0.008732 0.000000 0.000000 0.000000 0.008732 0.000000 0.000000 0.000000 0.008732 0.00000 0.00000 0.00000 Atugi, T. Kanazawa, H. Sugiyama, Y. Fujiwara, S. Ono, A. Kondo, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 48 90.00 90.00 90.00 114.523 114.523 114.523 C9 H12 Br N2 O8 P 387.078 n 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking N 1 N N N 2 N C N 3 N N N 4 N C N 5 N C N 6 N C N 7 N O N 8 N O N 9 N BR N 10 R C N 11 N C N 12 S C N 13 R C N 14 N O N 15 N O N 16 N C N 17 N O N 18 N P N 19 N O N 20 N O N 21 N O N 22 N H N 23 N H 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 O N 35 N P N 36 N O N 37 N O N 38 N O N 39 N C N 40 R C N 41 N O N 42 S C N 43 N O N 44 N C N 45 R C Y 46 N N Y 47 N C Y 48 N N Y 49 N C Y 50 N C N 51 N N Y 52 N N Y 53 N C Y 54 N N Y 55 N C N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N O N 71 N P N 72 N O N 73 N O N 74 N O N 75 N C N 76 R C N 77 N O N 78 S C N 79 N O N 80 N C N 81 R C N 82 N N N 83 N C N 84 N O N 85 N N N 86 N C N 87 N N N 88 N C N 89 N C N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N O N 105 N P N 106 N O N 107 N O N 108 N O N 109 N C N 110 R C N 111 N O N 112 S C N 113 N O N 114 N C N 115 R C Y 116 N N Y 117 N C Y 118 N N Y 119 N C N 120 N C N 121 N O N 122 N N N 123 N C N 124 N N N 125 N N Y 126 N C N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N O N 142 N P N 143 N O N 144 N O N 145 N O N 146 N C N 147 R C N 148 N O N 149 S C N 150 N O N 151 N C N 152 R C N 153 N N N 154 N C N 155 N O N 156 N N N 157 N C N 158 N O N 159 N C N 160 N C N 161 N C N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N doub N 6 N sing N 7 N sing N 8 N sing N 9 N doub N 10 N doub 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 N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N doub N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N doub N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing Y 58 N sing Y 59 N sing Y 60 N doub N 61 N sing Y 62 N sing Y 63 N sing Y 64 N doub N 65 N sing Y 66 N doub N 67 N sing N 68 N sing Y 69 N sing Y 70 N doub N 71 N sing Y 72 N sing N 73 N sing N 74 N sing N 75 N doub 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 sing 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 doub N 99 N sing N 100 N doub N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N doub 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 sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing 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 Y 131 N sing Y 132 N sing Y 133 N doub N 134 N sing Y 135 N sing N 136 N sing Y 137 N doub N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N doub N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N doub N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing 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 sing 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 doub N 177 N sing N 178 N sing N 179 N doub N 180 N sing N 181 N sing N 182 N sing N 183 N sing To Be Published 0353 2,2'-bipyridine linked DNA oligomer (CGCGAAT[BrU]CGCG) in the presence of Ni2+ ion 10.2210/pdb9u9m/pdb pdb_00009u9m 100 1 N PIXEL 2023-11-26 DECTRIS EIGER X 16M SINGLE WAVELENGTH M x-ray 1 0.91962 1.0 BL-17A Photon Factory 