0.028903 0.000000 0.000000 0.000000 0.019601 0.000000 0.000000 0.000000 0.010843 0.00000 0.00000 0.00000 3.54356 2.42580 25.62398 1.50364 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 8.95735 7.27484 0.0 1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 0.51345 0.48472 24.73122 6.32584 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 16.37977 2.54835 4.54127 84.28225 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 4.01032 2.96436 19.97189 1.75589 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 9.38062 1.54875 3.38349 72.32734 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 4.49882 3.47563 15.80542 1.70748 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 9.51135 5.44231 1.42069 35.72801 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. Peng, X. Huang, L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.000 90.000 90.000 34.598 51.018 92.223 162781.574 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C19 H14 F2 N4 O2 368.337 (5Z)-3-(3H-benzimidazol-4-ylmethyl)-5-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]methylidene]-2-methyl-imidazol-4-one non-polymer C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C10 H16 N5 O14 P3 523.180 n GUANOSINE-5'-TRIPHOSPHATE non-polymer H2 O 18.015 WATER non-polymer K 1 39.098 POTASSIUM ION non-polymer Na 1 22.990 SODIUM ION non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H Y 38 N C Y 39 N C Y 40 N C Y 41 N C Y 42 N C Y 43 N C N 44 N C N 45 N C N 46 N C N 47 N C N 48 N C Y 49 N C Y 50 N C Y 51 N C Y 52 N C Y 53 N C Y 54 N C Y 55 N C N 56 N C N 57 N F N 58 N F N 59 N N N 60 N N Y 61 N N Y 62 N N N 63 N O N 64 N O N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N O N 80 N P N 81 N O N 82 N O N 83 N O N 84 N C N 85 R C N 86 N O N 87 S C N 88 N O N 89 R C N 90 N O N 91 R C N 92 N N N 93 N C N 94 N O N 95 N N N 96 N C N 97 N N N 98 N C N 99 N C N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N O N 115 N P N 116 N O N 117 N O N 118 N O N 119 N C N 120 R C N 121 N O N 122 S C N 123 N O N 124 R C N 125 N O N 126 R C Y 127 N N Y 128 N C Y 129 N N Y 130 N C N 131 N C N 132 N O N 133 N N N 134 N C N 135 N N N 136 N N Y 137 N C N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N P N 153 N O N 154 N O N 155 N O N 156 N O N 157 N P N 158 N O N 159 N O N 160 N O N 161 N P N 162 N O N 163 N O N 164 N O N 165 N C N 166 R C N 167 N O N 168 S C N 169 N O N 170 R C N 171 N O N 172 R C Y 173 N N Y 174 N C Y 175 N N Y 176 N C N 177 N C N 178 N O N 179 N N N 180 N C N 181 N N N 182 N N Y 183 N C N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N O N 201 N H N 202 N H N 203 N K N 204 N NA N 205 N O N 206 N P N 207 N O N 208 N O N 209 N O N 210 N C N 211 R C N 212 N O N 213 S C N 214 N O N 215 R C N 216 N O N 217 R C N 218 N N N 219 N C N 220 N O N 221 N N N 222 N C N 223 N O N 224 N