PCI-e x16 is for videocards and such, if you have two then you can run an SLI or CrossFire setup (two graphic cards; depending on the motherboard/cards).
If it has an Nvidia Chipset (680i/750i/780i) it will do SLI, if it's an Intel chipsets with atleast two PCI-e slots (preferably x16 ones) it will do CrossFire.
Though I'd advise to take a Q6600 or Q6700 and overclock it (q6600 only, Q6700 doesn't need overclocking to keep up with the Q9450) a bit, Q9450 is overpriced.
Though that P5E3 is only capable of running DDR3 memory, which is more expensive then DDR2 though it's better (but not all that much is you ask me). And it's an Intel chipset so it won't run SLI but only CF.