1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Shiflett, P.R. Taylor-McCabe, K.J. Michalczyk, R. Silks, L.A. Gupta, G. 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 Biochemistry BICHAW 0033 0006-2960 42 6078 6089 10.1021/bi034128f 12755609 Structural Studies on the Hairpins at the 3' Untranslated Region of an Anthrax Toxin Gene 2003 10.2210/pdb1ngu/pdb pdb_00001ngu Chirality error at C 15 in Chain A 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 3' UTR hairpin of pagA gene, noncoding strand 8225.333 5'-D(*CP*TP*CP*TP*CP*CP*TP*TP*GP*TP*AP*TP*TP*TP*CP*TP*TP*AP*CP*AP*AP*AP*AP*AP*GP*AP*G)-3' 1 syn polymer no no (DC)(DT)(DC)(DT)(DC)(DC)(DT)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DC)(DT)(DT)(DA)(DC)(DA) (DA)(DA)(DA)(DA)(DG)(DA)(DG) CTCTCCTTGTATTTCTTACAAAAAGAG A 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 12.541 1 19 A 1 A 27 -5.424 A_DC1:DG27_A 1 -21.495 -0.550 0.501 0.096 -0.119 1 20 A 2 A 26 -5.188 A_DT2:DA26_A 2 -27.793 0.622 0.278 -0.096 -18.112 1 19 A 3 A 25 -4.732 A_DC3:DG25_A 3 -17.143 1.072 0.694 -0.290 -14.629 1 20 A 4 A 24 -3.196 A_DT4:DA24_A 4 -4.680 0.801 1.005 -0.181 -24.209 A 5 A 23 -21.001 A_DC5:DA23_A 5 -43.353 0.848 0.392 0.124 -37.023 A 6 A 22 -24.135 A_DC6:DA22_A 6 -30.841 2.490 0.567 0.177 -32.552 1 20 A 8 A 20 8.263 A_DT8:DA20_A 7 -0.788 -0.691 -0.396 0.033 -19.633 1 19 A 9 A 19 -3.315 A_DG9:DC19_A 8 -22.793 -1.156 0.205 -0.275 -19.592 1 20 A 10 A 18 -3.434 A_DT10:DA18_A 9 -4.761 0.492 0.364 0.102 1.960 1 20 A 11 A 17 -23.405 A_DA11:DT17_A 10 29.291 0.856 -0.689 0.028 3.486 39.159 A A 1 2 0.141 A A 27 26 3.499 0.094 -0.098 -0.421 AA_DC1DT2:DA26DG27_AA 1 2.433 -3.632 39.086 -0.640 0.458 3.519 44.822 A A 2 3 0.561 A A 26 25 3.529 0.428 0.002 -0.416 AA_DT2DC3:DG25DA26_AA 2 -2.813 3.691 44.736 -0.587 -0.278 3.186 32.658 A A 3 4 -7.475 A A 25 24 3.145 -4.189 0.253 -0.696 AA_DC3DT4:DA24DG25_AA 3 -2.036 3.632 32.333 -0.531 -0.793 3.050 51.804 A A 4 5 -30.718 A A 24 23 3.445 -25.741 -2.288 0.415 AA_DT4DC5:DA23DA24_AA 4 -5.370 6.408 45.037 2.340 2.230 3.390 41.735 A A 5 6 0.232 A A 23 22 3.391 0.165 0.105 -0.620 AA_DC5DC6:DA22DA23_AA 5 2.073 -2.911 41.685 -0.889 0.079 5.008 79.704 A A 6 8 -18.466 A A 22 20 6.113 -23.389 1.231 3.124 AA_DC6DT8:DA20DA22_AA 6 -8.528 6.733 76.339 3.535 -1.360 2.960 46.015 A A 8 9 -34.878 A A 20 19 3.393 -25.815 -2.384 0.034 AA_DT8DG9:DC19DA20_AA 7 -2.566 3.467 38.337 2.428 2.813 3.258 42.626 A A 9 10 0.958 A A 19 18 3.261 0.696 0.278 -0.609 AA_DG9DT10:DA18DC19_AA 8 1.469 -2.021 42.597 -0.908 -0.235 2.966 28.253 A A 10 11 -18.309 A A 18 17 3.071 -8.728 -0.237 -0.522 AA_DT10DA11:DT17DA18_AA 9 5.971 -12.525 26.237 0.875 1.815 database_2 pdbx_nmr_software pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-06-10 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model NMR Structure of Putative 3' Terminator for B. Anthracis pagA Gene Coding Strand RCSB Y RCSB 2002-12-17 REL This sequence occurs on the noncoding strand of the 3' UTR of the pagA (110) gene of Bacillus anthracis. sample The structure was determined using standard 2D homonuclear techniques. Submitted conformers include minimized average from molecular dynamics and 4 representative diverging structures. 