0.025228 0.014566 0.000000 0.000000 0.029131 0.000000 0.000000 0.000000 0.010143 0.00000 0.00000 0.00000 Chen, S. Berman, H.M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 39.638 39.638 98.591 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 386 1054 1065 19244617 Signatures of protein-DNA recognition in free DNA binding sites. 2009 10.2210/pdb1hq7/pdb pdb_00001hq7 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 108 1 1 mirrors CCD 2000-06-07 ADSC QUANTUM 4r mirrors CCD 2000-08-21 ADSC QUANTUM 1 parabolic collimating mirror SINGLE WAVELENGTH M x-ray 1 parabolic collimating mirror MAD M x-ray 1 1.0722 1.0 1.5418 1.0 X8C NSLS 1.0722 SYNCHROTRON NSLS BEAMLINE X8C 1.5418 ROTATING ANODE OTHER DNA BINDING SEQUENCE FOR PURINE REPRESSOR PROTEIN 3662.404 5'-D(*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*C)-3' 2 syn polymer 18.015 water 100 nat water no no (DG)(DC)(DA)(DA)(DA)(DC)(DG)(DT)(DT)(DT)(DG)(DC) GCAAACGTTTGC A,B polydeoxyribonucleotide n n n n n n n n n n n n 2 2.94 58.12 VAPOR DIFFUSION, HANGING DROP 6.0 MPD, magnesium acetate, sodium cacodylate, spermine tetrahydrochloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K 277 MPD 1 magnesium acetate 1 sodium cacodylate 1 spermine tetrahydrochloride 1 MPD 2 -4.533 1 19 A 1 B 24 -1.923 A_DG1:DC24_B 1 -2.230 -0.125 -0.209 -0.217 2.791 1 19 A 2 B 23 -1.422 A_DC2:DG23_B 2 -4.678 0.348 -0.009 -0.158 14.135 1 20 A 3 B 22 2.867 A_DA3:DT22_B 3 -8.063 0.489 0.002 -0.059 9.261 1 20 A 4 B 21 2.234 A_DA4:DT21_B 4 -15.178 -0.151 0.121 -0.152 3.734 1 20 A 5 B 20 1.602 A_DA5:DT20_B 5 -11.929 0.037 0.297 -0.183 -1.830 1 19 A 6 B 19 1.215 A_DC6:DG19_B 6 -11.368 0.167 0.168 -0.269 -10.993 1 19 A 7 B 18 2.133 A_DG7:DC18_B 7 -11.628 -0.345 -0.113 -0.192 -4.803 1 20 A 8 B 17 3.773 A_DT8:DA17_B 8 -14.163 -0.060 0.038 -0.084 -9.129 1 20 A 9 B 16 -0.160 A_DT9:DA16_B 9 -17.664 -0.294 0.081 -0.280 -11.303 1 20 A 10 B 15 0.742 A_DT10:DA15_B 10 -12.864 -0.164 0.292 -0.060 -5.557 1 19 A 11 B 14 -0.463 A_DG11:DC14_B 11 -2.891 -0.360 -0.101 0.019 3.139 1 19 A 12 B 13 -1.628 A_DC12:DG13_B 12 -1.318 0.069 -0.080 -0.090 3.188 30.724 A A 1 2 0.962 B B 24 23 3.177 0.509 -0.326 -0.294 AA_DG1DC2:DG23DC24_BB 1 -2.823 5.335 30.593 -0.653 0.076 3.050 30.161 A A 2 3 11.895 B B 23 22 3.072 6.147 0.225 0.171 AA_DC2DA3:DT22DG23_BB 2 0.799 -1.545 29.532 -0.856 -0.279 3.285 39.449 A A 3 4 -7.744 B B 22 21 3.323 -5.208 -0.588 0.366 AA_DA3DA4:DT21DT22_BB 3 -3.146 4.678 38.996 1.166 0.493 3.272 39.001 A A 4 5 -3.688 B B 21 20 3.272 -2.461 0.184 -0.192 AA_DA4DA5:DT20DT21_BB 4 -1.028 1.541 38.913 0.010 -0.400 3.369 36.077 A A 5 6 -1.357 B B 20 19 3.347 -0.841 0.349 -0.693 AA_DA5DC6:DG19DT20_BB 5 0.856 -1.383 36.058 -0.996 -0.439 3.558 40.044 A A 6 7 9.378 B B 19 18 3.514 6.383 0.601 0.261 AA_DC6DG7:DC18DG19_BB 6 4.729 -6.949 39.280 -0.417 -0.286 3.059 32.189 A A 7 8 5.485 B B 18 17 3.071 3.035 -0.712 -0.442 AA_DG7DT8:DA17DC18_BB 7 -2.226 4.024 31.974 -1.306 0.910 3.388 38.521 A A 8 9 -3.582 B B 17 16 3.399 -2.362 -0.044 0.094 AA_DT8DT9:DA16DA17_BB 8 -0.055 0.084 38.451 0.445 0.060 3.414 31.764 A A 9 10 -3.444 B B 16 15 3.400 -1.881 -0.353 -0.018 AA_DT9DT10:DA15DA16_BB 9 -3.092 5.662 31.562 0.328 0.053 3.294 41.861 A A 10 11 2.179 B B 15 14 3.236 1.555 0.394 1.146 AA_DT10DG11:DC14DA15_BB 10 3.104 -4.350 41.724 