ArticleIUCrJ2024
Waterless structures in the Protein Data Bank.
Article in IUCrJ, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed.
- Lysozyme revisited: evaluating models of a reference protein in structural biology.Current research in structural biology · 2026Article
- The Advantages of AI for Computational Protein Studies and Looking Ahead at the Next Challenges: Single Structures Are Not Enough.Journal of molecular biology · 2026Review
- Comparative assessment of crystallographic and cryo-EM models in the Protein Data Bank.FEBS open bio · 2026Article
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- How to mitigate the caveat emptor burden of human and machine users of the Protein Data Bank.Acta crystallographica. Section D, Structural biology · 2026Article
- Role of restraints on hydrogen atoms in Hirshfeld atom refinement: the case of tri-aspartic acid trihydrate.Acta crystallographica Section B, Structural science, crystal engineering and materials · 2025Article
- A Critical Look at the Crystal Structures of cAMP-Dependent Protein Kinases.Kinases and phosphatases · 2025Article
- Duplicate entries in the Protein Data Bank: how to detect and handle them.Acta crystallographica. Section D, Structural biology · 2025Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The absence of solvent molecules in high-resolution protein crystal structure models deposited in the Protein Data Bank (PDB) contradicts the fact that, for proteins crystallized from aqueous media, water molecules are always expected to bind to the protein surface, as well as to some sites in the protein interior. An analysis of the contents of the PDB indicated that the expected ratio of the number of water molecules to the number of amino-acid residues exceeds 1.5 in atomic resolution structures, decreasing to 0.25 at around 2.5 Å resolution. Nevertheless, almost 800 protein crystal structures determined at a resolution of 2.5 Å or higher are found in the current release of the PDB without any water molecules, whereas some other depositions have unusually low or high occupancies of modeled solvent. Detailed analysis of these depositions revealed that the lack of solvent molecules might be an indication of problems with either the diffraction data, the refinement protocol, the deposition process or a combination of these factors. It is postulated that problems with solvent structure should be flagged by the PDB and addressed by the depositors.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.