I want to read out the taxonomy id of the source organism of a pdb entry using the xml-file of the entry that is provided under http://files.rcsb.org/view/{pdb_accession}-noatom.xml.

I have so far found the taxonomy id in the tag PDBx:entity_src_genCategory (example entry 1UKV) but also in the tag PDBx:entity_src_natCategory (example entry 2BWI).

XML for 1UKV with PDBx:entity_src_genCategory

  <PDBx:entity_src_gen entity_id="1" pdbx_src_id="1">
     <PDBx:gene_src_common_name>baker&apos;s yeast</PDBx:gene_src_common_name>
     <PDBx:host_org_species>Escherichia coli</PDBx:host_org_species>
     <PDBx:pdbx_gene_src_scientific_name>Saccharomyces cerevisiae</PDBx:pdbx_gene_src_scientific_name>
     <PDBx:pdbx_host_org_scientific_name>Escherichia coli BL21(DE3)</PDBx:pdbx_host_org_scientific_name>

XML for 2BWI with PDBx:entity_src_natCategory

  <PDBx:entity_src_nat entity_id="1" pdbx_src_id="1">
     <PDBx:pdbx_organism_scientific>ACHROMOBACTER CYCLOCLASTES</PDBx:pdbx_organism_scientific>

What is the difference between them? Are there other tags that contain information about the source organism of the entry? Can they occur together in one file? If so, is one of them more valid?


1 Answer 1


src_nat = isolated directly from a natural tissue

src_gen = the source was genetically manipulated

The files that you use (PDBML/XML) are derived from the primary PDB data format which is PDBx/mmCIF. The names in XML seem to correspond to mmCIF names, so you can read documentation on http://mmcif.wwpdb.org/, and here are direct links:

Can they occur together in one file? I suppose they can for complexes: one "entity" could be natural and another genetically manipulated.


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