1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Kaluarachchi, K. Gorenstein, D.G. Luxon, B.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 US J.Biomol.Struct.Dyn. JBSDD6 0646 0739-1102 Conversation 11 123 133 -1 How Do Proteins Recognize DNA? Solution Structure and Local Conformational Dynamics of Lac Operators by 2D NMR 2000 10.2210/pdb1k9h/pdb pdb_00001k9h 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 This sequence has been derived from the natural Lac Operator sequence by symmetrizing the minimum required length for lac repressor binding. 4280.792 5'-D(*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*A)-3' 2 syn polymer no no (DT)(DG)(DT)(DG)(DA)(DG)(DC)(DG)(DC)(DT)(DC)(DA)(DC)(DA) TGTGAGCGCTCACA A,B polydeoxyribonucleotide n n n n n n n n n n n n n n 23.054 1 20 A 1 B 28 5.687 A_DT1:DA28_B 1 -41.343 0.419 -0.275 -0.183 -5.776 1 19 A 2 B 27 -0.940 A_DG2:DC27_B 2 -8.346 -0.382 0.143 -0.265 -2.009 1 20 A 3 B 26 3.780 A_DT3:DA26_B 3 -12.567 0.110 0.185 -0.202 -21.363 1 19 A 4 B 25 0.029 A_DG4:DC25_B 4 -28.448 -0.391 -0.715 -0.336 -27.297 1 20 A 5 B 24 3.054 A_DA5:DT24_B 5 -13.066 -0.074 -0.416 -0.127 -3.060 1 19 A 6 B 23 -0.151 A_DG6:DC23_B 6 -7.235 -0.264 0.095 -0.214 -11.475 1 19 A 7 B 22 -3.467 A_DC7:DG22_B 7 0.479 0.195 0.282 -0.255 13.643 1 19 A 8 B 21 -2.777 A_DG8:DC21_B 8 1.109 -0.155 0.426 -0.232 4.128 1 19 A 9 B 20 -0.502 A_DC9:DG20_B 9 -6.864 0.278 0.039 -0.218 7.988 1 20 A 10 B 19 5.300 A_DT10:DA19_B 10 -1.703 0.039 0.239 -0.161 1.895 1 19 A 11 B 18 -3.053 A_DC11:DG18_B 11 -14.175 0.326 0.106 -0.287 2.525 1 20 A 12 B 17 -2.326 A_DA12:DT17_B 12 -13.667 -0.266 0.226 -0.277 1.562 1 19 A 13 B 16 1.339 A_DC13:DG16_B 13 -6.546 0.528 0.404 -0.241 0.170 1 20 A 14 B 15 -3.574 A_DA14:DT15_B 14 -31.247 -0.011 0.050 -0.216 2.855 46.966 A A 1 2 34.482 B B 28 27 3.619 25.932 -0.828 -0.548 AA_DT1DG2:DC27DA28_BB 1 -8.301 11.039 38.638 -3.044 0.285 3.053 35.399 A A 2 3 7.738 B B 27 26 3.127 4.692 0.013 -0.381 AA_DG2DT3:DA26DC27_BB 2 0.075 -0.124 35.096 -1.281 -0.011 2.922 38.626 A A 3 4 27.937 B B 26 25 3.575 17.661 0.193 -0.501 AA_DT3DG4:DC25DA26_BB 3 8.931 -14.128 33.338 -3.094 0.889 3.247 33.361 A A 4 5 8.443 B B 25 24 3.296 4.830 0.464 -0.003 AA_DG4DA5:DT24DC25_BB 4 -1.030 1.801 33.004 -0.811 -0.980 2.345 32.651 A A 5 6 29.758 B B 24 23 2.808 15.802 -0.451 -0.262 AA_DA5DG6:DC23DT24_BB 5 -9.311 17.534 27.129 -2.840 -0.595 3.360 41.028 A A 6 7 6.633 B B 23 22 3.432 4.638 -0.481 -0.633 AA_DG6DC7:DG22DC23_BB 6 -1.743 2.493 40.741 -1.430 0.488 2.623 26.912 A A 7 8 0.289 B B 22 21 2.634 0.134 0.002 -0.427 AA_DC7DG8:DC21DG22_BB 7 -2.161 4.649 26.826 -0.944 -0.450 3.470 39.753 A A 8 9 3.692 B B 21 20 3.469 2.505 0.525 -0.433 AA_DG8DC9:DG20DC21_BB 8 3.846 -5.667 39.497 -0.946 -0.297 2.447 39.370 A A 9 10 48.121 B B 20 19 3.481 28.880 1.206 -0.133 AA_DC9DT10:DA19DG20_BB 9 6.517 -10.858 26.248 -3.984 -0.936 3.123 32.847 A A 10 11 19.873 B B 19 18 3.373 11.026 -0.270 -0.140 AA_DT10DC11:DG18DA19_BB 10 1.731 -3.120 30.942 -2.183 0.781 3.072 32.798 A A 11 12 9.343 B B 18 17 3.144 5.252 -0.502 -0.357 AA_DC11DA12:DT17DG18_BB 11 -1.687 3.001 32.343 -1.495 0.612 3.335 37.514 A A 12 13 1.065 B B 17 16 3.347 0.685 0.225 0.038 AA_DA12DC13:DG16DT17_BB 12 -1.566 2.435 37.476 -0.033 -0.559 2.862 33.169 A A 