The domain of the store www.example.com
is connected to the folder where the website located. You can specify it with your hosting team.
All you need to do is to locate the file in your store folder (or create an additional one there, like "PDF") and set proper permissions so it could be available for all customers (777 if you don't mind about sharing it with all).
As a result you will access it as:
a) domain connected to the store folder - www.example.com/pdf_file.pdf
b) domain is connected to the root so store is located at - www.example.com/store/pdf_file.pdf