C N 225 N C N 226 N H N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing Y 40 N doub Y 41 N sing N 42 N sing Y 43 N sing N 44 N sing Y 45 N doub N 46 N sing Y 47 N sing Y 48 N doub N 49 N sing N 50 Z doub N 51 N sing N 52 N sing N 53 N doub N 54 N sing N 55 N doub N 56 N sing N 57 N sing N 58 N sing N 59 N sing Y 60 N doub Y 61 N sing Y 62 N sing Y 63 N sing Y 64 N sing Y 65 N doub Y 66 N sing Y 67 N doub Y 68 N sing Y 69 N doub N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N doub N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N doub N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N doub N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N doub N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing Y 144 N sing Y 145 N sing Y 146 N doub N 147 N sing Y 148 N sing N 149 N sing Y 150 N doub N 151 N doub N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N doub N 157 N sing N 158 N sing N 159 N sing N 160 N doub N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N doub N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N doub N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing Y 194 N sing Y 195 N sing Y 196 N doub N 197 N sing Y 198 N sing N 199 N sing Y 200 N doub N 201 N doub N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N doub N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N doub N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N doub N 239 N sing N 240 N sing N 241 N sing N 242 N doub N 243 N sing N 244 N doub N 245 N sing N 246 N sing To Be Published 0353 Crystal structure of Broccoli aptamer in with BI 10.2210/pdb9vmz/pdb pdb_00009vmz 100 1 N PIXEL 2022-03-11 DECTRIS PILATUS3 6M SINGLE WAVELENGTH M x-ray 1 0.97853 1.0 BL19U1 SSRF 0.97853 SYNCHROTRON SSRF BEAMLINE BL19U1 Fluorescent light-up aptamer 15874.386 RNA (49-MER) 1 syn polymer 523.180 GUANOSINE-5'-TRIPHOSPHATE 1 syn non-polymer 368.337 (5Z)-3-(3H-benzimidazol-4-ylmethyl)-5-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]methylidene]-2-methyl-imidazol-4-one 1 syn non-polymer 39.098 POTASSIUM ION 6 syn non-polymer 22.990 SODIUM ION 1 syn non-polymer 18.015 water 1 nat water no no GGGACGGUCGGGUCCAGAUAUUCGUAUCUGUCGAGUAGAGUGUGGGCUC GGGACGGUCGGGUCCAGAUAUUCGUAUCUGUCGAGUAGAGUGUGGGCUC A polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n 1 2.67 54 VAPOR DIFFUSION, HANGING DROP 0.04 M Lithium chloride, 0.08 M Strontium chloride hexahydrate, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 7.