What does ensemble-based model of enzyme mean?
An 'ensemble' is a set of related models of a structure. 

For example, conformational ensembles describe the structure of flexible proteins. There is a database of such structures here : http://pedb.vib.be/.

When NMR is used to determine a structure, the result is an ensemble of structures (see this paper for a comparison with crystallography). However, it is possible to see multiple structures for crystallography as well. This paper on "Accessing protein conformational ensembles using room-temperature X-ray crystallography" describes limitations to the idea of crystal structures having one unique structure.