You are getting a bit confused on the specs
- PCI-e slots will run at either x1 x4 x8 or x16 (this is the number of lanes the card will use to interconnect with the MOBO and does not deal with speed - so the x16 slot will be fine and will run the card at its full capacity.
As explained by the WIKI :
The PCIe 2.0 standard doubles the per-lane throughput from the PCIe 1.0 standard's 250 MB/s to 500 MB/s. This means a 32-lane PCI connector (x32) can support throughput up to 16 GB/s aggregate. The PCIe 2.0 standard uses a base clock speed of 5.0 GHz, while the first version operates at 2.5 GHz.
PCIe 2.0 motherboard slots are fully backward compatible with PCIe v1.x cards. PCIe 2.0 cards are also generally backward compatible with PCIe 1.x motherboards, using the available bandwidth of PCI Express 1.1. Overall, graphic cards or motherboards designed for v 2.0 will be able to work with the other being v 1.1 or v 1.0.
SO in your case the gts 250 will not fully saturate even a PCI-e 1.0 standard slot (It does not run at more than 4Gb\s throughput so will not fully use the available capacity) -so you will not notice any slow down due to using an older mobo -- The only time it will become a problem is if you have a card that can handle more than 4 GB\s throughput and then a PCI-e 2.0 spec MObo that can handle 8Gb\s throughput on a PCI-e x16 slot would help !)