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride 291 -5.784 1 28 A 2 A 48 0.105 A_G2:U48_A 1 -16.522 -1.525 0.174 -0.359 -15.080 1 19 A 3 A 47 -4.489 A_G3:C47_A 2 -21.243 -0.129 -0.011 -0.007 -19.615 1 8 A 4 A 46 -16.281 A_A4:G46_A 3 -9.581 0.102 -0.181 1.450 -11.041 A 5 A 45 -45.815 A_C5:G45_A 4 -8.576 0.367 -0.539 1.383 -21.019 A 36 A 43 -131.279 A_U36:U43_A 5 7.976 -1.304 0.767 -4.329 -0.076 3 6 A 7 A 35 89.471 A_G7:G35_A 6 4.241 -2.104 -0.233 -2.935 1.888 1 20 A 13 A 34 4.388 A_U13:A34_A 7 0.395 0.477 -0.112 0.080 10.665 1 19 A 14 A 33 4.911 A_C14:G33_A 8 -9.579 -0.122 0.005 -0.091 9.580 1 19 A 15 A 30 -2.588 A_C15:G30_A 9 -15.318 -0.165 0.314 -0.289 5.219 1 20 A 16 A 29 1.717 A_A16:U29_A 10 -14.855 -0.784 0.182 -0.160 2.471 1 19 A 17 A 28 -2.936 A_G17:C28_A 11 -17.103 -0.305 0.124 -0.483 0.346 1 20 A 18 A 27 1.816 A_A18:U27_A 12 -13.691 -0.450 0.437 -0.447 -0.188 1 20 A 19 A 26 -2.341 A_U19:A26_A 13 -10.665 0.053 0.005 -0.252 4.827 1 20 A 20 A 25 0.114 A_A20:U25_A 14 -3.398 0.373 0.548 -0.192 -16.730 6 A 21 A 24 -107.336 A_U21:G24_A 15 3.032 1.083 0.591 -5.131 3.176 38.777 A A 2 3 8.149 A A 48 47 3.433 5.394 -0.180 -1.675 AA_G2G3:C47U48_AA 1 0.469 -0.708 38.412 -3.192 0.329 2.617 36.355 A A 3 4 12.374 A A 47 46 3.095 7.657 -0.740 -1.663 AA_G3A4:G46C47_AA 2 3.181 -5.140 35.428 -3.609 1.579 2.785 31.195 A A 4 5 -0.177 A A 46 45 3.027 -0.094 -0.773 -2.246 AA_A4C5:G45G46_AA 3 7.131 -13.373 30.389 -4.161 2.659 -3.501 178.390 A A 5 36 -73.937 A A 45 43 -3.976 -147.699 1.928 -2.826 AA_C5U36:U43G45_AA 4 -91.193 45.650 150.929 -1.818 -0.714 6.460 -146.092 A A 7 13 1.612 A A 35 34 6.460 -3.084 1.386 -0.515 AA_G7U13:A34G35_AA 5 -1.182 -0.618 -146.077 0.297 0.714 1.930 30.607 A A 13 14 21.199 A A 34 33 2.859 10.940 0.666 -1.948 AA_U13C14:G33A34_AA 6 -2.618 5.072 28.511 -5.332 -1.655 3.026 48.590 A A 14 15 5.793 A A 33 30 3.154 4.760 1.295 -1.228 AA_C14C15:G30G33_AA 7 -0.050 0.061 48.371 -1.838 -1.578 2.266 30.041 A A 15 16 23.462 A A 30 29 3.133 11.841 0.072 -1.612 AA_C15A16:U29G30_AA 8 1.281 -2.538 27.629 -5.205 0.088 2.814 34.798 A A 16 17 12.145 A A 29 28 3.150 7.213 0.121 -1.334 AA_A16G17:C28U29_AA 9 -0.696 1.172 34.058 -3.244 -0.300 2.661 34.438 A A 17 18 10.798 A A 28 27 3.015 6.353 0.488 -1.455 AA_G17A18:U27C28_AA 10 -2.599 4.417 33.767 -3.325 -1.179 2.950 37.312 A A 18 19 5.116 A A 27 26 3.126 3.262 -0.254 -1.412 AA_A18U19:A26U27_AA 11 4.210 -6.601 36.944 -2.610 0.917 2.532 32.601 A A 19 20 8.700 A A 26 25 2.853 4.862 0.748 -1.592 AA_U19A20:U25A26_AA 12 -2.360 4.222 32.162 -3.538 -1.674 3.349 95.660 A A 20 21 4.550 A A 25 24 3.557 6.730 -1.510 -0.684 AA_A20U21:G24U25_AA 13 12.430 -8.403 94.862 -0.586 1.249 repository Initial release 1 0 2026-07-01 China National Natural Science Foundation of China (NSFC) 32171191 China National Natural Science Foundation of China (NSFC) 32400021 huanglin36@mail.sysu.edu.cn 0000-0002-2121-365X Lin Huang principal investigator/group leader N PDBJ N PDBC 2025-06-29 REL REL A1EST A1EST SUBJECT OF INVESTIGATION GTP GUANOSINE-5'-TRIPHOSPHATE A1EST (5Z)-3-(3H-benzimidazol-4-ylmethyl)-5-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]methylidene]-2-methyl-imidazol-4-one K POTASSIUM ION NA SODIUM ION