Biological Unit: Difference between revisions
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===Unreliability of REMARK 350 in the PDB File Header=== | ===Unreliability of REMARK 350 in the PDB File Header=== | ||
When a structure is deposited in the [[PDB]], the authors are required to specify the biological unit if it is known. This is given in REMARK 350 in the header of the [[PDB file format]]. Unfortunately, information in REMARK 350 is often incorrect (see [https://lists.wwpdb.org/empathy/thread/DNQIHDGCX3E64AJT5ABCTNFW2EJZTGAS discussion of this problem by Roland Dunbrack])<ref name="xudunbrackpreprint" /><ref name="xudunbrack" />. There are numerous examples in which the authors state that the biological unit is a monomer in REMARK 350, but provide good experimental evidence in the paper reporting the structure that the biological unit is a dimer. Jose Duarte provided a [https://lists.wwpdb.org/empathy/thread/FNLXQHDEEHGFT7UID3WDYWUFFARTMTN7 list of examples]. | When a structure is deposited in the [[PDB]], the authors are required to specify the biological unit if it is known. This is given in REMARK 350 in the header of the [[PDB file format]]. Unfortunately, information in REMARK 350 is often incorrect (see [https://lists.wwpdb.org/empathy/thread/DNQIHDGCX3E64AJT5ABCTNFW2EJZTGAS discussion of this problem by Roland Dunbrack])<ref name="xudunbrackpreprint" /><ref name="xudunbrack" />. There are numerous examples in which the authors state that the biological unit is a monomer in REMARK 350, but provide good experimental evidence in the paper reporting the structure that the biological unit is a dimer. Jose Duarte provided a [https://lists.wwpdb.org/empathy/thread/FNLXQHDEEHGFT7UID3WDYWUFFARTMTN7 list of examples]. | ||
Also unfortunately, in 2022, the wwPDB is adding REMARK 350 to PDB-format files originally | |||
deposited without that remark, mostly models determined by [[NMR]]. What is unfortunate is that the added REMARK 350 specifies "AUTHOR DETERMINED", although it appears that the authors are not being consulted. An example is [[2z59]], which lacked REMARK 350 until it was added on March 16, 2022 (see the REVDAT records in the PDB format file). | |||
In some cases, more than one putative biological unit is specified in REMARK 350. Biological units specified by the author(s) are distinguished from those predicted by software. An example is [[3fad]], which is explained in [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies Introduction to Biological Assemblies and the PDB Archive]. | In some cases, more than one putative biological unit is specified in REMARK 350. Biological units specified by the author(s) are distinguished from those predicted by software. An example is [[3fad]], which is explained in [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies Introduction to Biological Assemblies and the PDB Archive]. | ||
