Structural determination and refinement

        The crystals of the complex, which grown in the optimized condition [0.1 M Hepes (pH 6.8) and 1.5% PEG-6000] were collected by the cryoprotectant made from mother liquor supplemented with 20 to 30% glycerol before flash-freezing in liquid nitrogen. 

        Datasets of these crystals were collected in BL17U1 of the Shanghai Synchrotron Radiation Facility (China) and processed with HKL2000 and CCP4.The structure of the KdpDE complex was solved by molecular replacement in Phaser. One of the MR templates is from the solved and published structure of KdpE (PDB ID: 4KNY). During the structure determination, considering the whole conformation of KdpE in the two structures is different, we just isolated RD and DBD structures of KdpE (PDB ID: 4KNY), which is helpful to determine the KdpE structure in the KdpD-KdpE complex dataset. And the other is form the KdpD-CA domain structure modeled in Phyre used as reference models, because there is no published KdpD cytoplasmic domain structure currently. After molecular replacement that have initially solved the complex structure, the structure was further refined in Phenix and manually rebuilt in Coot. The quality of the structure was also checked in MolProbity. Details of the data collection and refinement statistics are summarized in table S1. The atomic coordinates of the final KdpDE complex structure reported in this paper have been deposited in PDB (www.rcsb.org) under the accession number 6LGQ and the structure was also released.