This isn't a new topic, we covered PDFs and duplicate content before, but this morning John Mueller was more specific.
On Twitter John Mueller of Google said that if you offer a PDF download link that lets users download the web content they are looking at, it is not a problem with Google.
So for example, if I offer a link to download this exact page's content as a PDF, Google would not see that as duplicate and shouldn't hurt your rankings at all.
Here are the tweets:
@davebuts I don't see a problem with that. If your users are also consuming your content like that, then go for it.
— John Mueller (@JohnMu) August 11, 2016
Yes, John Mueller went with the do what is best for the user response here by saying "If your users are also consuming your content like that, then go for it."
Forum discussion at Twitter.