Databases in general are made for handling multiple connections and requests at the same time through locking mechanism. The problem I might see in your scenario is more related to caching on the side of the database client applications.
Refer to the documentation of Hibernate and PDO and understand what and how their caching works.
You might want to check out JPA's @Version annotation. I don't know if PDO has a similar mechanism. If not, you'll have to implement it yourself.
Another option you have would be adding an abstraction layer between the Java side and PHP side, for instance a REST Service. So your PHP and Java clients would talk to the REST service alone and that service will handle database access for you. Has the nice advantage that you can add other client types and languages easily as long as they can talk HTTP.