1- Decrease the IPTG concentration (try different IPTG concentration in small volume cultures 0.2 mM- 0.5 mM).
2- Decrease the temperature, try 18 or 25C instead of 37C and increase the induction time to 18-24 hours.
3- Test these conditions in 5 ml volume first. Then check your protein in different conditions with dot plot if you have the antibody for HSP90. If you have a tag on protein you can check the tag with its Ab too. (with SDS page you could not check 50 conditions at the same time. If you have a signal in any dot plot, try that condition/s for further experiments)
The idea of decreasing the temperature and IPTG concentration also decrease the growth rate of bacteria and induction rate of Lac operon respectively. In this way, you can give the time to bacteria for completing the whole protein. your protein is 90kDa and it needs time to be completed.
Thanks a lot for your valuable comments. I tried with decreased IPTG concentration but did not check with decreased temperature. I shall definitely do that. Thanks Again.