There are several ways how to do this:
1. /rcon PB_SV_Update
2.if you have access via ssh to your server, in pb folder run pbweb.x86( or pbweb.exe )
3.visit this link , download all necessary files and upload them to pb folder . You can find instructions on that link.
4.If your PB Server has enabled Web Interface, go to PB_SV_HttpAddr:PB_SV_HttpPort and there you should find update button