ArticleActa crystallographica. Section D, Structural biology2022
Updated restraint dictionaries for carbohydrates in the pyranose form.
Article in Acta crystallographica. Section D, Structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- Methods for detecting, building, and improving tryptophan mannosylation in glycoprotein structures.Protein science : a publication of the Protein Society · 2025Article
- Post-translational modifications in the Protein Data Bank.Acta crystallographica. Section D, Structural biology · 2024Review
- Online carbohydrate 3D structure validation with the Privateer web app.Acta crystallographica. Section F, Structural biology communications · 2024Article
- Monitoring carbohydrate 3D structure quality with theBeilstein journal of organic chemistry · 2024Article
- The CCP4 suite: integrative software for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- Analysis and validation of overall N-glycan conformation in Privateer.Acta crystallographica. Section D, Structural biology · 2023Article
- In situ ligand restraints from quantum-mechanical methods.Acta crystallographica. Section D, Structural biology · 2023Article
- Native glycosylation and binding of the antidepressant paroxetine in a low-resolution crystal structure of human myeloperoxidase.Acta crystallographica. Section D, Structural biology · 2022Article
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4 authors.
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Abstract
Restraint dictionaries are used during macromolecular structure refinement to encapsulate intramolecular connectivity and geometric information. These dictionaries allow previously determined `ideal' values of features such as bond lengths, angles and torsions to be used as restraint targets. During refinement, restraints influence the model to adopt a conformation that agrees with prior observation. This is especially important when refining crystal structures of glycosylated proteins, as their resolutions tend to be worse than those of nonglycosylated proteins. Pyranosides, the overwhelming majority component in all forms of protein glycosylation, often display conformational errors in crystal structures. Whilst many of these flaws usually relate to model building, refinement issues may also have their root in suboptimal restraint dictionaries. In order to avoid subsequent misinterpretation and to improve the quality of all pyranose monosaccharide entries in the CCP4 Monomer Library, new dictionaries with improved ring torsion restraints, coordinates reflecting the lowest-energy ring pucker and updated geometry have been produced and evaluated. These new dictionaries are now part of the CCP4 Monomer Library and will be released with CCP4 version 8.0.
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