To integrate Neo4j Enterprise Edition with an LDAP protocol connector, you need to define settings in the neo4j.conf configuration file, such as specifying the endpoint for the LDAP service and providing details on your user graph structure. The LDAP connector is used to manage federated users, while role-based access control is still performed in Neo4j. You can configure encrypted LDAPS and specify credentials for a special LDAP system account with read access to all users and groups. Proper configuration of the LDAP connector requires settings such as user_dn_template, user_search_filter, user_search_base, group_membership_attributes, and group_to_role_mapping. With the right settings, you can manage your existing directory of users outside of Neo4j while mapping them to pre-defined or custom roles for access to the graph database. The integration allows for easy management of federated users via the LDAP protocol, enabling secure access control and authorization.