If you have all pdb files, keep them in a directory, run the following. At the end you will get a file organ.txt, contains the information as follows

3adk
ORGANISM: SUS SCROFA;
5pti
ORGANISM: BOS TAURUS;

Script

#!/bin/bash

for f in *.pdb
do
  sed -n "/ORGANISM_SCIENTIFIC:/p" $f > ""$f".orga"
done

for f in *.orga
do
  echo "$f" >> organisms.txt
  cat $f >> organisms.txt
done

sed "s/.orga//" organisms.txt | sed "s/SOURCE   2 //" | sed "s/_SCIENTIFIC//" > organ.txt

rm *.orga

Otherwise run the following. Keep all ids in a file called pdb_ids.txt. It retrieves the pdb header of every pdb id in your file from PDBeurope database, then the organism name of every id.

pdb_ids.txt

5pti
3adk
..

​Script

#!/bin/bash

while read -r I 
do
  wget -O ""$i".header" "http://www.ebi.ac.uk/pdbe/static/entry/$i.header"
  sed -n "/ORGANISM_SCIENTIFIC:/p" ""$i".header" > ""$i".orga"
done < pdb_ids.txt

for f in *.orga
do
  echo "$f" >> organisms.txt
  cat $f >> organisms.txt
done

sed "s/.orga//" organisms.txt | sed "s/SOURCE 2 //" | sed "s/_SCIENTIFIC//" > organ.txt

rm *.header
rm *.orga

```

Keep the script in a file biostar.bash and execute bash biostar.bash