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Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?статья
Статья опубликована в высокорейтинговом журнале
Информация о цитировании статьи получена из
Web of Science,
Scopus
Статья опубликована в журнале из списка Web of Science и/или Scopus
Дата последнего поиска статьи во внешних источниках: 15 июля 2021 г.
- Авторы: Garbuzynskiy Sergiy O., Melnik Bogdan S., Lobanov Michail Yu, Finkelstein Alexei V., Galzitskaya Oxana V.
- Журнал: Proteins: Structure, Function and Bioinformatics
- Том: 60
- Номер: 1
- Год издания: 2005
- Издательство: Wiley-Liss Inc
- Местоположение издательства: United States
- Первая страница: 139
- Последняя страница: 147
- DOI: 10.1002/prot.20491
- Аннотация: We have compared structures of 78 proteins determined by both NMR and X-ray methods. It is shown that X-ray and NMR structures of the same protein have more differences than various X-ray structures obtained for the protein, and even more than various NMR structures of the protein. X-ray and NMR structures of 18 of these 78 proteins have obvious large-scale structural differences that seem to reflect a difference of crystal and solution structures. The other 60 pairs of structures have only small-scale differences comparable with differences between various X-ray or various NMR structures of a protein; we have analyzed these structures more attentively. One of the main differences between NMR. and X-ray structures concerns the number of contacts per residue: (1) NMR structures presented in PDB have more contacts than X-ray structures at distances below 3.0 angstrom and 4.5- 6.5 angstrom, and fewer contacts at distances of 3.0-4.5 angstrom and 6.5-8.0 angstrom; (2) this difference in the number of contacts is greater for internal residues than for external ones, and it is larger for beta-containing proteins than for all-alpha proteins. Another significant difference is that the main-chain hydrogen bonds identified in X-ray and NMR structures often differ. Their correlation is 69% only. However, analogous difference is found for refined and rerefined NMR structures, allowing us to suggest that the observed difference in interresidue contacts of X-ray and NMR structures of the same proteins is due mainly to a difference in mathematical treatment of experimental results. (c) 2005 Wiley-Liss, Inc.
- Добавил в систему: Финкельштейн Алексей Витальевич