IMB Jena Image Library of Biological Macromolecules ----------------------------------------------------------------- Comprehensive Bending Classification of Nucleic Acid Double Helix Structures Bending classification of helical axis - Single-kink line ----------------------------------------------------------------- Table 1a: Structures for which the helical axis is best described by a single-kink line. Sigma2 of a single-kink line is only slightly smaller (< 0.2) than for the next best model(s). All structures have 13 or more base pairs and, therefore, an unambigious classification as single-kink structure is possible, in principle, even though the goodness-of-fit difference to the next-best model is small. The structures are listed by the kink angle alpha (a). Number of structures: 30 PDB NDB bp molecule method helical s(2) r a/a1 a2 o l1 l2 l3 type axis shape 1imh pd0214 13 prot-nuc diff single-kink 0.169 5 5 7 circular 0.188 320 double-kink 0.194 10 7 -140 4 3 6 straight 0.209 1fos pdt014 19 prot-nuc diff single-kink 0.130 7 11 8 double-kink 0.143 8 7 149 2 8 9 circular 0.149 301 1jnm pd0241 20 prot-nuc diff single-kink 0.203 7 17 3 circular 0.221 924 straight 0.227 double-kink 0.233 4 6 8 3 14 3 1mnn pd0341 13 prot-nuc diff single-kink 0.182 7 9 4 double-kink 0.210 8 8 -164 2 6 4 circular 0.215 343 straight 0.222 1mhd pd0243 13 prot-nuc diff single-kink 0.123 9 10 3 double-kink 0.130 6 10 -143 3 7 3 straight 0.221 circular 0.284 >1000 3kbd ------ 16 nuc NMR single-kink 0.161 11 5 11 double-kink 0.191 11 3 109 5 4 6 circular 0.229 191 1gtw ------ 15 prot-nuc diff single-kink 0.199 12 10 5 double-kink 0.212 8 16 164 5 4 6 circular 0.341 158 1ig9 pd0212 13 prot-nuc diff single-kink 0.106 12 4 9 double-kink 0.110 13 6 151 5 4 4 circular 0.216 148 1a0a pdt046 17 prot-nuc diff single-kink 0.370 13 12 4 double-kink 0.421 28 12 34 1 11 4 circular 0.540 223 1gu4 ------ 15 prot-nuc diff single-kink 0.153 13 10 5 double-kink 0.196 5 16 155 6 3 5 circular 0.301 147 1a02 pdt050 18 prot-nuc diff single-kink 0.101 15 11 7 double-kink 0.126 14 4 65 11 2 4 circular 0.288 132 1b8i pd0042 13 prot-nuc diff single-kink 0.173 18 7 6 circular 0.205 74 double-kink 0.299 5 16 34 3 5 5 1ig7 pd0211 13 prot-nuc diff single-kink 0.185 18 8 5 double-kink 0.187 12 18 -18 7 4 2 circular 0.190 74 1pdn pdr018 13 prot-nuc diff single-kink 0.280 18 5 8 double-kink 0.344 21 8 -153 5 4 3 4gat ------ 13 prot-nuc NMR single-kink 0.108 18 7 6 double-kink 0.118 11 12 -39 6 3 4 circular 0.185 80 1h9t pd0232 19 prot-nuc diff single-kink 0.369 20 10 9 double-kink 0.377 22 15 -117 9 2 8 1kqq ------ 15 prot-nuc NMR single-kink 0.248 22 7 8 double-kink 0.263 21 9 70 7 6 2 circular 0.283 77 1tsr pdr022 20 prot-nuc diff single-kink 0.287 22 4 16 double-kink 0.309 21 3 22 4 10 5 1tup pdr027 20 prot-nuc diff single-kink 0.282 22 4 16 double-kink 0.301 21 4 23 4 10 5 141d ------ 13 nuc NMR single-kink 0.070 23 6 7 circular 0.073 50 double-kink 0.085 13 13 -7 5 3 5 1rna arn035 14 nuc diff single-kink 0.080 23 8 6 double-kink 0.108 5 21 -14 4 4 6 circular 0.162 50 5gat ------ 13 prot-nuc NMR single-kink 0.173 23 7 6 double-kink 0.186 10 18 -56 6 2 5 circular 0.262 63 1f44 pd0166 15 prot-nuc diff single-kink 0.276 27 8 7 double-kink 0.277 13 21 -55 6 3 6 circular 0.470 55 1skn pdt064 13 prot-nuc diff single-kink 0.196 27 7 6 double-kink 0.272 10 20 -5 6 2 5 circular 0.281 49 1kbu pd0271 16 prot-nuc diff single-kink 0.352 33 8 8 double-kink 0.407 17 19 32 7 3 6 1lbg pdr026 16 prot-nuc diff single-kink 0.666 44 8 8 double-kink 0.834 43 8 83 8 4 4 1j5n ------ 15 prot-nuc NMR single-kink 0.419 48 10 5 double-kink 0.455 7 51 146 5 5 5 1hbx pd0233 25 prot-nuc diff single-kink 1.881 57 16 9 double-kink 1.920 9 59 -146 6 10 9 1e3m pd0201 17 prot-nuc diff single-kink 1.164 70 8 9 double-kink 1.206 25 51 20 6 2 9 1ng9 pd0367 17 prot-nuc diff single-kink 1.020 71 7 10 double-kink 1.105 30 46 21 6 2 9 -------------------------------------------------------------------------- Abbreviations -------------------------------------------------------------------------- PDB Protein Data Bank NDB Nucleic Acid Database bp base pair number diff diffraction model theoretical model NMR nuclear magnetic resonance spectroscopy prot protein nuc nucleic acid prot-nuc protein-nucleic acid complex carb carbohydrate plane plane s(2) goodness of fit r radius of curvature (circular line) a kink angle (single-kink line) a1, a2 kink angles (double-kink line) o twist angle (double-kink line) l1, l2, l3 lenght of segments 1, 2, and 3 measured in bp (double-kink model)