One was Electro-Motive Sibanye, a joint venture between the recently established Electro-Motive Diesel (EMD) and Sibanye Trade and Services, a South African Black Economic Empowerment (BEE) company which dealt in locomotives and spare parts.

Furthermore, when serious tender irregularities came to light, the locomotive rebuilding deal between Transnet and Sibanye was cancelled.

It was later hired or leased to the Khumani iron ore mine in the Northern Cape, where it was renumbered again to LC9-1.

These five were tested and approved by Transnet and placed in service between April 2006 and 2009 as the Class 39-000, numbered in the range from 39-001 to 39-005.

[2][7][8] Improvements over the pre-rebuilt locomotives which were realised in the Class 39-000 include microprocessor control, 26% more maximum continuous tractive effort and 15% more tractive horse-power, and a Knorr-Bremse electronic brake rack (EBR) to replace the old pneumatic braking controls.

By 2013, once the Class 39-200 locomotive fleet had also entered service, they were redeployed to the Thabazimbi iron ore line and shedded at Pyramid South.