0.040290 0.000000 0.000000 -0.000000 0.022779 0.000000 0.000000 -0.000000 0.021473 0.00000 0.00000 0.00000 Hall, J.P. Ruiz-Morte, S. Murray, C.A. Cardin, C.J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 24.820 43.900 46.570 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 To be Published 0353 GGGCATGCCC in the A-DNA Form 10.2210/pdb4izq/pdb pdb_00004izq 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 PIXEL 2012-10-13 DECTRIS PILATUS 6M Si(111) dual crystal SINGLE WAVELENGTH M x-ray 1 1.7712 1.0 I02 Diamond 1.7712 SYNCHROTRON DIAMOND BEAMLINE I02 3045.993 DNA (5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3') 2 syn polymer 18.015 water 22 nat water no no (DG)(DG)(DG)(DC)(DA)(DT)(DG)(DC)(DC)(DC) GGGCATGCCC A,B polydeoxyribonucleotide n n n n n n n n n n 1 2.08 40.93 VAPOR DIFFUSION, SITTING DROP 7.0 0.1mM 2-phenylpyridine-Pd12-cyanurate, 80mM KCl, 40mM Na-cacodylate, 20mM BaCl2, 12mM spermine, 10%(v/v) 2-methyl-2,4-pentanediol, 1ml 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K 298 -7.680 1 19 A 1 B 10 -2.007 A_DG1:DC10_B 1 -2.514 -0.530 -0.148 -0.195 -5.384 1 19 A 2 B 9 2.798 A_DG2:DC9_B 2 -14.720 -0.162 -0.086 -0.274 -11.060 1 19 A 3 B 8 -0.082 A_DG3:DC8_B 3 -14.906 -0.446 0.022 -0.172 -9.669 1 19 A 4 B 7 -1.100 A_DC4:DG7_B 4 -11.771 -0.070 0.232 -0.198 -7.912 1 20 A 5 B 6 1.612 A_DA5:DT6_B 5 -10.182 -0.323 0.071 -0.249 0.270 1 20 A 6 B 5 -0.672 A_DT6:DA5_B 6 -17.280 0.462 -0.064 -0.160 11.196 1 19 A 7 B 4 1.962 A_DG7:DC4_B 7 -2.623 0.152 0.265 -0.148 10.702 1 19 A 8 B 3 4.229 A_DC8:DG3_B 8 -14.663 0.289 -0.229 -0.139 3.447 1 19 A 9 B 2 0.916 A_DC9:DG2_B 9 -12.735 0.077 -0.096 -0.185 4.486 1 19 A 10 B 1 -3.216 A_DC10:DG1_B 10 0.705 0.125 -0.122 -0.065 3.146 35.322 A A 1 2 6.228 B B 10 9 3.308 3.770 0.651 -1.689 AA_DG1DG2:DC9DC10_BB 1 1.973 -3.258 35.073 -3.335 -0.784 3.257 28.949 A A 2 3 5.980 B B 9 8 3.460 2.984 0.010 -1.829 AA_DG2DG3:DC8DC9_BB 2 0.332 -0.666 28.796 -4.338 0.056 2.977 37.990 A A 3 4 10.050 B B 8 7 3.153 6.499 -1.128 -1.429 AA_DG3DC4:DG7DC8_BB 3 -4.252 6.575 37.216 -2.980 1.219 1.934 27.593 A A 4 5 33.543 B B 7 6 3.198 15.083 0.981 -1.597 AA_DC4DA5:DT6DG7_BB 4 4.053 -9.013 22.819 -6.520 -1.204 2.693 39.706 A A 5 6 18.014 B B 6 5 3.151 12.057 -0.271 -1.081 AA_DA5DT6:DA5DT6_BB 5 0.620 -0.926 37.897 -2.877 0.465 1.898 25.744 A A 6 7 26.482 B B 5 4 2.968 11.375 0.946 -1.476 AA_DT6DG7:DC4DA5_BB 6 -2.980 6.937 22.942 -5.829 -2.783 3.130 31.580 A A 7 8 5.220 B B 4 3 3.327 2.836 -0.370 -1.783 AA_DG7DC8:DG3DC4_BB 7 1.957 -3.602 31.396 -3.797 1.040 2.565 32.633 A A 8 9 20.914 B B 3 2 3.370 11.496 -0.494 -1.827 AA_DC8DC9:DG2DG3_BB 8 -2.881 5.242 30.459 -5.128 0.408 3.098 31.923 A A 9 10 8.929 B B 2 1 3.406 4.892 -0.246 -1.827 AA_DC9DC10:DG1DG2_BB 9 -0.526 0.961 31.551 -4.211 0.352 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model repository Initial release Data collection Database references Refinement description 1 0 2014-02-05 1 1 2024-03-20 1 2 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y PDBJ 2013-01-30 REL REL HOH water Purchased from ATDBio sample Ideal A-DNA from Coot Other in silico model HOH 2 2 HOH HOH 101 A HOH 9 2 HOH HOH 102 A HOH 10 2 HOH HOH 103 A HOH 11 2 HOH HOH 104 A HOH 12 2 HOH HOH 105 A HOH 13 2 HOH HOH 106 A HOH 14 2 HOH HOH 107 A HOH 15 2 HOH HOH 108 A HOH 16 2 HOH HOH 109 A HOH 17 2 HOH HOH 110 A HOH 18 2 HOH HOH 111 A HOH 20 2 HOH