Everything, whatever you do in SOA suite runs inside a JTA transactions at runtime (read everything that goes through BPEL, Mediator or is initiated by an adapter)
In SOA Suite 10.1.3 on OC4J - there were two knobs that people could tweak to prolong the time of a jta-transaction. The global jta transaction timeout could be set in transaction-manager.xml.
Now BPEL PM overwrote this setting in its own EJBs - e.g. Dispatcher Bean, Cube Engine and Delivery Bean. So the change could be done in $SOA_SUITE_HOME/j2ee\
As OESB used User Managed Transactions, the setting there was in $SOA_SUITE_HOME\integration\esb\config esb_config.ini - namely through xa_timeout
On weblogic in SOA Suite 11g - the same idea applies, except that the place to set those is little different.
Globally, the transaction timeout can be set via the weblogic console / JTA and for BPEL specific beans, go to deployments / scroll to soa-infra and expand it. Now scroll down to EJBs and find "BPELEngineBean" - in the configuration section, all the way down you find the transaction timeout - set to 300 seconds by default.
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