The Museum Company Inc., the 99-store chain and Web site, filed for Chapter 11 bankruptcy protection late last month in New York City. According to documents filed with the court, the company, which sells art reproductions, jewelry, music and books, many licensed from museums, has liabilities of $54.6 million and $73.5 million in assets. Some publishers, particularly the high-end gift and art book publishers carried by the firm, such as Workman and Chronicle, are among the company's creditors. To cut costs, Museum Company will close its flagship store on 42nd Street in New York City, as well as seven other stores, by the end of February.