HOH water 32630 synthetic construct sample 1 49 Y N 8K7W PDB experimental model GTP 1 2 GTP GTP 101 A DRG 101 3 A1EST A1EST 102 A K 1 4 K K 103 A K 2 4 K K 104 A K 3 4 K K 105 A K 4 4 K K 106 A K 5 4 K K 107 A K 6 4 K K 108 A NA 1 5 NA NA 109 A HOH 1 6 HOH HOH 201 A n 1 1 A G 2 n 2 G 2 A G 3 n 3 G 3 A A 4 n 4 A 4 A C 5 n 5 C 5 A G 6 n 6 G 6 A G 7 n 7 G 7 A U 8 n 8 U 8 A C 9 n 9 C 9 A G 10 n 10 G 10 A G 11 n 11 G 11 A G 12 n 12 G 12 A U 13 n 13 U 13 A C 14 n 14 C 14 A C 15 n 15 C 15 A A 16 n 16 A 16 A G 17 n 17 G 17 A A 18 n 18 A 18 A U 19 n 19 U 19 A A 20 n 20 A 20 A U 21 n 21 U 21 A U 22 n 22 U 22 A C 23 n 23 C 23 A G 24 n 24 G 24 A U 25 n 25 U 25 A A 26 n 26 A 26 A U 27 n 27 U 27 A C 28 n 28 C 28 A U 29 n 29 U 29 A G 30 n 30 G 30 A U 31 n 31 U 31 A C 32 n 32 C 32 A G 33 n 33 G 33 A A 34 n 34 A 34 A G 35 n 35 G 35 A U 36 n 36 U 36 A A 37 n 37 A 37 A G 38 n 38 G 38 A A 39 n 39 A 39 A G 40 n 40 G 40 A U 41 n 41 U 41 A G 42 n 42 G 42 A U 43 n 43 U 43 A G 44 n 44 G 44 A G 45 n 45 G 45 A G 46 n 46 G 46 A C 47 n 47 C 47 A U 48 n 48 U 48 A C 49 n 49 C 49 A 4.33006957331 -0.202909504859 1.86755133336 4.40455901833 -0.978113033252 7.93108815877 0.0689440950226 0.0746214759134 -0.390946355179 -0.60017646664 0.330197444448 0.00318563878202 0.360442056043 0.0898330068551 -0.308303959049 0.701996346837 -0.0586766066372 -0.0124277028423 0.508650129039 0.0743084214398 0.285148022215 refined 9.66487653999 7.43314775185 13.0639773907 X-RAY DIFFRACTION 0.499677846374 -1.66458798745 -1.75579699623 5.63968687084 4.4352942367 5.73173783605 -0.107726007362 -0.203025836449 0.305210637536 0.123250080319 0.433468621442 -0.562009902771 -0.062390549192 0.30434458076 -0.204716562361 0.662639399261 0.0648168057632 0.0268230153751 0.592176739321 -0.00814023694831 0.427930860639 refined 6.74735858233 20.8312160148 31.9781182371 X-RAY DIFFRACTION 5.52537362375 0.5044803215 -0.783089785654 6.58477960096 -1.23999920411 2.05245709879 0.383720666548 0.118160836951 -0.322870815233 0.295416788546 0.156825652389 0.383127612257 -0.0250171718695 -0.964955108908 -0.64101145957 0.646313855702 -0.00580262932931 -0.13782563597 0.55020070546 0.0944124973418 0.38118112353 refined 3.13487525537 5.61006631252 12.7198140462 X-RAY DIFFRACTION A 2 B A 11 B X-RAY DIFFRACTION 1 chain 'A' and (resid 2 through 11 ) A 12 B A 36 B X-RAY DIFFRACTION 2 chain 'A' and (resid 12 through 36 ) A 37 B A 49 B X-RAY DIFFRACTION 3 chain 'A' and (resid 37 through 49 ) author_and_software_defined_assembly PISA 2 dimeric none 2460 -23 17090 A C 5 A O2 C 5 1_555 A NA 109 J NA NA 1_555 A U 36 A O4 U 36 1_555 85.8 A G 6 A O6 G 6 1_555 A K 103 D K K 1_555 A G 7 A O6 G 7 1_555 77.3 A G 6 A O6 G 6 1_555 A K 103 D K K 1_555 A G 10 A O6 G 10 1_555 75.4 A G 7 A O6 G 7 1_555 A K 103 D K K 1_555 A G 10 A O6 G 10 1_555 90.3 A G 6 A O6 G 6 1_555 A K 103 D K K 1_555 