To support digital signing certificate must have digitalSignature
option in it's keyUsage
field (and codeSigning
option in it's extendedKeyUsage
field if your want to sign programs with it).
Signing may be done with existing tools or manually (java example, you are not asking for it, but this code snippet might be useful anyway):
byte[] bytesToSign = loadMyData();
KeyStore ks = KeyStore.getInstance("pkcs12", "SunJSSE");
ks.load(new FileInputStream("cert.p12"), "passwd1".toCharArray());
PrivateKey privateKey = (PrivateKey) ks.getKey("myalias", "passwd2".toCharArray());
Signature sig = Signature.getInstance("SHA1withRSA", ks.getProvider());
sig.initSign(privateKey);
sig.update(bytesToSign);
byte[] signature = sig.sign();
To make your own not self-signed certificate with openssl see this SO answer.
Also curious about signing PDF's - aren't separate hash sums of these files enough in your case?
edit: if you want any sign, not exactly X.509 sign by existing tools, you can extract RSA key from your cert and do signing without bothering about keyUsage
field.