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After I have fiddled with the folders /usr/bin, /usr/lib and /usr/lib64 I restored them, but was not able to su into root (and probably other accounts too):

Permissions on the password database may be too restrictive

This error shows only for unprivileged users. Furthermore this causes problems with programs that require root privileges too, therefore rendering me unable to "switch" into administration mode from my normal user account.

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It turned out that this was caused by the fact that not all permissions had been restored. Specifically the setuid bit on /usr/bin/su was not set.

After fixing this (as root) with:

chmod u+s /usr/bin/su

I was able to su as an unprivileged user and use the graphical tools that rely on root permissions.

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