She took a pen out of her pocket.

Literal

She [topic-は] pen [object-を] pocket [from-から] took-out.

取り出す is a compound verb (取る 'take' + 出す 'put out') meaning 'to take out, extract, produce from.' Such 取り~ compounds are highly productive: 取り戻す (take back), 取り消す (cancel), 取り替える (replace). から marks the source of the motion. Two katakana loanwords (ペン and ポケット) sit in a single sentence — both early Meiji-era borrowings from English.