My grandpa usually eats breakfast at six.

Literal

I [of-の] grandpa [topic-は], usually [topic-は] 6 o'clock [at-に] breakfast [object-を] takes.

朝食を取る ('to have breakfast') treats the meal as something 'taken' — a common formal expression. Paradox of Japanese: this collocation sounds more literary or formal even though 取る is itself a very basic verb — because pairing 取る with a meal noun is the formal register's signature. You'd see this in news writing or hotel signs more than at the breakfast table.