A G 11 A O6 G 11 1_555 146.3 A G 7 A O6 G 7 1_555 A K 103 D K K 1_555 A G 11 A O6 G 11 1_555 84.7 A G 10 A O6 G 10 1_555 A K 103 D K K 1_555 A G 11 A O6 G 11 1_555 76.4 A G 6 A O6 G 6 1_555 A K 103 D K K 1_555 A G 35 A O6 G 35 1_555 94.3 A G 7 A O6 G 7 1_555 A K 103 D K K 1_555 A G 35 A O6 G 35 1_555 69.7 A G 10 A O6 G 10 1_555 A K 103 D K K 1_555 A G 35 A O6 G 35 1_555 159.2 A G 11 A O6 G 11 1_555 A K 103 D K K 1_555 A G 35 A O6 G 35 1_555 106.0 A G 6 A O6 G 6 1_555 A K 103 D K K 1_555 A G 38 A O6 G 38 1_555 77.2 A G 7 A O6 G 7 1_555 A K 103 D K K 1_555 A G 38 A O6 G 38 1_555 124.9 A G 10 A O6 G 10 1_555 A K 103 D K K 1_555 A G 38 A O6 G 38 1_555 128.3 A G 11 A O6 G 11 1_555 A K 103 D K K 1_555 A G 38 A O6 G 38 1_555 135.8 A G 35 A O6 G 35 1_555 A K 103 D K K 1_555 A G 38 A O6 G 38 1_555 64.5 A G 6 A O6 G 6 1_555 A K 103 D K K 1_555 A G 40 A O6 G 40 1_555 152.7 A G 7 A O6 G 7 1_555 A K 103 D K K 1_555 A G 40 A O6 G 40 1_555 114.7 A G 10 A O6 G 10 1_555 A K 103 D K K 1_555 A G 40 A O6 G 40 1_555 126.4 A G 11 A O6 G 11 1_555 A K 103 D K K 1_555 A G 40 A O6 G 40 1_555 61.0 A G 35 A O6 G 35 1_555 A K 103 D K K 1_555 A G 40 A O6 G 40 1_555 69.6 A G 38 A O6 G 38 1_555 A K 103 D K K 1_555 A G 40 A O6 G 40 1_555 75.9 A G 6 A O6 G 6 1_555 A K 103 D K K 1_555 A G 42 A O6 G 42 1_555 109.1 A G 7 A O6 G 7 1_555 A K 103 D K K 1_555 A G 42 A O6 G 42 1_555 158.0 A G 10 A O6 G 10 1_555 A K 103 D K K 1_555 A G 42 A O6 G 42 1_555 71.8 A G 11 A O6 G 11 1_555 A K 103 D K K 1_555 A G 42 A O6 G 42 1_555 78.8 A G 35 A O6 G 35 1_555 A K 103 D K K 1_555 A G 42 A O6 G 42 1_555 129.0 A G 38 A O6 G 38 1_555 A K 103 D K K 1_555 A G 42 A O6 G 42 1_555 77.0 A G 40 A O6 G 40 1_555 A K 103 D K K 1_555 A G 42 A O6 G 42 1_555 69.4 A G 6 A O6 G 6 1_555 A K 104 E K K 1_555 A G 38 A O6 G 38 1_555 67.9 A G 6 A O6 G 6 1_555 A K 104 E K K 1_555 A G 42 A O6 G 42 1_555 104.6 A G 38 A O6 G 38 1_555 A K 104 E K K 1_555 A G 42 A O6 G 42 1_555 69.2 A G 6 A O6 G 6 1_555 A K 104 E K K 1_555 A U 43 A O2' U 43 1_555 150.6 A G 38 A O6 G 38 1_555 A K 104 E K K 1_555 A U 43 A O2' U 43 1_555 88.5 A G 42 A O6 G 42 1_555 A K 104 E K K 1_555 A U 43 A O2' U 43 1_555 81.5 A G 6 A O6 G 6 1_555 A K 104 E K K 1_555 A U 43 A O2 U 43 1_555 77.1 A G 38 A O6 G 38 1_555 A K 104 E K K 1_555 A U 43 A O2 U 43 1_555 71.2 A G 42 A O6 G 42 1_555 A K 104 E K K 1_555 A U 43 A O2 U 43 1_555 135.8 A U 43 A O2' U 43 1_555 A K 104 E K K 1_555 A U 43 A O2 U 43 1_555 78.8 A G 6 A O6 G 6 1_555 A K 104 E K K 1_555 A G 44 A O6 G 44 1_555 96.8 A G 38 A O6 G 38 1_555 A K 104 E K K 1_555 A G 44 A O6 G 44 1_555 155.3 A G 42 A O6 G 42 1_555 A K 104 E K K 1_555 A G 44 A O6 G 44 1_555 98.0 A U 43 A O2' U 43 1_555 A K 104 E K K 1_555 A G 44 A O6 G 44 1_555 111.0 A U 43 A O2 U 43 1_555 A K 104 E K K 1_555 A G 44 A O6 G 44 1_555 125.9 A U 21 A O4 U 21 1_555 A K 107 H K K 1_555 