0.91962 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 3728.262 DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*(BRU)P*CP*GP*CP*G)-3') 1 syn polymer no yes (DC)(DG)(DC)(DG)(DA)(DA)(DT)(BRU)(DC)(DG)(DC)(DG) CGCGAATUCGCG A polydeoxyribonucleotide n n n n n n n n n n n n 1 8.39 85.35 VAPOR DIFFUSION, SITTING DROP 7.0 MOPS, hexaamminecobalt(III) chloride, Potassium chloride, PEG3350 293 -3.808 1 19 A 2 A 11 1.915 A_DG2:DC11_A 1 5.466 -0.667 -0.077 0.074 2.837 1 A 3 A 10 8.099 A_DC3:DG10_A 2 3.390 -0.982 -0.079 0.538 14.351 1 19 A 4 A 9 9.109 A_DG4:DC9_A 3 -3.608 -0.319 0.461 0.316 3.162 1 20 A 5 A 8 -2.205 A_DA5:BRU8_A 4 -14.869 1.003 0.391 -0.141 -0.411 1 20 A 6 A 7 -0.306 A_DA6:DT7_A 5 -18.506 0.374 0.710 -0.169 0.411 1 20 A 7 A 6 -0.306 A_DT7:DA6_A 6 -18.506 -0.374 0.710 -0.169 -3.162 1 20 A 8 A 5 -2.205 A_BRU8:DA5_A 7 -14.869 -1.003 0.391 -0.141 -14.351 1 19 A 9 A 4 9.109 A_DC9:DG4_A 8 -3.608 0.319 0.461 0.316 -2.837 1 A 10 A 3 8.099 A_DG10:DC3_A 9 3.390 0.982 -0.079 0.538 3.808 1 19 A 11 A 2 1.915 A_DC11:DG2_A 10 5.466 0.667 -0.077 0.074 3.113 29.515 A A 2 3 -1.887 A A 11 10 3.132 -0.961 0.979 0.017 AA_DG2DC3:DG10DC11_AA 1 -0.505 0.992 29.496 0.229 -2.024 3.244 36.043 A A 3 4 6.538 A A 10 9 3.121 4.033 -0.518 1.010 AA_DC3DG4:DC9DG10_AA 2 -3.022 4.899 35.701 1.072 0.419 3.497 46.134 A A 4 5 -2.498 A A 9 8 3.443 -1.955 -0.866 -0.183 AA_DG4DA5:BRU8DC9_AA 3 -3.203 4.092 45.990 -0.056 0.813 3.302 32.501 A A 5 6 -16.315 A A 8 7 3.232 -9.006 0.209 -0.818 AA_DA5DA6:DT7BRU8_AA 4 -2.849 5.161 31.133 0.148 -0.883 3.086 31.200 A A 6 7 -2.614 A A 7 6 3.046 -1.405 0.000 -0.977 AA_DA6DT7:DA6DT7_AA 5 0.000 0.000 31.169 -1.566 0.000 3.302 32.501 A A 7 8 -16.315 A A 6 5 3.232 -9.006 -0.209 -0.818 AA_DT7BRU8:DA5DA6_AA 6 2.849 -5.161 31.133 0.148 0.883 3.497 46.134 A A 8 9 -2.498 A A 5 4 3.443 -1.955 0.866 -0.183 AA_BRU8DC9:DG4DA5_AA 7 3.203 -4.092 45.990 -0.056 -0.813 3.244 36.043 A A 9 10 6.538 A A 4 3 3.121 4.033 0.518 1.010 AA_DC9DG10:DC3DG4_AA 8 3.022 -4.899 35.701 1.072 -0.419 3.113 29.515 A A 10 11 -1.887 A A 3 2 3.132 -0.961 -0.979 0.017 AA_DG10DC11:DG2DC3_AA 9 0.505 -0.992 29.496 0.229 2.024 repository Initial release 1 0 2026-04-01 Japan Japan Agency for Medical Research and Development (AMED) JP23ama121014 Japan Japan Society for the Promotion of Science (JSPS) 21H01956 j.kondo@sophia.ac.jp 0000-0002-5682-3685 Jiro Kondo principal investigator/group leader N PDBJ Y PDBJ 2025-03-28 REL REL 32630 synthetic construct sample 1 12 N N DC 1 n 1 DC 1 A DG 2 n 2 DG 2 A DC 3 n 3 DC 3 A DG 4 n 4 DG 4 A DA 5 n 5 DA 5 A DA 6 n 6 DA 6 A DT 7 n 7 DT 7 A BRU 8 n 8 BRU 8 A DC 9 n 9 DC 9 A DG 10 n 10 DG 10 A DC 11 n 11 DC 11 A DG 12 n 12 DG 12 A author_and_software_defined_assembly PISA 2 dimeric none 2040 7 4670 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 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 46_455 z-1/4,-y+3/4,x+1/4 crystal symmetry operation -28.6307500000 85.8922500000 28.6307500000 0.2479 0.2636 0.2620 3.20 33.06 225 3956 10.01 98.68 0.12 1 FREE R-VALUE 1.93 SAD 29.95 0.90 1.10 ML FLAT BULK SOLVENT MODEL 3.20 33.06 0 243 0 243 0 0.012 272 1.753 418 35.494 110 0.167 46 0.005 12 0.2939 0.3031 3.67 129 1154 96.00 0.2536 0.2811 4.61 135 1189 