1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Gollmick, F.A. Lorenz, M. Dornberger, U. von Langen, J. Diekmann, S. Fritzsche, H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 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 UK Nucleic Acids Res. NARHAD 0389 0305-1048 30 2669 2677 10.1093/nar/gkf375 12060684 Solution structure of dAATAA and dAAUAA DNA bulges. 2002 10.2210/pdb1jrw/pdb pdb_00001jrw 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 5220.412 5'-D(*GP*CP*AP*TP*CP*GP*AP*AP*TP*AP*AP*GP*CP*TP*AP*CP*G)-3' 1 syn polymer 3663.392 5'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3' 1 syn polymer no no (DG)(DC)(DA)(DT)(DC)(DG)(DA)(DA)(DT)(DA)(DA)(DG)(DC)(DT)(DA)(DC)(DG) GCATCGAATAAGCTACG A polydeoxyribonucleotide no no (DC)(DG)(DT)(DA)(DG)(DC)(DC)(DG)(DA)(DT)(DG)(DC) CGTAGCCGATGC B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n -0.074 1 19 A 2 B 28 -3.576 A_DC2:DG28_B 1 8.348 -0.223 -0.077 -0.046 0.624 1 20 A 3 B 27 5.187 A_DA3:DT27_B 2 -11.465 -0.429 0.129 -0.107 -12.544 1 20 A 4 B 26 -1.988 A_DT4:DA26_B 3 -14.075 -0.033 0.656 -0.146 -13.881 1 19 A 5 B 25 -1.484 A_DC5:DG25_B 4 -12.635 -0.209 0.265 0.052 -8.485 1 19 A 6 B 24 -2.101 A_DG6:DC24_B 5 5.445 0.253 0.645 -0.100 11.670 1 19 A 12 B 23 -1.809 A_DG12:DC23_B 6 13.913 -0.166 0.286 -0.030 -6.933 1 19 A 13 B 22 -2.388 A_DC13:DG22_B 7 -3.841 -0.387 0.955 -0.123 5.182 1 20 A 14 B 21 -8.217 A_DT14:DA21_B 8 -3.342 0.234 0.536 -0.140 9.329 1 20 A 15 B 20 0.492 A_DA15:DT20_B 9 -7.136 -0.471 0.667 -0.198 -0.184 1 19 A 16 B 19 -0.530 A_DC16:DG19_B 10 -1.287 0.091 0.454 -0.064 13.891 1 19 A 17 B 18 -12.919 A_DG17:DC18_B 11 7.118 1.278 -1.630 -0.566 3.118 38.396 A A 2 3 18.764 B B 28 27 3.208 12.121 -0.213 0.195 AA_DC2DA3:DT27DG28_BB 1 -4.197 6.498 36.267 -1.211 -0.199 3.540 31.485 A A 3 4 1.271 B B 27 26 3.507 0.687 -0.588 -0.677 AA_DA3DT4:DA26DT27_BB 2 -4.733 8.755 31.129 -1.386 0.126 3.089 36.127 A A 4 5 10.595 B B 26 25 3.106 6.509 0.411 0.028 AA_DT4DC5:DG25DA26_BB 3 5.844 -9.512 35.087 -0.838 0.132 3.332 34.501 A A 5 6 23.867 B B 25 24 3.413 13.750 -0.216 0.483 AA_DC5DG6:DC24DG25_BB 4 -4.095 7.108 31.459 -1.494 -0.322 3.744 38.037 A A 12 13 2.683 B B 23 22 3.786 1.743 -0.250 -0.866 AA_DG12DC13:DG22DC23_BB 5 -5.159 7.941 37.659 -1.585 -0.374 2.820 30.636 A A 13 14 2.200 B B 22 21 2.910 1.159 -0.412 -0.459 AA_DC13DT14:DA21DG22_BB 6 3.788 -7.189 30.385 -1.069 1.437 2.761 38.373 A A 14 15 29.231 B B 21 20 3.189 18.468 0.115 -0.117 AA_DT14DA15:DT20DA21_BB 7 -0.933 1.477 33.771 -2.424 -0.288 3.459 33.097 A A 15 16 1.699 B B 20 19 3.477 0.968 0.078 -0.543 AA_DA15DC16:DG19DT20_BB 8 -0.495 0.869 33.079 -1.127 -0.225 3.410 38.541 A A 16 17 0.805 B B 19 18 3.555 0.524 -0.053 0.229 AA_DC16DG17:DC18DG19_BB 9 10.813 -16.589 37.045 0.276 1.536 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 2002-08-28 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 1QSK contains a similar pentanucleotide DNA bulge with AAAAA in the bulge loop 1JRV IS the SOLUTION STRUCTURE OF DAATAA DNA BULGE (ENSEMBLE) 1JS5 IS the AVERAGED SOLUTION STRUCTURE OF DAAUAA DNA BULGE 1JS7 IS the SOLUTION STRUCTURE (ENSEMBLE) OF DAAUAA DNA BULGE RCSB Y RCSB 2001-08-15 REL THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY COORDINATE AVERAGING OF THE FINAL ENSEMBLE OF STRUCTURES, FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. This structure was determined using standard 2D homonuclear and heteronuclear techniques. 