[NMR paper] Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
Related ArticlesComparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
Proteins. 2005 Jul 1;60(1):139-47
Authors: Garbuzynskiy SO, Melnik BS, Lobanov MY, Finkelstein AV, Galzitskaya OV
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 A and 4.5-6.5 A, and fewer contacts at distances of 3.0-4.5 A and 6.5-8.0 A; (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.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Open Biochem J. 2010;4:83-95
Authors: Sikic K, Tomic S, Carugo O
Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in...
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02-05-2011 05:28 PM
[NMR paper] NMR structures of three single-residue variants of the human prion protein.
NMR structures of three single-residue variants of the human prion protein.
Related Articles NMR structures of three single-residue variants of the human prion protein.
Proc Natl Acad Sci U S A. 2000 Jul 18;97(15):8340-5
Authors: Calzolai L, Lysek DA, Guntert P, von Schroetter C, Riek R, Zahn R, Wüthrich K
The NMR structures of three single-amino acid variants of the C-terminal domain of the human prion protein, hPrP(121-230), are presented. In hPrP(M166V) and hPrP(R220K) the substitution is with the corresponding residue in murine PrP, and in...
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11-19-2010 08:29 PM
[NMR paper] Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex.
Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex.
Related Articles Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex.
Nat Struct Biol. 1998 Aug;5(8):692-7
Authors: Fraenkel E, Pabo CO
Homeodomains are one of the key families of eukaryotic DNA-binding motifs and provide an important model system for studying protein-DNA interactions. We have crystallized the Antennapedia homeodomain-DNA complex and solved this structure at 2.4 A resolution. NMR and molecular dynamics studies...
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11-17-2010 11:15 PM
Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
Related Articles Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1381-92
Authors: Mohanty B, Serrano P, Pedrini B, Jaudzems K, Geralt M, Horst R, Herrmann T, Elsliger MA, Wilson IA, Wüthrich K
The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for...
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10-16-2010 03:56 PM
[NMR paper] Comparison of the NMR and X-ray structures of the HIV-1 matrix protein: evidence for
Comparison of the NMR and X-ray structures of the HIV-1 matrix protein: evidence for conformational changes during viral assembly.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Comparison of the NMR and X-ray structures of the HIV-1 matrix protein: evidence for conformational changes during viral assembly.
Protein Sci. 1996...
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08-22-2010 02:20 PM
[NMR paper] Comparison of protein structures in solution using local conformations derived from N
Comparison of protein structures in solution using local conformations derived from NMR data: application to cytochrome c.
Related Articles Comparison of protein structures in solution using local conformations derived from NMR data: application to cytochrome c.
J Biomol Struct Dyn. 1994 Dec;12(3):527-58
Authors: Kar L, Sherman SA, Johnson ME
Structural comparisons of proteins in solution are often required to examine structure-functional relationships, study structural effects of mutations or distinguish between various forms of the same...
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08-22-2010 03:29 AM
[NMR paper] Comparison of protein structures determined by NMR in solution and by X-ray diffracti
Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals.
Related Articles Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals.
Q Rev Biophys. 1992 Aug;25(3):325-77
Authors: Billeter M