Atanasova, Mihaela, Nicholls, Robert A., Joosten, Robbie P. et al. (1 more author) (2022) Updated restraint dictionaries for carbohydrates in the pyranose form. Acta Crystallographica Section D: Structural Biology. pp. 455-465. ISSN 2059-7983
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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | Funding Information: This work was supported by the Medical Research Council as part of United Kingdom Research and Innovation (also known as UK Research and Innovation; MRC file reference No. MC_UP_A025_1012), by the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 871037 (iNEXT-Discovery) and by CCP4. Mihaela Atanasova is funded by the UK Engineering and Physical Sciences Research Council (EPSRC; grant No. EP/R513386/ 1). Robert Nicholls is funded by the BBSRC (reference BB/ S007083/1). Jon Agirre is the Royal Society Olga Kennard Research Fellow (award No. UF160039). Publisher Copyright: © 2022. |
Keywords: | carbohydrates,dictionaries,pyranose,restraints,ring conformation. |
Dates: |
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Institution: | The University of York |
Academic Units: | The University of York > Faculty of Sciences (York) > Chemistry (York) |
Depositing User: | Pure (York) |
Date Deposited: | 22 Apr 2022 11:00 |
Last Modified: | 12 Nov 2024 01:18 |
Published Version: | https://doi.org/10.1107/S2059798322001103 |
Status: | Published |
Refereed: | Yes |
Identification Number: | 10.1107/S2059798322001103 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:186022 |
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Description: Updated restraint dictionaries for carbohydrates in the pyranose form
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