100.00 0.2290 0.2431 33.06 132 1217 100.00 3.20 33.1 9U9M 3997 0.9990000000000001 0.155 0.156 1 30.58 82.8 100 0.13 3.21 3.29 302 1.0 0.131 1 0.324 3.29 3.38 284 1.0 0.326 1 0.708 3.38 3.48 271 0.98 0.713 1 0.415 3.48 3.59 280 0.996 0.418 1 0.311 3.59 3.7 258 0.996 0.313 1 0.43799999999999994 3.70 3.83 259 0.995 0.441 1 0.39299999999999996 3.83 3.98 246 0.996 0.395 1 0.264 3.98 4.14 243 0.9990000000000001 0.265 1 0.20600000000000002 4.14 4.33 221 0.9990000000000001 0.207 1 0.16699999999999998 4.33 4.54 219 0.9990000000000001 0.168 1 0.174 4.54 4.78 206 0.9990000000000001 0.175 1 0.162 4.78 5.07 191 0.9990000000000001 0.163 1 0.13 5.07 5.42 193 0.9990000000000001 0.131 1 0.115 5.42 5.86 160 1.0 0.115 1 0.11699999999999999 5.86 6.42 154 1.0 0.11800000000000001 1 0.105 6.42 7.17 144 0.9990000000000001 0.106 1 0.094 7.17 8.28 131 0.9990000000000001 0.095 1 0.1 8.28 10.15 103 0.9990000000000001 0.10099999999999999 1 0.102 10.15 14.35 85 0.9990000000000001 0.10300000000000001 1 0.099 14.35 33.1 47 0.998 0.1 1 refinement PHENIX (1.20.1_4487: ???) data scaling XSCALE data reduction XDS phasing AutoSol N 2,2'-bipyridine linked DNA oligomer (CGCGAAT[BrU]CGCG) in the presence of Ni2+ ion 1 N N covale 1.605 both A DT 7 A O3' DT 7 1_555 A BRU 8 A P BRU 8 1_555 covale 1.608 both A BRU 8 A O3' BRU 8 1_555 A DC 9 A P DC 9 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 A DC 11 A N3 DC 11 46_455 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 A DC 11 A O2 DC 11 46_455 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 A DC 11 A N4 DC 11 46_455 hydrog DC-DG PAIR A DC 3 A O2 DC 3 1_555 A DG 10 A N2 DG 10 46_455 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 A DC 9 A N3 DC 9 46_455 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 A DC 9 A O2 DC 9 46_455 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 A DC 9 A N4 DC 9 46_455 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 A BRU 8 A N3 BRU 8 46_455 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 A BRU 8 A O4 BRU 8 46_455 hydrog TYPE_1_PAIR A DA 6 A N1 DA 6 1_555 A DA 6 A N6 DA 6 46_455 hydrog TYPE_1_PAIR A DA 6 A N6 DA 6 1_555 A DA 6 A N1 DA 6 46_455 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 A DT 7 A N3 DT 7 46_455 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 A DT 7 A O4 DT 7 46_455 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 A DA 6 A N1 DA 6 46_455 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 A DA 6 A N6 DA 6 46_455 hydrog WATSON-CRICK A BRU 8 A N3 BRU 8 1_555 A DA 5 A N1 DA 5 46_455 hydrog WATSON-CRICK A BRU 8 A O4 BRU 8 1_555 A DA 5 A N6 DA 5 46_455 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 A DG 4 A N1 DG 4 46_455 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 A DG 4 A O6 DG 4 46_455 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 A DG 4 A N2 DG 4 46_455 hydrog DG-DC PAIR A DG 10 A N2 DG 10 1_555 A DC 3 A O2 DC 3 46_455 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 A DG 2 A N1 DG 2 46_455 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 A DG 2 A O6 DG 2 46_455 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 A DG 2 A N2 DG 2 46_455 DNA DNA, oligomer 9U9M PDB 1 1 9U9M 1 12 9U9M 1 12 9U9M A 1 1 12 214 I 41 3 2