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Before episode one I figured C-3PO was a special protocol droid built by governments for governments. Considering he is in the company of an ambassador.

If we are to believe that a young impoverished slave boy assembled C-3PO from miscellaneous parts, where did Anakin acquire a database with over 6 million forms of communication?

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Anakin did not actually build C-3PO. He rebuilt him.

From Wookieepedia:

Originally activated on Affa in 112 BBY, C-3PO had served as a protocol droid to the emissary of the Manakron system. Nearly eighty years later, he was gutted and discarded on the streets of Mos Espa, a city on the Outer Rim world of Tatooine. After being rebuilt by the Human slave Anakin Skywalker, C-3PO served Skywalker and his mother Shmi for over ten years, performing household chores and helping Skywalker earn his freedom by winning a pod race.

So your assumption was correct: C-3PO was built by a government for government use, and his first use was to accompany an ambassador, much like when we first see him in A New Hope.

When Anakin found him, C-3PO was a head and a gutted chassis. However, he still boasted sound wiring, as well as a standard protocol droid verbobrain and communicator module. The communicator module in particular is where the linguistic skills demonstrated by C-3PO originated:

The TranLang III Communicator module was a late generation communication module incorporating millions of galactic languages, installed in 3PO-series protocol droids and LOM-series protocol droids.

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It appears that the language database was still intact within the TranLang III Communicator module of the discarded robot head that Anakin used to reconstruct C3PO. From Wookieepedia:

[C3PO's] head and gutted chassis had been discarded in a street of the city of Mos Espa on Tatooine, and were discovered by two Human youths, Anakin Skywalker and Kitster Banai.

...

C-3PO's gyro-balance circuitry was several decades old, but Skywalker was able to use scrounged and improvised replacement parts to make the droid functional again. C-3PO boasted sound wiring, as well as a standard protocol droid verbobrain and communicator module, but Skywalker could not afford even the simplest of droid coverings, and as such, left the droid's wiring exposed.

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