A G 24 A OP1 G 24 1_555 60.9 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_556 -x,y,-z+1 crystal symmetry operation 0.0000000000 0.0000000000 92.2230000000 1 A G 1 A G 1 1 Y 1 -3.70 0.60 125.10 121.40 A A A C6 N1 C2 G G G 35 35 35 N 1 3.79 0.60 125.90 129.69 A A A C5 C4 O4 U U U 43 43 43 N 65.85 0.2816 0.2389 0.2410 2.44 28.63 313 6079 6392 4.90 98.51 0.3673 1 FREE R-VALUE 1.48 MOLECULAR REPLACEMENT 33.3429 0.9000 1.1100 GeoStd + Monomer Library + CDL v1.2 FLAT BULK SOLVENT MODEL 2.44 28.63 1 1097 66 1030 0 0.0085 1216 1.1031 1896 0.0474 246 0.0134 53 15.5226 603 0.3664 0.3025 3.07 159 2972 98.68 0.2621 0.2229 28.63 154 3107 98.37 51.301 2.44 32.39 9VMZ 6439 0.999 0.113 0.034 1 10.4 12.0 99.8 0.910 2.44 2.48 2.3 623 0.455 0.277 1 refinement PHENIX 1.20.1_4487 refinement PHENIX 1.20.1_4487 data reduction xia2 data scaling xia2 phasing PHASER 18 orthorhombic P 21 2 21 P 2 2ab (y,z,x) x,y,z x+1/2,-y,-z+1/2 -x,y,-z -x+1/2,-y,z+1/2 N Crystal structure of Broccoli aptamer in with BI 1 N N 2 N N 3 N N 4 N N 4 N N 4 N N 4 N N 4 N N 4 N N 5 N N 6 N N covale 1.629 both A G 2 A P G 2 1_555 A GTP 101 B O3' GTP 1_555 metalc 3.136 A C 5 A O2 C 5 1_555 A NA 109 J NA NA 1_555 metalc 2.803 A G 6 A O6 G 6 1_555 A K 103 D K K 1_555 metalc 2.924 A G 6 A O6 G 6 1_555 A K 104 E K K 1_555 metalc 2.947 A G 7 A O6 G 7 1_555 A K 103 D K K 1_555 metalc 2.828 A G 7 A OP2 G 7 1_555 A K 105 F K K 1_555 metalc 2.862 A G 10 A O6 G 10 1_555 A K 103 D K K 1_555 metalc 2.724 A G 11 A O6 G 11 1_555 A K 103 D K K 1_555 metalc 2.637 A U 21 A O4 U 21 1_555 A K 107 H K K 1_555 metalc 3.399 A G 24 A OP1 G 24 1_555 A K 107 H K K 2_556 metalc 3.383 A G 35 A O6 G 35 1_555 A K 103 D K K 1_555 metalc 3.067 A U 36 A O4 U 36 1_555 A NA 109 J NA NA 1_555 metalc 2.611 A G 38 A O6 G 38 1_555 A K 103 D K K 1_555 metalc 3.126 A G 38 A O6 G 38 1_555 A K 104 E K K 1_555 metalc 2.948 A G 40 A O6 G 40 1_555 A K 103 D K K 1_555 metalc 2.993 A G 42 A O6 G 42 1_555 A K 103 D K K 1_555 metalc 3.043 A G 42 A O6 G 42 1_555 A K 104 E K K 1_555 metalc 2.583 A U 43 A O2' U 43 1_555 A K 104 E K K 1_555 metalc 2.576 A U 43 A O2 U 43 1_555 A K 104 E K K 1_555 metalc 3.006 A G 44 A O6 G 44 1_555 A K 104 E K K 1_555 hydrog TYPE_28_PAIR A G 2 A N1 G 2 1_555 A U 48 A O2 U 48 1_555 hydrog TYPE_28_PAIR A G 2 A O6 G 2 1_555 A U 48 A N3 U 48 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 A C 47 A N3 C 47 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 A C 47 A O2 C 47 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 A C 47 A N4 C 47 1_555 hydrog TYPE_8_PAIR A A 4 A N1 A 4 1_555 A G 46 A N1 G 46 1_555 hydrog TYPE_8_PAIR A A 4 A N6 A 4 1_555 A G 46 A O6 G 46 1_555 hydrog C-G PAIR A C 5 A N4 C 5 1_555 A G 45 A O6 G 45 1_555 hydrog TYPE_6_PAIR A G 6 A N1 G 6 1_555 A G 10 A O6 G 10 1_555 hydrog TYPE_6_PAIR A G 6 A N2 G 6 1_555 A G 10 A