We extend a recently proposed dipole model which relates the virtual photon-proton cross section to the dipole-proton forward scattering amplitude in momentum space investigating the effects of the gluon number fluctuations. The model interpolates between well known asymptotic behaviours predicted by perturbative QCD from the Balitsky-Kovchegov equation, which describes the rapidity evolution of the dipole-proton scattering amplitude in the mean field approximation. The model was shown to be successful in describing the last HERA data for the case where the strong coupling constant αs is fixed, showing also some important advantages when compared with other dipole models - all of them in coordinate space - in the literature. Based on the fact that the fluctuations may be important in the small-x evolution and on recent results obtained in coordinate space beyond the mean field approximation, we use this model to parametrize the proton structure function and confront it to HERA data using the average (physical) amplitude - then including fluctuations - within the momentum space framework.