In an MXF file there are 4 timecode sources:
The most likely and convenient start timecode candidate in an MXF file is the start of the timecode track in the Material Package. In bits and bytes, this is not a timecode but an integer number that represents a number of edit units. In D10 the edit unit is a frame, e.g. 1/25th second in PAL. There are other timecode tracks in the MXF file (notably the one in the File Package) which may be used in certain applications. Furthermore, D10 files must carry a System Item in the Essence Container that contains the timecode of each frame (like a label). In addition to this, many essence streams contain timecode information in the elementary bit stream, but it is not recommended to use these because these are difficult to access and modify.
There is no PTS/DTS/PCR in an MXF file. Instead, for frame-wrapped content such as D10, synchronicity is achieved by interleaving video and audio on a frame-by-frame basis so there can be no confusion about which audio goes with which video.