What this paper is saying is that the researchers found a new gene with little similarity to known DNA-binding proteins, and showed that it's both a DNA-binding protein, and that it binds specific DNA sequences. An implication is that we might not know as much as we think we do about the kinds of proteins that bind to DNA, since we're still finding new stuff. However, for all we know, this protein could work just like one of the known DNA-binding proteins, just using a different protein sequence. That would be weird, but not exceptionally weird.
It's possible that this is a pretty rare find, and that we really do know most of the basic protein structures that bind DNA sequences. But at the same time...there are tons of weird microbes out there whose genes we know nothing about. The world is a big place.
That said, we're still not any closer to making velociraptors.
Proteins are immensely cool.
When I worked in structural bio, one of my colleagues was studying a protein [complex] that had a prominent structure homologous to a helicase, but no DNA-unwinding activity whatsoever. To this day it's unknown what that structure does.
I'm excited to more progress linking structure to function, even if this is very very difficult.
My point: great comment, makes me want to learn.
in terms of predicting the protein's structure, the challenge is the sheer number of computations, the dynamics the protein goes through, and the effects of any environmental factors as the protein is synthesized or folded.
i spent much of a decade (mid 90's to early 00s) studying folding with an aim to getting into enzyme engineering. fun stuff, but i have since left biochem.
The title would be better if it said "protein family" or "protein class". New transcription factors are discovered fairly often. Humans have around ~2K transcription factors. New families, less often.