My arrival to Shanghai Pudong airport will be around 05:45 am.So can I get into shuttle bus line 5 to local railway station, right?

Yes, you are right and you can take the shuttle bus line 5.
I do not think you can catch the first bus and maybe you need to take the second one. The bus' interval is around 15 to 25 minutes.
From the airport to the railway station, it takes about an hour to an hour and thirty minutes. The bus fare is around 30RMB.