Here the procedure to use Let’s Encrypt certificate with freeIPA

Download isrgrootx1 certificate:

# wget https://letsencrypt.org/certs/isrgrootx1.pem.txt
# mv isrgrootx1.pem.txt isrgrootx1.pem

Download letsencryptauthorityx3 certificate:

# wget https://letsencrypt.org/certs/letsencryptauthorityx3.pem.txt
# mv letsencryptauthorityx3.pem.txt letsencryptauthorityx3.pem

Install CA to freeIPA

# ipa-cacert-manage install isrgrootx1.pem -n ISRGRootX1 -t ,,
# ipa-cacert-manage install letsencryptauthorityx3.pem -n letsencryptx3 -t C,,

I added DSTRootCAX3 certificate, but I'm not sure if it's necessary

# crete a file DSTRootCAX3.pem with the content of 
https://www.identrust.com/certificates/trustid/root-download-x3.html
# ipa-cacert-manage install DSTRootCAX3.pem -n DSTRootCAX3 -t ,,

Update certificates

# kinit admin
# ipa-certupdate

Install Let’s Encrypt certificate (I used a DNS-01 challenge: 
http://letsencrypt.readthedocs.io/en/latest/challenges.html)

# ipa-server-certinstall -w -d /etc/letsencrypt/live/your.doma.in/privkey.pem 
/etc/letsencrypt/live/your.doma.in/fullchain.pem --pin=

Restart the system

# systemctl restart httpd.service
# systemctl restart dirsrv@BLACKPOINTS-CH.service

or 

# ipactl restart

That's all
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