0.024877 0.000000 0.000000 0.000000 0.024877 0.000000 0.000000 0.000000 0.012931 0.000000 0.000000 0.000000 Ng, H.L. Kopka, M.L. Dickerson, R.E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 40.197 40.197 77.336 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 H2 O 18.015 WATER non-polymer 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 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C 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 H N 35 N H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C 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 H N 71 N O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C 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 H N 105 N H N 106 N H N 107 N H N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C 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 H N 142 N H N 143 N H N 144 N O N 145 N H N 146 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 Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub 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 N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub 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 Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub 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 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 doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 97 2035 2039 10.1073/pnas.040571197 10688897 The structure of a stable intermediate in the A ;-> B DNA helix transition 2000 10.2210/pdb1dc0/pdb pdb_00001dc0 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 110 1 AREA DETECTOR SINGLE WAVELENGTH M x-ray 1 0.978 1.0 NSLS 0.978 SYNCHROTRON NSLS 3663.392 DNA (5'-D(*CP*AP*TP*GP*GP*GP*CP*CP*CP*AP*TP*G)-3') 2 syn polymer 18.015 water 93 nat water no no (DC)(DA)(DT)(DG)(DG)(DG)(DC)(DC)(DC)(DA)(DT)(DG) CATGGGCCCATG A,B polydeoxyribonucleotide n n n n n n n n n n n n 1 2.13 42.30 VAPOR DIFFUSION, SITTING DROP 7.0 2.3MM DUPLEX DNA, 120 MM CALCIUM ACETATE, 4.8 MM SPERMINE, 60 MM SODIUM CACODYLATE BUFFER, PH 7.0, 9.5% MPD IN DROP, 25% MPD IN RESERVOIR, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 CALCIUM ACETATE 1 SPERMINE 1 SODIUM CACODYLATE 1 MPD 1 MPD 2 -2.789 1 19 A 1 B 24 -0.829 A_DC1:DG24_B 1 -5.711 0.137 0.041 -0.180 0.144 1 20 A 2 B 23 6.141 A_DA2:DT23_B 2 -6.665 -0.042 0.098 -0.184 -1.114 1 20 A 3 B 22 3.771 A_DT3:DA22_B 3 -8.777 -0.125 0.130 -0.117 0.462 1 19 A 4 B 21 0.703 A_DG4:DC21_B 4 -8.478 -0.190 0.128 -0.128 -6.622 1 19 A 5 B 20 -3.104 A_DG5:DC20_B 5 -11.684 -0.187 -0.006 -0.169 -7.518 1 19 A 6 B 19 0.380 A_DG6:DC19_B 6 -7.991 -0.281 0.086 -0.121 6.919 1 19 A 7 B 18 -2.665 A_DC7:DG18_B 7 -7.525 0.141 0.101 -0.113 9.406 1 19 A 8 B 17 -0.308 A_DC8:DG17_B 8 -12.582 0.047 -0.024 -0.144 4.308 1 19 A 9 B 16 1.123 A_DC9:DG16_B 9 -9.123 0.226 0.007 -0.155 -0.819 1 20 A 10 B 15 4.985 A_DA10:DT15_B 10 -7.750 0.068 0.035 -0.179 2.099 1 20 A 11 B 14 2.361 A_DT11:DA14_B 11 -1.917 -0.012 0.039 -0.127 23.520 1 19 A 12 B 13 -0.876 A_DG12:DC13_B 12 6.996 -0.260 0.318 -0.066 2.853 32.715 A A 1 2 11.321 B B 24 23 3.161 6.338 0.725 -1.370 AA_DC1DA2:DT23DG24_BB 1 0.343 -0.612 32.110 -3.448 -1.231 3.422 33.432 A A 2 3 -0.451 B B 23 22 3.407 -0.259 0.054 -2.013 AA_DA2DT3:DA22DT23_BB 2 -0.133 0.232 33.430 -3.454 -0.116 2.901 27.468 A A 3 4 7.902 B B 22 21 3.150 3.740 -0.603 -1.795 AA_DT3DG4:DC21DA22_BB 3 -0.950 2.007 27.201 -4.636 1.053 3.364 33.658 A A 4 5 4.160 B B 21 20 3.484 2.407 -0.404 -1.505 AA_DG4DG5:DC20DC21_BB 4 0.596 -1.031 33.569 -3.010 0.800 3.000 32.892 A A 5 6 7.529 B B 20 19 3.225 4.250 0.471 -1.713 