2.4 Structure solution and refinement
For Ec ppnP, the diffraction data set was processed and scaled using HKL3000 7. The phase was determined by Selenomethionine-derived Ec ppnP using the program hkl2map8. And all the native ppnP structures are solved by Phaser with the structure of Se-Ec ppnP as the search model 9. Cycles of refinement and model building were carried out using REFMAC5 10, COOT11, and PHENIX 12 until the crystallography reached a reasonable range. The details of data collection and processing are presented in Table 1 . All structure figures were prepared with PyMOL (DeLano Scientific). The coordinates that support the findings of this study have been deposited in the Protein Data Bank with accession codes for 7EYJ for NativeEc ppnP, 7EYK for Se-Ec ppnP, 7EYP for Pa ppnP, 7EYL for St ppnP, and 7EYM for Vc ppnP, respectively.