N7 G 10 1_555 hydrog TYPE_6_PAIR A G 6 A N7 G 6 1_555 A G 38 A N2 G 38 1_555 hydrog TYPE_6_PAIR A G 6 A O6 G 6 1_555 A G 38 A N1 G 38 1_555 hydrog TYPE_6_PAIR A G 7 A N1 G 7 1_555 A G 11 A O6 G 11 1_555 hydrog TYPE_6_PAIR A G 7 A N2 G 7 1_555 A G 11 A N7 G 11 1_555 hydrog TYPE_6_PAIR A G 7 A N7 G 7 1_555 A G 35 A N2 G 35 1_555 hydrog TYPE_6_PAIR A G 7 A O6 G 7 1_555 A G 35 A N1 G 35 1_555 hydrog C-U MISPAIR A C 9 A N4 C 9 1_555 A U 36 A O4 U 36 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 A G 44 A N1 G 44 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 A G 44 A O6 G 44 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 A G 44 A N2 G 44 1_555 hydrog TYPE_6_PAIR A G 10 A N1 G 10 1_555 A G 42 A O6 G 42 1_555 hydrog TYPE_6_PAIR A G 10 A N2 G 10 1_555 A G 42 A N7 G 42 1_555 hydrog TYPE_6_PAIR A G 11 A N1 G 11 1_555 A G 40 A O6 G 40 1_555 hydrog TYPE_6_PAIR A G 11 A N2 G 11 1_555 A G 40 A N7 G 40 1_555 hydrog WATSON-CRICK A U 13 A N3 U 13 1_555 A A 34 A N1 A 34 1_555 hydrog WATSON-CRICK A U 13 A O4 U 13 1_555 A A 34 A N6 A 34 1_555 hydrog WATSON-CRICK A C 14 A N3 C 14 1_555 A G 33 A N1 G 33 1_555 hydrog WATSON-CRICK A C 14 A N4 C 14 1_555 A G 33 A O6 G 33 1_555 hydrog WATSON-CRICK A C 14 A O2 C 14 1_555 A G 33 A N2 G 33 1_555 hydrog WATSON-CRICK A C 15 A N3 C 15 1_555 A G 30 A N1 G 30 1_555 hydrog WATSON-CRICK A C 15 A N4 C 15 1_555 A G 30 A O6 G 30 1_555 hydrog WATSON-CRICK A C 15 A O2 C 15 1_555 A G 30 A N2 G 30 1_555 hydrog WATSON-CRICK A A 16 A N1 A 16 1_555 A U 29 A N3 U 29 1_555 hydrog WATSON-CRICK A A 16 A N6 A 16 1_555 A U 29 A O4 U 29 1_555 hydrog WATSON-CRICK A G 17 A N1 G 17 1_555 A C 28 A N3 C 28 1_555 hydrog WATSON-CRICK A G 17 A N2 G 17 1_555 A C 28 A O2 C 28 1_555 hydrog WATSON-CRICK A G 17 A O6 G 17 1_555 A C 28 A N4 C 28 1_555 hydrog WATSON-CRICK A A 18 A N1 A 18 1_555 A U 27 A N3 U 27 1_555 hydrog WATSON-CRICK A A 18 A N6 A 18 1_555 A U 27 A O4 U 27 1_555 hydrog WATSON-CRICK A U 19 A N3 U 19 1_555 A A 26 A N1 A 26 1_555 hydrog WATSON-CRICK A U 19 A O4 U 19 1_555 A A 26 A N6 A 26 1_555 hydrog WATSON-CRICK A A 20 A N1 A 20 1_555 A U 25 A N3 U 25 1_555 hydrog WATSON-CRICK A A 20 A N6 A 20 1_555 A U 25 A O4 U 25 1_555 hydrog U-G MISPAIR A U 21 A O2 U 21 1_555 A G 24 A N1 G 24 1_555 hydrog HOOGSTEEN A U 31 A N3 U 31 1_555 A A 34 A N7 A 34 1_555 hydrog HOOGSTEEN A U 31 A O4 U 31 1_555 A A 34 A N6 A 34 1_555 hydrog TYPE_6_PAIR A G 35 A N7 G 35 1_555 A G 40 A N2 G 40 1_555 hydrog TYPE_6_PAIR A G 35 A O6 G 35 1_555 A G 40 A N1 G 40 1_555 hydrog U-U MISPAIR A U 36 A O2 U 36 1_555 A U 43 A N3 U 43 1_555 hydrog TYPE_6_PAIR A G 38 A N7 G 38 1_555 A G 42 A N2 G 42 1_555 hydrog TYPE_6_PAIR A G 38 A O6 G 38 1_555 A G 42 A N1 G 42 1_555 RNA Fluorescent light-up aptamer, Broccoli aptamer, BI, RNA 9VMZ PDB 1 1 9VMZ 1 49 9VMZ 1 49 9VMZ A 1 1 49 18 P 21 2 21 P 2 2ab (y,z,x)