AA_DG5DG6:DC19DC20_BB 5 1.348 -2.388 32.596 -3.719 -0.611 2.830 30.602 A A 6 7 9.194 B B 19 18 2.991 4.833 -0.531 -0.840 AA_DG6DC7:DG18DC19_BB 6 -0.268 0.509 30.226 -2.448 0.958 3.083 32.850 A A 7 8 4.757 B B 18 17 3.193 2.687 0.329 -1.266 AA_DC7DC8:DG17DG18_BB 7 0.170 -0.301 32.743 -2.681 -0.555 3.352 33.602 A A 8 9 3.738 B B 17 16 3.465 2.159 0.125 -1.552 AA_DC8DC9:DG16DG17_BB 8 -1.622 2.808 33.497 -3.054 -0.493 3.021 30.664 A A 9 10 9.891 B B 16 15 3.347 5.205 0.343 -1.603 AA_DC9DA10:DT15DG16_BB 9 -1.107 2.104 30.209 -4.036 -0.862 3.457 32.477 A A 10 11 -3.517 B B 15 14 3.337 -1.966 -0.376 -2.002 AA_DA10DT11:DA14DT15_BB 10 -0.796 1.424 32.410 -3.221 0.527 2.013 24.679 A A 11 12 25.385 B B 14 13 2.844 10.495 -1.159 -1.588 AA_DT11DG12:DC13DA14_BB 11 -2.443 5.909 22.235 -6.224 2.127 chem_comp_atom chem_comp_bond database_2 repository Initial release Version format compliance Version format compliance Structure summary Data collection Database references 1 0 2000-03-06 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-02-01 1 4 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 1999-11-03 REL REL HOH water HOH 103 2 HOH HOH 103 A HOH 105 2 HOH HOH 105 A HOH 109 2 HOH HOH 109 A HOH 111 2 HOH HOH 111 A HOH 113 2 HOH HOH 113 A HOH 115 2 HOH HOH 115 A HOH 117 2 HOH HOH 117 A HOH 118 2 HOH HOH 118 A HOH 119 2 HOH HOH 119 A HOH 121 2 HOH HOH 121 A HOH 123 2 HOH HOH 123 A HOH 124 2 HOH HOH 124 A HOH 125 2 HOH HOH 125 A HOH 126 2 HOH HOH 126 A HOH 131 2 HOH HOH 131 A HOH 132 2 HOH HOH 132 A HOH 134 2 HOH HOH 134 A HOH 136 2 HOH HOH 136 A HOH 137 2 HOH HOH 137 A HOH 138 2 HOH HOH 138 A HOH 139 2 HOH HOH 139 A HOH 140 2 HOH HOH 140 A HOH 144 2 HOH HOH 144 A HOH 145 2 HOH HOH 145 A HOH 146 2 HOH HOH 146 A HOH 147 2 HOH HOH 147 A HOH 148 2 HOH HOH 148 A HOH 149 2 HOH HOH 149 A HOH 150 2 HOH HOH 150 A HOH 152 2 HOH HOH 152 A HOH 153 2 HOH HOH 153 A HOH 154 2 HOH HOH 154 A HOH 159 2 HOH HOH 159 A HOH 162 2 HOH HOH 162 A HOH 163 2 HOH HOH 163 A HOH 164 2 HOH HOH 164 A HOH 167 2 HOH HOH 167 A HOH 168 2 HOH HOH 168 A HOH 169 2 HOH HOH 169 A HOH 173 2 HOH HOH 173 A HOH 174 2 HOH HOH 174 A HOH 175 2 HOH HOH 175 A HOH 176 2 HOH HOH 176 A HOH 178 2 HOH HOH 178 A HOH 180 2 HOH HOH 180 A HOH 185 2 HOH HOH 185 A HOH 187 2 HOH HOH 187 A HOH 192 2 HOH HOH 192 A HOH 101 2 HOH HOH 101 B HOH 102 2 HOH HOH 102 B HOH 104 2 HOH HOH 104 B HOH 106 2 HOH HOH 106 B HOH 107 2 HOH HOH 107 B HOH 108 2 HOH HOH 108 B HOH 110 2 HOH HOH 110 B HOH 112 2 HOH HOH 112 B HOH 114 2 HOH HOH 114 B HOH 116 2 HOH HOH 116 B HOH 120 2 HOH HOH 120 B HOH 122 2 HOH HOH 122 B HOH 127 2 HOH HOH 127 B HOH 128 2 HOH HOH 128 B HOH 129 2 HOH HOH 129 B HOH 130 2 HOH HOH 130 B HOH 133 2 HOH HOH 133 B HOH 135 2 HOH HOH 135 B HOH 141 2 HOH HOH 141 B HOH 142 2 HOH HOH 142 B HOH 143 2 HOH HOH 143 B HOH 151 2 HOH HOH 151 B HOH 155 2 HOH HOH 155 B HOH 156 2 HOH HOH 156 B HOH 157 2 HOH HOH 157 B HOH 158 2 HOH HOH 158 B HOH 160 2 HOH HOH 160 B HOH 161 2 HOH HOH 161 B HOH 165 2 HOH HOH 165 B HOH 166 2 HOH HOH 166 B HOH 170 2 HOH HOH 170 B HOH 171 2 HOH HOH 171 B HOH 172 2 HOH HOH 172 B HOH 177 2 HOH HOH 177 B HOH 179 2 HOH HOH 179 B HOH 181 2 HOH HOH 181 B HOH 182 2 HOH HOH 182 B HOH 183 2 HOH HOH 183 B HOH 184 2 HOH HOH 184 B HOH 186 2 HOH HOH 186 B HOH 188 2 HOH HOH 188 B HOH 189 2 HOH HOH 189 B HOH 190 2 HOH HOH 190 B HOH 191 2 HOH HOH 191 B HOH 193 2 HOH HOH 193 B C 1 n 1 DC 1 A A 2 n 2 DA 2 A T 3 n 3 DT 3 A G 4 n 4 DG 4 A G 5 n 5 DG 5 A G 6 n 6 DG 6 A C 7 n 7 DC 7 A C 8 n 8 DC 8 A C 9 n 9 DC 9 A A 10 n 10 DA 10 A T 11 n 11 DT 11 A G 12 n 12 DG 12 A C 13 n 1 DC 13 B A 14 n 2 DA 14 B T 15 n 