"As a sampling frequency, I have chosen the frequency that I have also set the pulse generator (5Mhz)."
There's your problem; you must sample at least twice the highest frequency in the signal (look up "Nyquist frequency").
Commercial O-scopes sample at much higher multiples than that in their auto modes; the Fmax of the plot you show is 10 MHz; if the scope uses only a simple baseband FFT, then you can presume a sample rate of 20 MHz.
You should be able to also download the sampling parameters from the scope to confirm the settings besides just the time trace values; see the doc for the instrument for how...
Also there's some inconsistency in the frequency vector and normalization; the Matlab FFT is two-sided in frequency; see the example in
to see the generic way to pick the positive frequency and to normalize the one-sided PSD as there is only a single DC and Fmax array element.