proteins from an organism

Hello,

I would like to get all proteins from an organism but proteins from
cholorplasts or with chrystal structures or something else.

I tried to obtain these proteins by send a query 'Arabidopsis 
thaliana[organism]'
with Bio::DB::GenBank and fetch the gi numbers from the cds.
But on the one pc I get 6000 proteins and on another pc I get 46000 proteins
although Arabidopsis thaliana has 25000 genes.

Thank you for your help.