3 DT 15 B G 16 n 4 DG 16 B G 17 n 5 DG 17 B G 18 n 6 DG 18 B C 19 n 7 DC 19 B C 20 n 8 DC 20 B C 21 n 9 DC 21 B A 22 n 10 DA 22 B T 23 n 11 DT 23 B G 24 n 12 DG 24 B author_defined_assembly 2 dimeric 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 1.97 0.30 108.30 110.27 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 4.03 0.30 108.30 112.33 A A A O4' C1' N9 DG DG DG 12 12 12 N 1 -2.49 0.40 104.50 102.01 B B B O4' C4' C3' DC DC DC 13 13 13 N 1 -2.82 0.40 104.50 101.68 B B B O4' C4' C3' DT DT DT 15 15 15 N 1 -3.22 0.40 104.50 101.28 B B B O4' C4' C3' DC DC DC 19 19 19 N 1 3.29 0.50 106.80 110.09 B B B O4' C1' C2' DT DT DT 23 23 23 N 1 -5.54 0.80 109.40 103.86 B B B O5' C5' C4' DG DG DG 24 24 24 N 1 -5.24 0.70 108.00 102.76 B B B O4' C1' N9 DG DG DG 24 24 24 N 1 A A C3' C2' DC DC 1 1 -0.050 0.008 1.516 1.466 N 1 A A C3' C2' DG DG 12 12 -0.053 0.008 1.516 1.463 N 1 B B C3' C2' DG DG 24 24 -0.049 0.008 1.516 1.467 N 0.1900000 0.1680000 0.1720000 0.1720000 1.3 20. 800 16111 16111 5 99.5 RANDOM 1 THROUGHOUT 0 0 SIRAS BASED ON THE IODINATED SEQUENCE D(CAT(IODO-G)GGCCCATG) 1.3 20. 93 579 0 486 0 0.007 0.016 1.3 25. 1DC0 16190 16190 0 0 0.0890000 1 43.6 13.0 99.1 0.1790000 1.30 1.35 1 91.2 model building DM refinement SHELXL-97 data reduction DENZO data scaling SCALEPACK phasing DM CRYSTAL STRUCTURE OF AN A/B-DNA INTERMEDIATE CATGGGCCCATG 1 N N 1 N N 2 N N 2 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 24 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 24 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 24 B N2 DG 12 1_555 hydrog WATSON-CRICK A DA 2 A N1 DA 2 1_555 B DT 23 B N3 DT 11 1_555 hydrog WATSON-CRICK A DA 2 A N6 DA 2 1_555 B DT 23 B O4 DT 11 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B DA 22 B N1 DA 10 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B DA 22 B N6 DA 10 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 21 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 21 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 21 B N4 DC 9 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 B DC 20 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 B DC 20 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 B DC 20 B N4 DC 8 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 19 B N3 DC 7 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 19 B O2 DC 7 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 19 B N4 DC 7 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 18 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 18 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 18 B N2 DG 6 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 17 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 17 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 17 B N2 DG 5 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 16 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 16 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 16 B N2 DG 4 1_555 hydrog WATSON-CRICK A DA 10 A N1 DA 10 1_555 B DT 15 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 10 A N6 DA 10 1_555 B DT 15 B O4 DT 3 1_555 hydrog WATSON-CRICK A DT 11 A N3 DT 11 1_555 B DA 14 B N1 DA 2 1_555 hydrog WATSON-CRICK A DT 11 A O4 DT 11 1_555 B DA 14 B N6 DA 2 1_555 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 B DC 13 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 13 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 13 B N4 DC 1 1_555 DNA A-DNA, B-DNA, INTERMEDIATE, DNA 1DC0 PDB 1 1DC0 1 12 1DC0 1 12 1DC0 A 1 1 12 13 24 1DC0 13 24 1DC0 B 1 1 12 92 tetragonal P 41 21 2