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Correcting cis-trans-transgressions in macromolecular structure models.

Franz Waibl1, Klaus R Liedl1, Bernhard Rupp2,3

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Summary
This summary is machine-generated.

Many protein structure models in the Protein Data Bank (PDB) incorrectly depict the cis-trans stereochemistry of unsaturated fatty acid ligands. This study identifies common errors and provides guidance for correction to ensure accurate molecular models.

Keywords:
X-ray crystallographycis-trans isomerscryo-EMmacromolecular modelsstereochemical restraintsunsaturated fatty acids

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Area of Science:

  • Structural Biology
  • Biochemistry
  • Computational Biology

Background:

  • Macromolecular structure models in the Protein Data Bank (PDB) frequently include biologically relevant small molecule ligands with unsaturated fatty acid acyl chains.
  • A significant number of these deposited models contain errors in the cis-trans stereochemistry of these unsaturated fatty acid chains.

Purpose of the Study:

  • To identify and document common errors in cis-trans stereochemistry of unsaturated fatty acid ligands within PDB structures.
  • To provide resources and guidance for correcting these stereochemical inaccuracies in macromolecular models.

Main Methods:

  • Analysis of case studies involving frequently occurring small molecule ligands with unsaturated fatty acid chains in PDB.
  • Compilation and listing of identified cis-trans geometry errors (C-C=C-C torsion angles) in deposited structure models.
  • Review of stereochemical restraint file definitions and model building practices.

Main Results:

  • Identified frequent occurrences of incorrect cis-trans stereochemistry in unsaturated fatty acid ligands within PDB models.
  • Demonstrated that the same ligand can be present in both incorrect (cis/trans) isomeric configurations within deposited models.
  • Provided detailed listings of cis/trans torsion angles for commonly occurring molecules to aid in error identification.

Conclusions:

  • Incorrect cis-trans stereochemistry in unsaturated fatty acid ligands is a prevalent issue in macromolecular structure databases.
  • Standardized restraint file definitions and careful model building are crucial to prevent and correct these errors.
  • The provided data and guidance can help users avoid inadvertently using incorrect models and assist modelers in refinement.