It sounds natural enough, but "I won't be but a minute" doesn't necessarily imply an intent to purchase, so it strikes me as just a tiny bit odd. In that same situation I would make it clear to the clerk that a) I wanted to buy something (if you stay open another five minutes you can make money) and b) exactly what it was, in order to make the transaction as quick as possible. Sorry, we're closed for the night.
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