HOH 112 A HOH 5 2 HOH HOH 101 B HOH 1 2 HOH HOH 102 B HOH 3 2 HOH HOH 103 B HOH 4 2 HOH HOH 104 B HOH 6 2 HOH HOH 105 B HOH 7 2 HOH HOH 106 B HOH 8 2 HOH HOH 107 B HOH 19 2 HOH HOH 108 B HOH 21 2 HOH HOH 109 B HOH 22 2 HOH HOH 110 B DG 1 n 1 DG 1 A DG 2 n 2 DG 2 A DG 3 n 3 DG 3 A DC 4 n 4 DC 4 A DA 5 n 5 DA 5 A DT 6 n 6 DT 6 A DG 7 n 7 DG 7 A DC 8 n 8 DC 8 A DC 9 n 9 DC 9 A DC 10 n 10 DC 10 A DG 1 n 1 DG 1 B DG 2 n 2 DG 2 B DG 3 n 3 DG 3 B DC 4 n 4 DC 4 B DA 5 n 5 DA 5 B DT 6 n 6 DT 6 B DG 7 n 7 DG 7 B DC 8 n 8 DC 8 B DC 9 n 9 DC 9 B DC 10 n 10 DC 10 B author_and_software_defined_assembly PISA 2 dimeric 970 -5 3760 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 -8.16 0.90 105.70 97.54 A A A O5' P OP2 DG DG DG 7 7 7 N 1 -5.71 0.90 105.70 99.99 A A A O5' P OP2 DC DC DC 9 9 9 N 1 -3.06 0.40 104.50 101.44 B B B O4' C4' C3' DC DC DC 4 4 4 N 25.844 -2.70 0.00 0.00 1.04 -0.00 1.66 0.961 0.963 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.25227 0.19703 0.19970 2.04 31.94 137 3301 3001 4.4 89.33 6.187 0.154 RANDOM 1 THROUGHOUT MOLECULAR REPLACEMENT 0.243 0.205 0.80 0.80 1.20 Ideal A-DNA from Coot MAXIMUM LIKELIHOOD MASK 2.04 31.94 22 426 0 404 0 0.010 0.011 452 0.003 0.020 224 1.549 1.157 694 1.469 3.000 528 0.086 0.200 60 0.014 0.020 242 0.002 0.020 108 0.459 0.311 2.094 9 132 20 55.08 2.04 31.94 4IZQ 3153 3153 2 1 90.7 2.04 2.09 1 57.3 data collection GDA phasing PHASER refinement REFMAC 5.7.0029 data reduction XDS data scaling Aimless GGGCATGCCC in the A-DNA Form 1 N N 1 N N 2 N N 2 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 10 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 10 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 10 B N4 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 9 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 9 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 9 B N4 DC 9 1_555 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 B DC 8 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B DC 8 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B DC 8 B N4 DC 8 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 B DG 7 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 B DG 7 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 B DG 7 B N2 DG 7 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 6 B N3 DT 6 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 6 B O4 DT 6 1_555 hydrog WATSON-CRICK A DT 6 A N3 DT 6 1_555 B DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 6 A O4 DT 6 1_555 B DA 5 B N6 DA 5 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 4 B N3 DC 4 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 4 B O2 DC 4 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 4 B N4 DC 4 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 3 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 3 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 3 B N2 DG 3 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 2 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 2 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 2 B N2 DG 2 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 1 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 1 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 1 B N2 DG 1 1_555 DNA A-DNA, DNA 4IZQ PDB 1 4IZQ 1 10 4IZQ 1 10 4IZQ A 1 1 10 1 10 4IZQ 1 10 4IZQ B 1 1 10 19 P 21 21 21