13 14 21.124 B B 16 15 3.157 11.693 0.406 -0.300 AA_DC13DA14:DT15DG16_BB 13 7.939 -14.343 30.083 -2.427 0.581 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2001-11-07 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name 1k9l is the Solution structure of the DNA oligomer TATGAGCGCTCATA. RCSB Y RCSB 2001-10-29 REL This structure was determined using standard homonuclear techniques. back calculated data agree with experimental NOESY spectrum,structures with the lowest energy 2 1 2D NOESY 2D TOCSY 150 mM KCl 7.4 ambient 298 K molecular dynamics, matrix relaxation, simulated annealing closest to the average 3.6 mM oligonucleotide, 55 mM potassium phosphate, 150 mM KCl, 0.1mM NaN3 99.96% D2O Kollman. P. refinement Amber versions 3-5 Meadows. R.P. refinement MORASS 1.0 500 Varian VXRS 600 Varian VXRS THY 1 n 1 DT 1 A GUA 2 n 2 DG 2 A THY 3 n 3 DT 3 A GUA 4 n 4 DG 4 A ADE 5 n 5 DA 5 A GUA 6 n 6 DG 6 A CYT 7 n 7 DC 7 A GUA 8 n 8 DG 8 A CYT 9 n 9 DC 9 A THY 10 n 10 DT 10 A CYT 11 n 11 DC 11 A ADE 12 n 12 DA 12 A CYT 13 n 13 DC 13 A ADE 14 n 14 DA 14 A THY 15 n 1 DT 15 B GUA 16 n 2 DG 16 B THY 17 n 3 DT 17 B GUA 18 n 4 DG 18 B ADE 19 n 5 DA 19 B GUA 20 n 6 DG 20 B CYT 21 n 7 DC 21 B GUA 22 n 8 DG 22 B CYT 23 n 9 DC 23 B THY 24 n 10 DT 24 B CYT 25 n 11 DC 25 B ADE 26 n 12 DA 26 B CYT 27 n 13 DC 27 B ADE 28 n 14 DA 28 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 A DG 4 0.079 SIDE CHAIN 1 A DA 5 0.076 SIDE CHAIN 1 A DC 7 0.074 SIDE CHAIN 1 A DA 12 0.094 SIDE CHAIN 1 B DT 15 0.088 SIDE CHAIN 1 B DG 16 0.067 SIDE CHAIN 1 B DG 18 0.097 SIDE CHAIN 1 B DA 19 0.056 SIDE CHAIN 1 B DC 25 0.093 SIDE CHAIN 1 3.86 0.30 108.30 112.16 A A A O4' C1' N1 DT DT DT 1 1 1 N 1 8.21 0.30 108.30 116.51 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 3.18 0.50 113.10 116.28 A A A N7 C8 N9 DG DG DG 4 4 4 N 1 -3.24 0.40 106.40 103.16 A A A C8 N9 C4 DG DG DG 4 4 4 N 1 1.85 0.30 108.30 110.15 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 3.66 0.30 108.30 111.96 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 14.99 1.60 120.90 135.89 A A A P O5' C5' DC DC DC 9 9 9 N 1 2.05 0.30 108.30 110.35 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 -4.25 0.70 102.20 97.95 A A A C4' C3' C2' DT DT DT 10 10 10 N 1 7.93 1.20 102.50 110.43 A A A C3' C2' C1' DT DT DT 10 10 10 N 1 3.18 0.30 108.30 111.48 A A A O4' C1' N1 DC DC DC 11 11 11 N 1 4.48 0.60 106.00 110.48 A A A O4' C4' C3' DA DA DA 12 12 12 N 1 -9.90 0.70 102.20 92.30 A A A C4' C3' C2' DA DA DA 12 12 12 N 1 -4.93 0.80 105.90 100.97 A A A O4' C1' C2' DA DA DA 12 12 12 N 1 4.30 0.30 108.30 112.60 A A A O4' C1' N9 DA DA DA 12 12 12 N 1 3.64 0.30 108.30 111.94 A A A O4' C1' N1 DC DC DC 13 13 13 N 1 2.89 0.30 108.30 111.19 A A A O4' C1' N9 DA DA DA 14 14 14 N 1 2.41 0.30 108.30 110.71 B B B O4' C1' N1 DT DT DT 15 15 15 N 1 7.56 0.30 108.30 115.86 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 -2.49 0.40 106.40 103.91 B B B C8 N9 C4 DG DG DG 18 18 18 N 1 3.24 0.30 108.30 111.54 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 4.24 0.60 106.00 110.24 B B B O4' C4' C3' DT DT DT 24 24 24 N 1 -4.93 0.70 102.20 97.27 B B B C4' C3' C2' DT DT DT 24 24 24 N 1 7.99 1.20 102.50 110.49 B B B C3' C2' C1' DT DT DT 24 24 24 N 1 4.71 0.30 108.30 113.01 B B B O4' C1' N1 