DOI: 10.1002/prot.20491. Comparison of X‐ray and NMR structures: Is there a systematic difference in residue contacts between X‐ray‐ and NMR‐resolved protein structures?

Comparison of X‐ray and NMR structures: Is there a systematic difference in residue contacts between X‐ray‐ and NMR‐resolved protein structures?

10.1002/prot.20491

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractWe 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 Å and 4.5–6.5 Å, and fewer contacts at distances of 3.0–4.5 Å and 6.5–8.0 Å; (2) this difference in the number of contacts is greater for internal residues than for external ones, and it is larger for β‐containing proteins than for all‐α 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. Proteins 2005. © 2005 Wiley‐Liss, Inc.

Bibliography

Garbuzynskiy, S. O., Melnik, B. S., Lobanov, M. Yu., Finkelstein, A. V., & Galzitskaya, O. V. (2005). Comparison of Xâray and NMR structures: Is there a systematic difference in residue contacts between Xârayâ and NMRâresolved protein structures? Proteins: Structure, Function, and Bioinformatics, 60(1), 139â147. Portico.

Authors 5

Sergiy O. Garbuzynskiy (first)
Bogdan S. Melnik (additional)
Michail Yu. Lobanov (additional)
Alexei V. Finkelstein (additional)
Oxana V. Galzitskaya (additional)

References 23 Referenced 73

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10.1111/j.1432-1033.1977.tb11885.x
10.1017/S0033583500004261
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{'key': 'e_1_2_6_19_2', 'volume-title': 'Program FITT for rmsd calculation', 'author': 'Finkelstein AV', 'year': '1987'} / Program FITT for rmsd calculation by Finkelstein AV (1987)
10.1107/S0108767386099786
{'key': 'e_1_2_6_21_2', 'volume-title': 'Statistics. Lectures on elementary statistics and probability', 'author': 'Hudson DJ', 'year': '1964'} / Statistics. Lectures on elementary statistics and probability by Hudson DJ (1964)
10.1006/jmbi.2000.3750
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Dates

Type	When
Created	20 years, 3 months ago (April 26, 2005, 1:50 p.m.)
Deposited	1 year, 10 months ago (Oct. 16, 2023, 12:29 a.m.)
Indexed	3 weeks, 2 days ago (Aug. 2, 2025, 12:07 a.m.)
Issued	20 years, 3 months ago (April 26, 2005)
Published	20 years, 3 months ago (April 26, 2005)
Published Online	20 years, 3 months ago (April 26, 2005)
Published Print	20 years, 1 month ago (July 1, 2005)

Funders 0

None

BibTeX

@article{Garbuzynskiy_2005, title={Comparison of X‐ray and NMR structures: Is there a systematic difference in residue contacts between X‐ray‐ and NMR‐resolved protein structures?}, volume={60}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.20491}, DOI={10.1002/prot.20491}, number={1}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Garbuzynskiy, Sergiy O. and Melnik, Bogdan S. and Lobanov, Michail Yu. and Finkelstein, Alexei V. and Galzitskaya, Oxana V.}, year={2005}, month=apr, pages={139–147} }

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