1.441 -0.228 3.105 31.647 A A 11 12 0.682 B B 14 13 3.107 0.372 -0.065 -0.176 AA_DG11DC12:DG13DC14_BB 11 -0.023 0.042 31.645 -0.389 0.115 diffrn_source chem_comp_atom chem_comp_bond database_2 repository Initial release Version format compliance Version format compliance Data collection Data collection Database references 1 0 2003-07-07 1 1 2008-04-27 1 2 2011-07-13 1 3 2018-04-04 1 4 2024-02-07 _diffrn_source.type _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2000-12-14 REL REL HOH water solid-phase DNA synthesis sample WAT 28 2 HOH HOH 28 A WAT 29 2 HOH HOH 29 A WAT 30 2 HOH HOH 30 A WAT 32 2 HOH HOH 32 A WAT 33 2 HOH HOH 33 A WAT 35 2 HOH HOH 35 A WAT 39 2 HOH HOH 39 A WAT 40 2 HOH HOH 40 A WAT 44 2 HOH HOH 44 A WAT 45 2 HOH HOH 45 A WAT 46 2 HOH HOH 46 A WAT 48 2 HOH HOH 48 A WAT 49 2 HOH HOH 49 A WAT 50 2 HOH HOH 50 A WAT 51 2 HOH HOH 51 A WAT 52 2 HOH HOH 52 A WAT 53 2 HOH HOH 53 A WAT 54 2 HOH HOH 54 A WAT 55 2 HOH HOH 55 A WAT 57 2 HOH HOH 57 A WAT 58 2 HOH HOH 58 A WAT 59 2 HOH HOH 59 A WAT 62 2 HOH HOH 62 A WAT 66 2 HOH HOH 66 A WAT 68 2 HOH HOH 68 A WAT 69 2 HOH HOH 69 A WAT 72 2 HOH HOH 72 A WAT 73 2 HOH HOH 73 A WAT 75 2 HOH HOH 75 A WAT 77 2 HOH HOH 77 A WAT 78 2 HOH HOH 78 A WAT 79 2 HOH HOH 79 A WAT 80 2 HOH HOH 80 A WAT 81 2 HOH HOH 81 A WAT 82 2 HOH HOH 82 A WAT 84 2 HOH HOH 84 A WAT 86 2 HOH HOH 86 A WAT 87 2 HOH HOH 87 A WAT 90 2 HOH HOH 90 A WAT 93 2 HOH HOH 93 A WAT 94 2 HOH HOH 94 A WAT 95 2 HOH HOH 95 A WAT 98 2 HOH HOH 98 A WAT 103 2 HOH HOH 103 A WAT 106 2 HOH HOH 106 A WAT 107 2 HOH HOH 107 A WAT 108 2 HOH HOH 108 A WAT 112 2 HOH HOH 112 A WAT 113 2 HOH HOH 113 A WAT 114 2 HOH HOH 114 A WAT 115 2 HOH HOH 115 A WAT 120 2 HOH HOH 120 A WAT 121 2 HOH HOH 121 A WAT 122 2 HOH HOH 122 A WAT 124 2 HOH HOH 124 A WAT 25 2 HOH HOH 25 B WAT 26 2 HOH HOH 26 B WAT 27 2 HOH HOH 27 B WAT 31 2 HOH HOH 31 B WAT 34 2 HOH HOH 34 B WAT 36 2 HOH HOH 36 B WAT 37 2 HOH HOH 37 B WAT 38 2 HOH HOH 38 B WAT 41 2 HOH HOH 41 B WAT 42 2 HOH HOH 42 B WAT 43 2 HOH HOH 43 B WAT 47 2 HOH HOH 47 B WAT 56 2 HOH HOH 56 B WAT 60 2 HOH HOH 60 B WAT 61 2 HOH HOH 61 B WAT 63 2 HOH HOH 63 B WAT 64 2 HOH HOH 64 B WAT 65 2 HOH HOH 65 B WAT 67 2 HOH HOH 67 B WAT 70 2 HOH HOH 70 B WAT 71 2 HOH HOH 71 B WAT 74 2 HOH HOH 74 B WAT 76 2 HOH HOH 76 B WAT 83 2 HOH HOH 83 B WAT 85 2 HOH HOH 85 B WAT 88 2 HOH HOH 88 B WAT 89 2 HOH HOH 89 B WAT 91 2 HOH HOH 91 B WAT 92 2 HOH HOH 92 B WAT 96 2 HOH HOH 96 B WAT 97 2 HOH HOH 97 B WAT 99 2 HOH HOH 99 B WAT 100 2 HOH HOH 100 B WAT 101 2 HOH HOH 101 B WAT 102 2 HOH HOH 102 B WAT 104 2 HOH HOH 104 B WAT 105 2 HOH HOH 105 B WAT 109 2 HOH HOH 109 B WAT 110 2 HOH HOH 110 B WAT 111 2 HOH HOH 111 B WAT 116 2 HOH HOH 116 B WAT 117 2 HOH HOH 117 B WAT 118 2 HOH HOH 118 B WAT 119 2 HOH HOH 119 B WAT 123 2 HOH HOH 123 B GUA 1 n 1 DG 1 A CYT 2 n 2 DC 2 A ADE 3 n 3 DA 3 A ADE 4 n 4 DA 4 A ADE 5 n 5 DA 5 A CYT 6 n 6 DC 6 A GUA 7 n 7 DG 7 A THY 8 n 8 DT 8 A THY 9 n 9 DT 9 A THY 10 n 10 DT 10 A GUA 11 n 11 DG 11 A CYT 12 n 12 DC 12 A GUA 13 n 1 DG 13 B CYT 14 n 2 DC 14 B ADE 15 n 3 DA 15 B ADE 16 n 4 DA 16 B ADE 17 n 5 DA 17 B CYT 18 n 6 DC 18 B GUA 19 n 7 DG 19 B THY 20 n 8 DT 20 B THY 21 n 9 DT 21 B THY 22 n 10 DT 22 B GUA 23 n 11 DG 23 B CYT 24 n 12 DC 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 B HOH 67 D