If you were to use suPHP, you could allow the script to run under the same user for the script that owns the key.
EDIT:
Based on your clarification (and others comments), it would likely be best to generate a new key specifically for the purpose of your script and give it the permissions of your web user. It is usually best to have a new key set up per user/script.
For more information on why this is best practice, have a look at thisthis and thisthis link.