Autonomy is the frontier of research in robotic surgery and its aim is to improve the quality of surgical procedures in the next future. One fundamental requirement for autonomy is advanced perception capability through vision sensors. In this paper, we propose a novel calibration technique for a surgical scenario with da Vinci robot. Calibration of the camera and the robot is necessary for precise positioning of the tools in order to emulate the high performance surgeons. Our calibration technique is tailored for RGB-D camera. Different tests performed on relevant use cases for surgery prove that we significantly improve precision and accuracy with respect to the state of the art solutions for similar devices on a surgical-size setup. Moreover, our calibration method can be easily extended to standard surgical endoscope to prompt its use in real surgical scenario.