Introduction

Toward the goal of sustaining Core Archives of biostructure data and metadata to promote basic and applied research and education, the wwPDB strives to make biostructure data Findable, Accessible, Interoperable, and Reusable (FAIR). Owing to unique properties of metals, standard software and procedures developed for organic compounds do not always provide accurate data on metal-containing compounds, which poses major obstacles for data Reusability. Further, the metalloprotein research community has expressed a need for enhanced metal annotation, which would support Findability and Reusability of metalloprotein data. Based on identification of issues that could lead to widespread error propagation and on feedback from the community, metalloproteins were identified as a target for improvement ("remediation").

To improve accuracy and enhance annotation, a new data model for metalloproteins has been developed in consultation with the metalloprotein research community. In addition to providing valuable feedback, the metalloprotein research community served a crucial role in this remediation by providing tools that enable error correction and support enhanced annotation of metalloproteins.

The PDBx/mmCIF dictionary extensions, examples of PDBx/mmCIF files of remediated data representing various cases, and the corresponding proposed Chemical Component Dictionary definitions are provided at github https://github.com/wwPDB/metallo-extension for testing and adoption by key stakeholders during the development stage, including the metalloprotein community, refinement software developers, cheminformaticians, and 3D visualization software.

Scope

For this project, the ~900 metal-containing CCDs (80 metal ions and ~820 polyatomic metal chemical components) will be remediated. The focus of the remediation is on polyatomic metal chemical components, which tend to have more challenges in their definition and representation versus metal ions. Specifically, the ~13,000 entries containing polyatomic metal chemical components will be remediated. Entries containing only metal ions will not be impacted.

Corrections

As a key step of the remediation, Chemical Component Dictionary (CCD) files will be corrected as needed to ensure data accuracy and reusability. The following corrections will be completed:

• Standardization of charge on metals and metal-coordinating atoms.
• Generation of proper ideal coordinates for metal-containing chemical components.
• Splitting or merging metal-containing chemical components where required if:
  • for splitting, the metal is not part of a standalone coordination compound.
  • for merging, the metal coordination is more complete upon merging two components.
• Corrections of inaccuracies in the definition (such as incorrect bond order or missing hydrogens).

Providing such corrections is crucial for mitigating error propagation. For example, if the PDB provides incorrect ideal coordinates in our CCD, these are then reused in future structures, leading to incorrect geometries in new depositions (see CCD F3S in Figure 1 below).

Enhanced Annotation

Enhanced annotations in the CCD files include:

• For metal ions and polyatomic metal-containing chemical components:
  • Indicating the component type (metal cation or metal-containing ligand).

• For polyatomic metal-containing chemical components only:
  • Adopting metalloprotein community software (FindGeo from MetalPDB and MetalCoord from CCP4) for metal coordination annotation (coordination number, coordination geometry, and coordination descriptor).
  • Annotation of metal-protein interaction.
  • Flagging metal coordination and metal-pi bonds.

Enhanced annotations in the coordinate files include:

• Adopting metalloprotein community software (FindGeo from MetalPDB and MetalCoord from CCP4) for metal coordination annotation (coordination number, coordination geometry, and coordination descriptor).
• Annotation of metal-protein interaction.

For future consideration, depositors may provide metal properties such as metal identity and/or oxidation state and their experimental evidence.