A community resource of experimental data for NMR / X-ray crystal structure pairs

Abstract

We have developed an online NMR / X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of targeted protein domain families. In some cases, structures for identical (or nearly identical) constructs were determined by both NMR and X-ray crystallography. NMR spectroscopy and X-ray diffraction data for 41 of these "NMR / X-ray" structure pairs determined using conventional triple-resonance NMR methods with extensive sidechain resonance assignments have been organized in an online NMR / X-ray Structure Pair Data Repository. In addition, several NMR data sets for perdeuterated, methyl-protonated protein samples are included in this repository. As an example of the utility of this repository, these data were used to revisit questions about the precision and accuracy of protein NMR structures first outlined by Levy and coworkers several years ago (Andrec et al., Proteins 2007;69:449-465). These results demonstrate that the agreement between NMR and X-ray crystal structures is improved using modern methods of protein NMR spectroscopy. The NMR / X-ray Structure Pair Data Repository will provide a valuable resource for new computational NMR methods development.

Keywords: X-ray crystallography; accuracy and precision of NMR structures; protein NMR spectroscopy; structural bioinformatics.

Figure 1

Backbone RMSDs to the medoid conformer within NMR ensembles are generally smaller than RMSDs between the medoid conformer and the corresponding X‐ray crystal structure. Histogram plots of backbone RMSDs within each NMR ensemble (RMS_ens—red solid lines), and between the medoid NMR conformer and the X‐ray crystal structure (RMS_Xtal—blue dashed lines), showing the numbers of structure (n) in each 0.2 Å bin. Data are presented for NMR / X‐ray pairs of A: PDB set of 145 pairs, B: NESG set of 41 pairs, and C: NESG/R3 set of 39 pairs, a subset of the NESG set that have been energy minimized using the restrained Rosetta protocol.8 These sets of NMR / X‐ray pairs are defined in the text.

Figure 2

NESG NMR structures are more like corresponding X‐ray crystal structures than the PDB NMR structures. Scatter plots between RMS_ens, providing an estimate of the convergence of the NMR ensemble, and RMS_Xtal, comparing the medoid NMR conformer with the corresponding X‐ray crystal structure. The three solid lines in each plot indicate the points for which RMS_Xtal/RMS_ens ratios are 1:1, 2:1, and 3:1, respectively. A: Comparison of PDB set (open black circles) and NESG set (closed red circles) NMR / X‐ray structure pairs. B: Comparison of PDB set (open black circles) and NESG/R3 set (closed red circles) of NMR / X‐ray structure pairs.

Figure 3

Examples of NESG NMR / X‐ray pairs with low Γ = RMS_Xtal/RMS_ens. Nine NMR / X‐ray pairs, from the NESG or NESG/R3 sets, with lowest values of Γ. For each ensemble, the superimposed backbone (N, Cα, C′) trace of the X‐ray crystal structure (gold) and representative NMR conformer (dark blue) are shown, together with the converged well‐defined (blue) and non‐converged ill‐defined (gray) backbone structures of the ensemble of the NMR conformers. Ill‐defined N‐ and C‐terminal segments are excluded from these images, but ill‐defined internal loops are included. The PDB id of the NMR structure is followed by the PDB id of the X‐ray structure. NMR structures refined with restrained Rosetta are indicated with asterisk following the PDB id.

Figure 4

Examples of NESG NMR / X‐ray pairs with high RMS_Xtal / RMS_ens. Nine NMR / X‐ray pairs, from the NESG or NESG/R3 sets, with highest values of Γ. The color coding of backbone traces is the same as in the legend of Figure 3. The PDB id of the NMR structure is followed by the PDB id of the X‐ray structure. NMR structures refined with restrained Rosetta are indicated with asterisk following the PDB id.

Figure 5

Examples of NMR / X‐ray pairs with lower structural similarity. The three NMR / X‐ray pairs from the NESG set with RMS_Xtal > 2.5 Å. The color coding of backbone traces is the same as in the legend of Figure 3. The PDB id of the NMR structure is followed by the PDB id of the X‐ray structure.

Figure 6

Examples of NMR / X‐ray pairs with very low structural similarity. Eight NMR / X‐ray pairs from the PDB set with low structural similarity (RMS_Xtal > 3.5 Å). The color coding of backbone traces is the same as in the legend of Figure 3. The PDB id of the NMR structure is followed by the PDB id of the X‐ray structure. These “outliers” were excluded from the statistical analyses.