The plasmid is permitted to replicate in Agrobacterium, but with low copy number. Isolation of plasmids from Agrobacterium mostly give you low amount of DNA. Generally, people use E Coli to produce enough plasmids for digestion, sequencing and transformation. Once the digestion and sequence are verified correct; then it is used to transfer into Agrobacterium for genetic transformation. The selection marker will be used to identify those Agrobacterium colonies harboring the plasmids. There are also kits such as Qiagen Maxi and Mega prep kits available, if you really need to isolate high quantity of plasmids from Agrobacterium.