Catalyzes the dehydration of 6-phospho-D-gluconate to 2-dehydro-3-deoxy-6-phospho-D-gluconate. 6-phospho-D-gluconate = 2-dehydro-3-deoxy-6-phospho-D-gluconate + H2O Binds 1 [4Fe-4S] cluster. Carbohydrate metabolism; Entner-Doudoroff pathway. Belongs to the IlvD/Edd family.