Table 1. List of the 39 Protein Structures Solved by X-ray Diffraction Used in This Studya.
PDB ID | protein name | organism | NR | 310 (%)b | α (%)b | β (%)b | pH | res. [Å] | Rwork | Rfree | force field |
---|---|---|---|---|---|---|---|---|---|---|---|
4LFQ | potassium channel toxin L-ShK | Stichodactyla helianthus | 35 | 9 | 34 | – | 7.0 | 1.1 | 0.13 | 0.16 | all |
2NLS | human β-defensin-1, mutant Q24A | Homo sapiens | 36 | – | 19 | 31 | 7.5 | 1.0 | 0.11 | 0.12 | 54A7/8 |
3E7U | plectasin | Pseudoplectania nigrella | 40 | 3 | 23 | 25 | 7.5 | 1.4 | 0.16 | 0.18 | all |
2GKT | turkey ovomucoid third domain | Meleagris gallopavo | 51 | – | 20 | 16 | 7.5 | 1.2 | 0.13 | 0.15 | all |
3CA7 | protein Spitz | Drosophila melanogaster | 52 | – | 12 | 38 | 6.5 | 1.5 | 0.2 | 0.24 | 54A7/8 |
1PGBc | protein G, B1 domain | Streptococcus sp. gx7805 | 56 | – | 25 | 43 | 4.5 | 1.9 | 0.20 | – | all |
1ZLM | osteoclast stimulating factor 1 | Homo sapiens | 58 | 5 | – | 48 | 7.5 | 1.1 | 0.16 | 0.21 | all |
1SHGc | α-spectrin | Gallus gallus | 62 | 5 | – | 49 | 4.0 | 1.8 | 0.2 | 0.28 | all |
1UCS | antifreeze peptide RD1 | Lycodichthys dearborni | 64 | 14 | 6 | 25 | 7.5 | 0.6 | 0.14 | 0.15 | all |
1ZVG | α-like neurotoxin BmK-I | Mesobuthus martensii | 66 | 2 | 15 | 30 | 6.0 | 1.2 | 0.16 | 0.16 | all |
1YU5c | villin headpiece | Gallus gallus | 67 | 10 | 45 | – | 7.0 | 1.4 | 0.19 | 0.22 | all |
1MJC | major cold shock protein | Escherichia coli | 69 | 4 | – | 46 | 7.5 | 2.0 | 0.19 | – | all |
1UBIc | ubiquitin | Homo sapiens | 76 | 8 | 16 | 33 | 5.6 | 1.8 | 0.17 | – | all |
2J8B | human CD59 glycoprotein | Homo sapiens | 79 | 8 | 10 | 32 | 7.5 | 1.1 | 0.17 | 0.2 | 54A7/8 |
2PNEd | glycine-rich antifreeze protein | Hypogastrura harveyi | 81 | – | – | – | 6.5 | 1.0 | 0.14 | 0.16 | all |
1ULRe | putative acylphosphatase | Thermus thermophilus | 88 | 1 | 28 | 38 | 7.0 | 1.3 | 0.19 | 0.22 | all |
1A19c | barstar, mutant C82A | Bacillus amyloliquefaciens | 90 | 2 | 44 | 17 | 6.5 | 2.8 | 0.2 | 0.29 | 54A7/8 |
4RWU | protein Sis1 | Saccharomyces cerevisiae s288c | 92 | – | 62 | – | 7.0 | 1.2 | 0.12 | 0.15 | 54A7/8 |
1T2I | ribonuclease Sa | Streptomyces aureofaciens | 96 | 3 | 11 | 22 | 7.2 | 1.1 | 0.13 | 0.17 | all |
2YXF | β-2-microglobulin | Homo sapiens | 100 | – | – | 49 | 7.0 | 1.1 | 0.18 | 0.2 | 54A7/8 |
2CWRc | chitin binding domain of chitinase | Pyrococcus furiosus | 103 | – | – | 62 | 6.5 | 1.7 | 0.19 | 0.23 | all |
2RB8 | tenascin | Homo sapiens | 104 | – | – | 48 | 7.5 | 1.4 | 0.17 | 0.2 | 54A7/8 |
1EW4 | CyaY | Escherichia coli | 106 | – | 31 | 32 | 5.1 | 1.4 | 0.19 | 0.21 | all |
2PPO | FK506 binding protein-12 (FKBP12), mutant E60A | Homo sapiens | 107 | 4 | 7 | 37 | 7.0 | 1.3 | 0.13 | 0.18 | all |
2PND | Murine CRIg | Mus musculus | 119 | 5 | – | 51 | 7.5 | 1.0 | 0.12 | 0.14 | 54A7/8 |
1FAZc | phospholipase A2 | Streptomyces violaceoruber | 122 | 10 | 57 | – | 6.0 | 1.4 | 0.19 | 0.23 | all |
1TVQc | chicken liver basic fatty acid binding protein | Gallus gallus | 125 | – | 11 | 58 | 7.5 | 2.0 | 0.23 | 0.27 | all |
1AKIc | lysozyme | Gallus gallus | 129 | 13 | 30 | 11 | 4.5 | 1.5 | 0.21 | – | all |
1UXZ | cellulase B | Cellvibrio mixtus | 131 | 2 | – | 56 | 7.0 | 1.4 | 0.16 | 0.18 | all |
1QK8 | tryparedoxin-I | Crithidia fasciculata | 146 | 8 | 27 | 22 | 7.5 | 1.4 | 0.19 | 0.22 | all |
1NG6 | hypothetical protein yqeY | Bacillus subtilis | 148 | 4 | 74 | – | 5.5 | 1.4 | 0.21 | 0.25 | all |
2WLW | TRIM5-CypA | Macaca mulatta | 165 | 3 | 12 | 32 | 7.4 | 1.5 | 0.16 | 0.19 | 54A7/8 |
3EYE | PTS system N-acetylgalactosamine-specific IIB component 1 | Escherichia coli o157:h7 | 168 | 5 | 35 | 24 | 7.0 | 1.4 | 0.19 | 0.22 | 54A7/8 |
1FL0 | endothelial monocyte-activating polypeptide II | Homo sapiens | 171 | 7 | 2 | 37 | 7.5 | 1.5 | 0.22 | 0.22 | all |
1AMM | γ-crystallin B | Bos taurus | 174 | 6 | 3 | 40 | 6.8 | 1.2 | 0.18 | – | all |
1TUAe | hypothetical protein APE0754 | Aeropyrum pernix | 191 | 7 | 53 | 18 | 7.0 | 1.5 | 0.21 | 0.23 | all |
2PTH | peptidyl-tRNA hydrolase | Escherichia coli | 193 | 7 | 38 | 21 | 7.5 | 1.2 | 0.2 | 0.21 | 54A7/8 |
3WP5 | xylanase CDBFV, mutant E109A | Neocallimastix patriciarum | 227 | 2 | 8 | 54 | 6.5 | 1.3 | 0.15 | 0.18 | all |
4MHP | putative glutaminyl cyclase | Ixodes scapularis | 326 | 6 | 33 | 17 | 7.5 | 1.1 | 0.17 | 0.19 | all |
Abbreviations: NR = number of residues; 310 = 310-helix; α = α-helix; β = β-strand + β-bridge.
Secondary structure percentages as assigned by DSSP.
Has a paired NMR structure.
Polyproline II spiral only, not detected by DSSP.
pH not reported, set to 7.0.