e.g. for purposes of homology modelling, ligand design, mutant design, or molecular replacement calculations.
To do this practical, all you need in principle is a modern browser that supports HTML5 and WebGL. To test this, follow this link: https://www.ebi.ac.uk/pdbe/entry/pdb/2yi7/bound/BZ8 and check if what you then see in your browser looks similar to this image (if you don't see any electron density simply click on any atom in the 3D viewer panel):
The following are useful links that you may want to explore:
- A glossary of terms related to structural quality: http://spdbv.vital-it.ch/TheMolecularLevel/ModQual/index.html
- An introduction to protein crystallography: http://www.ruppweb.org/Xray/101index.html
- List of wwPDB documents and resources related to validation and validation reports: https://wwpdb.org/validation/validation-reports
- Overview of wwPDB Validation Task Forces (VTFs) and their published recommendations: https://wwpdb.org/task/validation-task-forces
- The websites of the wwPDB partners, PDBe (http://pdbe.org), PDBj (http://pdbj.org) and RCSB PDB (https://rcsb.org)
- PDBReport, a collection of quality reports, generated by the program WHAT IF, for all models that have been deposited in the PDB, and an explanation of the WHAT IF output
- An extensive review of validation in protein crystallography: http://scripts.iucr.org/cgi-bin/paper?S0907444999016364
This practical should preferably be carried out in pairs and is self-explanatory. Please write down your answers to the questions on a piece of paper (or type them into a file) so that you can discuss them with your instructor. Have fun!
This is what students who have done this practical have said:
"Hard, but fun!"
"When I get home, I'm going to read my organic chemistry textbook again!"
"When I get home, I'm going to buy an organic chemistry textbook!"
"From now on, I'm going to use the European PDB!"
Please send feedback, corrections, etc. to Gerard Kleywegt.