HOH 1 B HOH 70 D HOH 1 A A OP2 O DG HOH 11 28 1.87 1 B B OP1 O DA HOH 16 60 2.19 1 B DT 21 0.070 SIDE CHAIN 1 8.66 1.10 110.50 119.16 B B B O3' P OP2 DA DC DC 17 18 18 Y 1 A A O3' C3' DA DA 3 3 -0.036 0.006 1.419 1.383 N 1 A A C4 C5 DT DT 8 8 0.060 0.009 1.445 1.505 N 1 A A N1 C2 DT DT 9 9 0.048 0.008 1.376 1.424 N 1 A A C5 C6 DG DG 11 11 -0.060 0.010 1.419 1.359 N 1 B B N1 C2 DT DT 22 22 0.049 0.008 1.376 1.425 N 1 A B O O HOH HOH 35 60 1.89 1_555 4_555 1 A A O O HOH HOH 49 50 1.93 1_555 4_555 1 B B O O HOH HOH 27 92 2.17 1_555 4_555 PROTEIN_REP.PARAM PROTEIN.TOP DNA-RNA_REP.PARAM DNA-RNA.TOP WATER_REP.PARAM WATER.TOP 41.6 -2.59 -13.62 0.00 -2.59 0.00 5.18 0.266 0.012 0.237 0.237 2.10 13 518 5310 9.8 94.6 RANDOM 466472.03 0.00 1 RESTRAINED THROUGHOUT 4.0 MAD FLAT MODEL 65.74 0.313 0.44 0.34 5.00 0.41 0.33 2.10 13 100 586 0 486 0 0.018 2.1 17.1 1.88 0.362 0.040 0.318 2.23 84 717 6 10.5 88 34.6 2.1 13 1HQ7 5576 54956 4 0.064 1,2 10.9 9.9 94.6 0.234 2.10 2.14 269 8.3 99.6 data reduction DENZO data scaling SCALEPACK phasing MLPHARE refinement CNS 1.0 CRYSTALLOGRAPHIC STUDIES OF A DODECAMER B-DNA D-(GCAAACGTTTGC)2 1 N N 1 N N 2 N N 2 N N The biological assembly is a DNA duplex hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 24 B N3 DC 12 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 24 B O2 DC 12 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 24 B N4 DC 12 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 23 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 23 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 23 B N2 DG 11 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 22 B N3 DT 10 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 22 B O4 DT 10 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 21 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 21 B O4 DT 9 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 20 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 20 B O4 DT 8 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 B DG 19 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 B DG 19 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 B DG 19 B N2 DG 7 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 18 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 18 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 18 B N4 DC 6 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 17 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 17 B N6 DA 5 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 16 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 16 B N6 DA 4 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 15 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 15 B N6 DA 3 1_555 hydrog WATSON-CRICK A DG 11 A N1 DG 11 1_555 B DC 14 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 11 A N2 DG 11 1_555 B DC 14 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 11 A O6 DG 11 1_555 B DC 14 B N4 DC 2 1_555 hydrog WATSON-CRICK A DC 12 A N3 DC 12 1_555 B DG 13 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 12 A N4 DC 12 1_555 B DG 13 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 12 A O2 DC 12 1_555 B DG 13 B N2 DG 1 1_555 DNA DOUBLE HELIX, DNA 1HQ7 PDB 1 1HQ7 1 12 1HQ7 1 12 1HQ7 A 1 1 12 13 24 1HQ7 13 24 1HQ7 B 1 1 12 152 P 31 2 1