Due 18 September, 2025
1
What is the file size in bytes of the passwd file (/etc/passwd) on our machine? Is the passwd file marked as executable? Can you read the contents of the passwd file? Is this a security concern?
2
Use the File Transfer Protocol to get a structure of T4 lysozyme (file pdb2lzm.ent) from the Protein Data Bank in Japan (host ftp.pdbj.org, login as anonymous). Classic PDB files are found in the directory /pub/pdb/data/structures/all/pdb/. Verify your success by presenting the reference to the paper publishing this structure (hint: you'll find the reference in the JRNL records).
3
What is the range of nominal resolution (small to large, Res column in the PDBselect list) for X-ray structures (Methd = X) in the
current PDBselect list to two decimal places? Provide not only the range, but also the command line(s) used to generate these data.
4
They say, "the dog is man's best friend." And while dogs are certainly nice for fetching slippers or as a hunting companion, they don't contribute much to biomedical research.
That's the domain of the mouse.
The PDB reflects the valuable contribution of the humble laboratory mouse—there are 1523 single chain structures of Mus musculus proteins currently in the PDB.
Single tryptophan proteins are holy grail of intrinsic fluorescence studies in biological chemistry. Each student has an archive of fifty single chain protein structures from Mus musculus. In each archive is one protein which has a single tryptophan in its sequence. Report the PDB code of that protein and explain how you found it.
Details on dealing with this file are given below. Some program output is omitted.
[user@451 ~]$ wget https://biochemistry.prof/451/ps/ps01/222222.tar.gz
[user@451 ~]$ tar zxvf 222222.tar.gz
[user@451 ~]$ cd 222222
[user@451 222222]$ ls *.pdb | wc -l
50
[user@451 ~]$
Last updated at 08:39:49 on 2025-12-04.
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