Rubén, the previous answer probably addresses your problem accurately.
However. If your protein of interest modifies DNA/RNA, it is quite common that your pET constructs will mutate rapidly in E.coli. Lac operons tend to leak quite a bit, which is not enough to detect the protein prior to induction but can definitely drive the selection for mutated plasmids in E.coli. We saw that behavior in a nuclease cloned from homogeneous genomic DNA. Every colony had a different mutant when grown on LB. Also mutants that do not appear to affect the enzyme activity judged by the structure. We assumed, that any mutation that slightly reduces the toxicity for E.coli will be selected for. So, if you experience the same issue again with synthetic DNA, or have the patience to repeat, try adding ~1% glucose to all media, liquid and solid. This will tighten up the Lac operon and worked well for our nuclease project. You still have to sequence every batch you purify. pLysS cells can also work, but we still ended up adding glucose because it is cheap and doesn't cause trouble downstream. Stefan
