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An iron-sulfur protein that contains either a [3Fe-4S] or a [4Fe-4S] cluster. This enzyme comprises a system in which ferredoxin is first reduced and subsequently reoxidized by an NAD(P)+-dependent reductase. This is the last enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. This pathway, also known as the 1-deoxy-D-xylulose 5-phosphate (DOXP) or as the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway, is found in most bacteria and in plant chloroplasts. The enzyme acts in the reverse direction, producing a 5:1 mixture of isopentenyl diphosphate and dimethylallyl diphosphate.