Remove the LDR from the PIR sensor.
Use the Arduino to read darkness levels (using LDR or other light sensor).
When dark enough have it switch on the sensor: high side PNP transistor or logic level P-MOSFET in the Vcc line to the sensor (LOW signal will switch ON the sensor, HIGH signal switches it off).
Or if you mean have the Arduino respond to the PIR signal:
Remove the LDR from the PIR sensor.
Use the Arduino to read darkness levels (using LDR or other light sensor).
When dark enough start acting on the signal coming from the sensor, otherwise simply ignore it.