DC DC DC 25 25 25 N 1 2.86 0.30 108.30 111.16 B B B O4' C1' N1 DC DC DC 27 27 27 N 1 2.38 0.30 108.30 110.68 B B B O4' C1' N9 DA DA DA 28 28 28 N 1 A A O5' C5' DT DT 1 1 -0.371 0.025 1.418 1.047 N 1 A A O4' C4' DT DT 1 1 -0.071 0.010 1.446 1.375 N 1 A A O3' C3' DT DT 1 1 -0.041 0.006 1.419 1.378 N 1 A A O4' C4' DT DT 3 3 -0.063 0.010 1.446 1.383 N 1 A A P OP1 DC DC 9 9 -0.132 0.017 1.485 1.353 N 1 A A P O5' DC DC 9 9 -0.125 0.010 1.593 1.468 N 1 A A O4' C4' DC DC 9 9 -0.062 0.010 1.446 1.384 N 1 B B O4' C4' DT DT 15 15 -0.068 0.010 1.446 1.378 N 1 B B O4' C4' DT DT 24 24 -0.060 0.010 1.446 1.386 N 1 B B O3' C3' DA DA 28 28 -0.050 0.006 1.419 1.369 N 1 B B C4 C5 DA DA 28 28 -0.046 0.007 1.383 1.337 N NMR structure of DNA TGTGAGCGCTCACA 1 N N 1 N N hydrog WATSON-CRICK A DT 1 A N3 DT 1 1_555 B DA 28 B N1 DA 14 1_555 hydrog WATSON-CRICK A DT 1 A O4 DT 1 1_555 B DA 28 B N6 DA 14 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 27 B N3 DC 13 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 27 B O2 DC 13 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 27 B N4 DC 13 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B DA 26 B N1 DA 12 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B DA 26 B N6 DA 12 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 25 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 25 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 25 B N4 DC 11 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 24 B N3 DT 10 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 24 B O4 DT 10 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 23 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 23 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 23 B N4 DC 9 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 22 B N1 DG 8 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 22 B O6 DG 8 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 22 B N2 DG 8 1_555 hydrog WATSON-CRICK A DG 8 A N1 DG 8 1_555 B DC 21 B N3 DC 7 1_555 hydrog WATSON-CRICK A DG 8 A N2 DG 8 1_555 B DC 21 B O2 DC 7 1_555 hydrog WATSON-CRICK A DG 8 A O6 DG 8 1_555 B DC 21 B N4 DC 7 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 20 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 20 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 20 B N2 DG 6 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 19 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 19 B N6 DA 5 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 18 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 18 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 18 B N2 DG 4 1_555 hydrog WATSON-CRICK A DA 12 A N1 DA 12 1_555 B DT 17 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 12 A N6 DA 12 1_555 B DT 17 B O4 DT 3 1_555 hydrog WATSON-CRICK A DC 13 A N3 DC 13 1_555 B DG 16 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 13 A N4 DC 13 1_555 B DG 16 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 13 A O2 DC 13 1_555 B DG 16 B N2 DG 2 1_555 hydrog WATSON-CRICK A DA 14 A N1 DA 14 1_555 B DT 15 B N3 DT 1 1_555 hydrog WATSON-CRICK A DA 14 A N6 DA 14 1_555 B DT 15 B O4 DT 1 1_555 DNA Lac operator, Double helix, DNA 1K9H PDB 1 1K9H 1 14 1K9H 1 14 1K9H A 1 1 14 15 28 1K9H 15 28 1K9H B 1 1 14