I would start with 1E4M (residue 361 of chain M) and 1QW9 (170 of
chain B). First show the model and then reveal the electron density.
This promotes a healthy skepticism of PDB models and enforces the
importance of always looking at a model in the context of the map.
For model building I would recommend 2PWJ and 3SQK. In 3SQK the
linker to the His tag in chain B was built using the wrong sequence.
It is fairly easy to build a sequence into the density and then
recognize what the linker actually is. In 2PWJ the wrong sequence was
used up to residue 31. I've never been able to figure out how this
error came to be. Some horrible, horrible mistake was made when
sequencing the gene and the person who built the model believed the
sequence more than the density. The model building required to correct
2PWJ is more challenging since a number of "short cuts" were made
cutting out loops. If I recall, my model has about 10 more amino acids
than the PDB model.
In all of these cases the majority of the resides in each model are
fine. 3SQK has been replaced with a corrected model (4F4J).
Dale Tronrud
On 10/17/2013 06:51 AM, Lucas wrote:
> Dear all,
>
> I've been lecturing in a structural bioinformatics course where graduate
> students (always consisting of people without crystallography background
> to that point) are expected to understand the basics on how x-ray
> structures are obtained, so that they know what they are using in their
> bioinformatics projects. Practices include letting them manually build a
> segment from an excellent map and also using Coot to check problems in
> not so good structures.
>
> I wonder if there's a list of problematic structures somewhere that I
> could use for that practice? Apart from a few ones I'm aware of because
> of (bad) publicity, what I usually do is an advanced search on PDB for
> entries with poor resolution and bound ligands, then checking then
> manually, hopefully finding some examples of creative map
> interpretation. But it would be nice to have specific examples for each
> thing that can go wrong in a PDB construction.
>
> Best regards,
> Lucas
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