Table 1.
Set of proteins for which the 13Cα chemical shift was computed
| PDB codea | Experimental conditionsb | Number of residuesc | BMRB accession coded |
ca-rmsde (ppm) | ca-rmsdf (ppm) |
|---|---|---|---|---|---|
| 1Z2F (20)g | NMR (N/A; 290 K; 5.7) | 121 (9) | [6111] | 3.5 | 4.25 (3.56) |
| 1M8N (1)g | X-ray (2.45 Å; 100 K; 5.2) | 120 (9) | 3.2 | 4.38 (3.68) | |
| 2I83 (20)h | NMR (N/A; 310 K; 6.7) | 158 (6) | [5903] | 2.45 | 2.21 (1.64) |
| 1UUH (1)h | X-ray (2.2 Å; 100 K; 5.5) | 150 (6) | 2.47 | 3.1 (2.35) | |
| 1HJD (20) | NMR (N/A; 300 K; 7.0) | 101(2) | [4731] | 6.08 | 4.13 (3.65) |
| 1I1J (1) | X-ray (1.39 Å; 100 K; 8.2) | 101 (2) | 5.16 | 3.81 (3.39) | |
| 1IK0 (30) | NMR (N/A; 298 K; 6.0) | 113 (4) | [5004] | 4.92 | 2.37 (2.01) |
| 3BPO (1) | X-ray (3.00 Å; 100 K; 6.0) | 98 (4) | 5.21 | 2.9 (2.62) | |
| 1D2B (29)i | NMR (N/A; 293 K; 6.0) | 119 (4) | [4327] | 2.61 | 2.74 (2.27) |
| 2J0T (1)i | X-ray (2.54 Å; 100 K; 7.5) | 119 (4) | 2.56 | 3.43 (2.84) | |
| 1BPI (1) | X-ray (1.09 Å; 125 K; N/A) | 58 (6) | [5359] | 1.67 [0.86] |
1.65 (2.03) |
| 1D0D (1) | X-ray (1.62 Å; 298 K; 6.5) | 58 (6) | 1.33 [1.09] |
1.94 (2.39) | |
| 1G6X (1) | X-ray (0.86 Å; 100 K; 7.5) | 58 (6) | 2.39 [1.05] |
1.78 (2.20) | |
| 1K6U (1) | X-ray (1.00 Å; 100 K; 7.5) | 58 (6) | 2.39 [0.97] |
2.02 (2.49) | |
| 5PTI (1) | X-ray (1.09 Å; N/A; N/A) | 57 (6) | 1.66 [1.08] |
1.69 (2.11) | |
| 6PTI (1)j | X-ray (1.7 Å; N/A; N/A) | 56 (6) | 2.37 [0.64] |
1.81 (2.29) | |
| 1HA8 (20) | NMR (N/A; 290 K; 4.6) | 51 (10) | [4979] | 4.42 | 3.16 (4.57) |
Four-symbol code for the deposited structure in the Protein Data Bank (Berman et al. 2000). In parentheses, the number of determined conformations for each protein
Experimental conditions under which the proteins listed in column one were determined. The resolution (Å), temperature (K) and pH, are in parentheses. For all the NMR structures, DSS was used as the reference for the observed 13Cα chemical shifts
Total number of residues for each protein listed in column one. The number of cysteine residues in cystine for each protein is indicated between parentheses. For the same protein, and for three out of five cases, the total number of residues of each structure solved by NMR spectroscopy and X-ray crystallography are not the same; the reasons for the observed experimental difference in the total number of residues, can be found in the original papers cited in “Materials and methods” section
BMRB (Ulrich et al. 2007) accession number under which the observed 13Cα chemical shifts can be found
ca-rmsd computed from only the cysteine residues in cystines. The ca-rmsd values without cysteine in position 14, only for the six BPTI models, are shown in brackets
ca-rmsd computed for non-cysteine residues; in parenthesis, the normalized size-independent ca-rmsd76
The all heavy-atom rmsd value between the (1Z2F) NMR- and the X-ray-determined (1M8N) structure is ~0.65 Å. Differences between the 1Z2F and 1M8N models are located mainly in two loop regions (Li et al. 2005), namely for residues 90–93 and 106–110, near the C-terminal region. The X-ray-determined structure (1M8N) was solved as a dimer, but such oligomerization is not observed in solution and, hence, the NMR-determined structure (1Z2F) was solved as a monomer (Li et al. 2005). There is an odd number (nine) of cysteines listed in parentheses in column three because the observed 13Cα chemical-shift value for one of the cysteines is missing
The X-ray determined model (1UUH) was solved without ligand bound, while the NMR-determined structure (2I83) was solved with bound ligand. Several regions of the Hyaluronan-binding domain of the CD 44 protein undergo conformational changes upon ligand binding, as reflected by a high (~7.7 Å) all-heavy-atom rmsd between the 1UUH and 2I83 protein models. Most of the conformational changes occur at the C-terminal portion, i.e., for the last ~39 residues of the protein. Excluding the C-terminal portion from the rmsd analysis, a value of ~1.8 Å is obtained, indicating that there are still significant conformational differences between the 1UUH and 2I83 protein models
The rmsd between the X-ray model (2J0T) and the average NMR-determined conformation (1D2B) is 1.49 Å (Iyer et al. 2007). Conceivably, most of the conformational differences between these models arise from the fact that the NMR-derived structure (1D2B) was solved as a monomer while the X-ray-determined protein (2J0T) was solved as a dimer
Protein refined by neutron diffraction data