<p><code>src_nat</code> = isolated directly from a natural tissue</p>

<p><code>src_gen</code> = the source was genetically manipulated</p>

<p>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 <a href="http://mmcif.wwpdb.org/" rel="nofollow noreferrer">http://mmcif.wwpdb.org/</a>, and here are direct links:</p>

<ul>
<li>category <a href="http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entity_src_nat.html" rel="nofollow noreferrer">entity_src_nat</a></li>
<li>category <a href="http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entity_src_gen.html" rel="nofollow noreferrer">entity_src_gen</a></li>
</ul>

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

CC BY-SA 3.0
2018-01-26T11:31:30.107Z
2018-01-26T11:31:30.107Z
marcin
<p>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 <code>http://files.rcsb.org/view/{pdb_accession}-noatom.xml</code>. </p>

<p>I have so far found the taxonomy id in the tag <strong>PDBx:entity_src_genCategory</strong> (example entry <a href="http://files.rcsb.org/view/1ukv-noatom.xml" rel="nofollow noreferrer">1UKV</a>) but also in the tag <strong>PDBx:entity_src_natCategory</strong> (example entry <a href="http://files.rcsb.org/view/2bwi-noatom.xml" rel="nofollow noreferrer">2BWI</a>).</p>

<p>XML for 1UKV with PDBx:entity_src_genCategory</p>

<pre><code>&lt;PDBx:entity_src_genCategory&gt;
  &lt;PDBx:entity_src_gen entity_id="1" pdbx_src_id="1"&gt;
     &lt;PDBx:gene_src_common_name&gt;baker&amp;apos;s yeast&lt;/PDBx:gene_src_common_name&gt;
     &lt;PDBx:gene_src_genus&gt;Saccharomyces&lt;/PDBx:gene_src_genus&gt;
     &lt;PDBx:host_org_genus&gt;Escherichia&lt;/PDBx:host_org_genus&gt;
     &lt;PDBx:host_org_species&gt;Escherichia coli&lt;/PDBx:host_org_species&gt;
     &lt;PDBx:pdbx_alt_source_flag&gt;sample&lt;/PDBx:pdbx_alt_source_flag&gt;
     &lt;PDBx:pdbx_gene_src_ncbi_taxonomy_id&gt;4932&lt;/PDBx:pdbx_gene_src_ncbi_taxonomy_id&gt;
     &lt;PDBx:pdbx_gene_src_scientific_name&gt;Saccharomyces cerevisiae&lt;/PDBx:pdbx_gene_src_scientific_name&gt;
     &lt;PDBx:pdbx_host_org_ncbi_taxonomy_id&gt;469008&lt;/PDBx:pdbx_host_org_ncbi_taxonomy_id&gt;
     &lt;PDBx:pdbx_host_org_scientific_name&gt;Escherichia coli BL21(DE3)&lt;/PDBx:pdbx_host_org_scientific_name&gt;
     &lt;PDBx:pdbx_host_org_strain&gt;BL21(DE3)&lt;/PDBx:pdbx_host_org_strain&gt;
     &lt;PDBx:pdbx_host_org_vector_type&gt;PLASMID&lt;/PDBx:pdbx_host_org_vector_type&gt;
     &lt;PDBx:plasmid_name&gt;pET19tev&lt;/PDBx:plasmid_name&gt;
  &lt;/PDBx:entity_src_gen&gt;
</code></pre>

<p></p>

<p>XML for 2BWI with PDBx:entity_src_natCategory</p>

<pre><code>&lt;PDBx:entity_src_natCategory&gt;
  &lt;PDBx:entity_src_nat entity_id="1" pdbx_src_id="1"&gt;
     &lt;PDBx:pdbx_alt_source_flag&gt;sample&lt;/PDBx:pdbx_alt_source_flag&gt;
     &lt;PDBx:pdbx_ncbi_taxonomy_id&gt;223&lt;/PDBx:pdbx_ncbi_taxonomy_id&gt;
     &lt;PDBx:pdbx_organism_scientific&gt;ACHROMOBACTER CYCLOCLASTES&lt;/PDBx:pdbx_organism_scientific&gt;
  &lt;/PDBx:entity_src_nat&gt;
</code></pre>

<p></p>

<p>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? </p>

<pdb><taxonomy>
What is the difference between the entity_src_genCategory tag and the entity_src_natCategory tag in pdb-xmls?
# What is the difference between the entity_src_genCategory tag and the entity_src_natCategory tag in pdb-xmls?

(Asked by: username_0 on 2018-01-26)

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

  
     baker's yeast
     Saccharomyces
     Escherichia
     Escherichia coli
     sample
     4932
     Saccharomyces cerevisiae
     469008
     Escherichia coli BL21(DE3)
     BL21(DE3)
     PLASMID
     pET19tev
  


XML for 2BWI with PDBx:entity_src_natCategory

  
     sample
     223
     ACHROMOBACTER CYCLOCLASTES
  


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?

**Tags:** pdb, taxonomy

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## 1 answers

### Answer by username_1 on 2018-01-26. Score: 1 | Accepted answer

`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:

* category [entity\_src\_nat](http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entity_src_nat.html)
* category [entity\_src\_gen](http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/entity_src_gen.html)

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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