PubReading [307] - Comparison of X-ray and NMR Structures- Is There a Systematic Difference in Residue Contacts between X-ray- and NMR-Resolved Protein Structures? - S. Garbuzynskiy, O. Galzitskaya et al.

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: 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; this difference in the number of contacts is greater for internal residues than for external ones, and it is larger for -containing proteins than for all 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.

DOI: 10.1002/prot.20491 - 2005