1 2D_NOESY E-COSY 31P-1H_correlated 100mm Na+ 7 ambient 300 K the structures are based on a total of 906 restraints, 645 are NOE-derived distance constraints, 235 dihedral angle restraints, 26 distance restraints from hydrogen bonds. matrix relaxation; torsion angle dynamics; energy minimization 1 minimized average structure 1.6mm in duplex; 10mm phosphate buffer; 100mm NaCl; 0.05mm EDTA; 100% D2O 100% D2O 1.6mm in duplex; 100mm NaCl; 0.05mm EDTA; 100% D2O 100% D2O Delaglio, F., et al. processing NMRPipe 3 Borgias, B.A., James, T.L. iterative matrix relaxation MARDIGRAS 3.2 Guentert, P., Mumenthaler, C., Wuetrich, K. structure solution DYANA 1.5 WEINER, S.J., KOLLMAN, P.A., NGUYEN, D.T., CASE, D.A. refinement Amber 5.0 WEINER, S.J., KOLLMAN, P.A., NGUYEN, D.T., CASE, D.A. data analysis Amber 5.0 500 Varian INOVA 600 Varian INOVA 750 Varian INOVA GUA 1 n 1 DG 1 A CYT 2 n 2 DC 2 A ADE 3 n 3 DA 3 A THY 4 n 4 DT 4 A CYT 5 n 5 DC 5 A GUA 6 n 6 DG 6 A ADE 7 n 7 DA 7 A ADE 8 n 8 DA 8 A THY 9 n 9 DT 9 A ADE 10 n 10 DA 10 A ADE 11 n 11 DA 11 A GUA 12 n 12 DG 12 A CYT 13 n 13 DC 13 A THY 14 n 14 DT 14 A ADE 15 n 15 DA 15 A CYT 16 n 16 DC 16 A GUA 17 n 17 DG 17 A CYT 18 n 1 DC 18 B GUA 19 n 2 DG 19 B THY 20 n 3 DT 20 B ADE 21 n 4 DA 21 B GUA 22 n 5 DG 22 B CYT 23 n 6 DC 23 B CYT 24 n 7 DC 24 B GUA 25 n 8 DG 25 B ADE 26 n 9 DA 26 B THY 27 n 10 DT 27 B GUA 28 n 11 DG 28 B CYT 29 n 12 DC 29 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 DA 3 0.059 SIDE CHAIN 1 B DC 18 0.086 SIDE CHAIN 1 B DG 19 0.086 SIDE CHAIN 1 B DG 25 0.063 SIDE CHAIN 1 B DT 27 0.061 SIDE CHAIN 1 2.15 0.30 108.30 110.45 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 5.75 0.60 106.00 111.75 A A A O4' C4' C3' DA DA DA 3 3 3 N 1 2.25 0.30 108.30 110.55 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 -4.89 0.60 122.90 118.01 A A A C6 C5 C7 DT DT DT 4 4 4 N 1 2.58 0.30 108.30 110.88 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 4.63 0.30 108.30 112.93 A A A O4' C1' N9 DA DA DA 7 7 7 N 1 6.37 0.30 108.30 114.67 A A A O4' C1' N9 DA DA DA 10 10 10 N 1 5.20 0.30 108.30 113.50 A A A O4' C1' N9 DA DA DA 11 11 11 N 1 4.78 0.60 106.00 110.78 A A A O4' C4' C3' DC DC DC 13 13 13 N 1 2.78 0.30 108.30 111.08 B B B O4' C1' N1 DT DT DT 20 20 20 N 1 3.81 0.60 106.00 109.81 B B B O4' C4' C3' DA DA DA 26 26 26 N minimized average Solution Structure of dAATAA DNA Bulge 1 N N 2 N N hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 28 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 28 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 28 B N2 DG 11 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 27 B N3 DT 10 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 27 B O4 DT 10 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B DA 26 B N1 DA 9 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 26 B N6 DA 9 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 25 B N1 DG 8 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 25 B O6 DG 8 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 25 B N2 DG 8 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 24 B N3 DC 7 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 24 B O2 DC 7 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 24 B N4 DC 7 1_555 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 B DC 23 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 23 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 23 B N4 DC 6 1_555 hydrog WATSON-CRICK A DC 13 A N3 DC 13 1_555 B DG 22 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 13 A N4 DC 13 1_555 B DG 22 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 13 A O2 DC 13 1_555 B DG 22 B N2 DG 5 1_555 hydrog WATSON-CRICK A DT 14 A N3 DT 14 1_555 B DA 21 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 14 A O4 DT 14 1_555 B DA 21 B N6 DA 4 1_555 hydrog WATSON-CRICK A DA 15 A N1 DA 15 1_555 B DT 20 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 15 A N6 DA 15 1_555 B DT 20 B O4 DT 3 1_555 hydrog WATSON-CRICK A DC 16 A N3 DC 16 1_555 B DG 19 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 16 A N4 DC 16 1_555 B DG 19 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 16 A O2 DC 16 1_555 B DG 19 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 17 A N1 DG 17 1_555 B DC 18 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 17 A N2 DG 17 1_555 B DC 18 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 17 A O6 DG 17 1_555 B DC 18 B N4 DC 1 1_555 DNA DNA BULGE, five-nucleotide bulge loop, deoxyribonucleic acid, DNA 1JRW PDB 1 1JRW 1JRW PDB 2 1JRW 1 17 1JRW 1 17 1JRW A 1 1 17 18 29 1JRW 18 29 1JRW B 2 1 12