TheDalet of the word 'echad' is made larger than the other letters. Indeed the the ruling is that it must be 4 times the size of a normal Dalet (though usually this is not the case as mezuzot are generally small). It is large to ensure that the word is not read as 'acher' meaning (heaven forbid) [God is] 'another'.
ed - witness

 In addition the custom is also to enlarge the letter Ayin so that both letters together read as 'ed' (witness) to complement the aural idea of Shema (hear).