<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><p class="wwpdb-page-news-date">Source: <a href="https://www.wwpdb.org/news/news?year=2021#604a60610769342b1f3d04b2" class="">https://www.wwpdb.org/news/news?year=2021#604a60610769342b1f3d04b2</a></p><p class="wwpdb-page-news-date">03/16/2021</p>
<h2 class="">Modifications to support for SHEET and ligand SITE records in June 2021</h2><p class=""><a href="https://www.wwpdb.org/news/news?year=2014#5764490799cccf749a90cde3" class="">In 2014, PDBx/mmCIF became the PDB’s archive format and the the legacy PDB file format was frozen</a>.
In addition to PDBx/mmCIF files for all entries, wwPDB produces PDB
format-formatted files for entries that can be represented in this
legacy file format (e.g., entries with over 99,999 atoms or with
multi-character chain IDs are only available in PDBx/mmCIF)</p><p class="">As the
size and complexity of PDB structures increases, additional limitations
of the legacy PDB format are becoming apparent and need to be
addressed.</p><h4 class="">Defining complex sheet records</h4><p class="">Restrictions in
the SHEET record fields in legacy the PDB file format do not allow for
the generation of complex beta sheet topology. Complex beta sheet
topologies include instances where beta strands are part of multiple
beta sheets and other cases where the definition of the strands within a
beta sheet cannot be presented in a linear description. For example, in
PDB entry 5wln a large beta barrel structure is created from multiple
copies of a single protein; within the beta sheet forming the barrel are
instances of a single beta strand making contacts on one side with
multiple other strands, even from different chains.</p><p class="">This
limitation, however, is not an issue in the PDBx/mmCIF formatted file,
where these complex beta sheet topology can be captured in <i class="">_struct_sheet</i>, <i class="">_struct_sheet_order</i>, <i class="">_struct_sheet_range</i>, and <i class="">_struct_sheet_hbond</i>.</p><p class="">Starting
June 8th 2021, legacy PDB format files will no longer be generated for
PDB entries where the SHEET topology cannot be generated. For these
structures, wwPDB will continue to provide secondary structure
information with helix and sheet information in the PDBx/mmCIF formatted
file.</p><h4 class="">Deprecation of _struct_site (SITE) records</h4><p class="">wwPDB regularly reviews the software used during OneDep biocuration. The <i class="">_struct_site</i> and <i class="">_struct_site_gen</i>
categories in PDBx/mmCIF (SITE records in the legacy PDB file format)
are generated by in-house software and based purely upon distance
calculations, and therefore may not reflect biological functional sites.</p><p class="">Starting in June 2021, the in-house legacy software which produces <i class="">_struct_site</i> and <i class="">_struct_site_gen</i>
records will be retired and wwPDB will no longer generate these
categories for newly-deposited PDB entries. Existing entries will be
unaffected.</p></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><img alt="<a href=/pdb?id=pdb_00005wln>PDB 5wln: Cryo-EM structure of the T2SS secretin XcpQ from <I>Pseudomonas aeruginosa</I></a>" class="img-responsive" apple-inline="yes" id="16FB8030-04BD-4A65-89A3-F15FFBC8C506" src="cid:487BD147-472C-4252-85B4-2229FE3B48EC"></div><div class=""><br class=""></div><br class="">
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