Crates can only be opened or closed with objects residing inside of them, Certain objects are "bad" however and do not fully sit inside the crate - You should not try to have something locked inside a crate that is larger than the crate as a result of this. It can result in "problems"
There's also an issue of "Something" in the "air" triggering the ability to close a crate.
resist doing so, This is a fool's choice.
It may become hard to open the crate later since nothing but air is inside of it, and it may even start to exhibit gravity issues, Spirally away from your hand in odd ways, or floating around like a crystal.
under normal circumstances though, You won't be able to open or close it if nothing is in it, the prompt appears (generally) when you put ore into it (as that's its most common use) and will remain present as long as items are inside it
If you must carry something bigger than the crate, ensure something smaller than the crate is also inside the crate, in a fairly central location, as it can be pushed to the limits if not.