100 5 2D NOESY 2D NOESY 2D TOCSY DQF-COSY 150mM NaCl 6.5 ambient 278 K Structure is derived from 206 NOEs of which, 23 NOEs involvE exchangeable protons in the stem, 131 NOEs involve non-exchangeable protons in the stem, 52 NOEs involve non-exchangeable protons in the loop, 46 Distance restraints involve hydrogen bonds, and 44 dihedral angle restraints. minimization molecular dynamics 1 minimized average structure 2mM 110NC DNA; 10mM phosphate buffer pH 6.5; 150mM NaCl; 90% H2O/10% D2O 2mM 110NC DNA; 10mM phosphate buffer pH 6.5; 150mM NaCl; 100% D2O Biosym data analysis Felix 98 Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P.K., and Kollman, P.A. structure solution Amber 4.1 Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P.K., and Kollman, P.A. refinement Amber 4.1 500 Bruker AVANCE C 1 n 1 DC 1 A T 2 n 2 DT 2 A C 3 n 3 DC 3 A T 4 n 4 DT 4 A C 5 n 5 DC 5 A C 6 n 6 DC 6 A T 7 n 7 DT 7 A T 8 n 8 DT 8 A G 9 n 9 DG 9 A T 10 n 10 DT 10 A A 11 n 11 DA 11 A T 12 n 12 DT 12 A T 13 n 13 DT 13 A T 14 n 14 DT 14 A C 15 n 15 DC 15 A T 16 n 16 DT 16 A T 17 n 17 DT 17 A A 18 n 18 DA 18 A C 19 n 19 DC 19 A A 20 n 20 DA 20 A A 21 n 21 DA 21 A A 22 n 22 DA 22 A A 23 n 23 DA 23 A A 24 n 24 DA 24 A G 25 n 25 DG 25 A A 26 n 26 DA 26 A G 27 n 27 DG 27 A author_defined_assembly 1 monomeric 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 C1' DC 15 WRONG HAND 2 A C1' DC 15 WRONG HAND 3 A C1' DC 15 WRONG HAND 4 A C1' DC 15 WRONG HAND 5 A C1' DC 15 WRONG HAND 1 A DC 6 0.063 SIDE CHAIN 1 A DT 14 0.085 SIDE CHAIN 1 A DA 20 0.067 SIDE CHAIN 2 A DT 14 0.060 SIDE CHAIN 2 A DT 16 0.071 SIDE CHAIN 2 A DA 20 0.071 SIDE CHAIN 3 A DC 6 0.065 SIDE CHAIN 3 A DA 20 0.077 SIDE CHAIN 4 A DT 10 0.062 SIDE CHAIN 4 A DA 11 0.071 SIDE CHAIN 4 A DT 14 0.066 SIDE CHAIN 4 A DA 20 0.088 SIDE CHAIN 5 A DA 20 0.070 SIDE CHAIN 1 2.64 0.30 108.30 110.94 A A A O4' C1' N1 DT DT DT 2 2 2 N 1 2.69 0.30 108.30 110.99 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 2.82 0.30 108.30 111.12 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 4.96 0.30 108.30 113.26 A A A O4' C1' N1 DC DC DC 6 6 6 N 1 3.23 0.30 108.30 111.53 A A A O4' C1' N1 DT DT DT 7 7 7 N 1 3.36 0.30 108.30 111.66 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 3.80 0.30 108.30 112.10 A A A O4' C1' N9 DG DG DG 9 9 9 N 1 4.56 0.30 108.30 112.86 A A A O4' C1' N9 DA DA DA 11 11 11 N 1 3.09 0.30 108.30 111.39 A A A O4' C1' N1 DT DT DT 12 12 12 N 1 -3.76 0.60 122.90 119.14 A A A C6 C5 C7 DT DT DT 12 12 12 N 1 2.15 0.30 108.30 110.45 A A A O4' C1' N1 DT DT DT 13 13 13 N 1 5.83 0.30 108.30 114.13 A A A O4' C1' N1 DT DT DT 14 14 14 N 1 -4.43 0.60 122.90 118.47 A A A C6 C5 C7 DT DT DT 14 14 14 N 1 8.05 0.30 108.30 116.35 A A A O4' C1' N1 DC DC DC 15 15 15 N 1 2.67 0.30 108.30 110.97 A A A O4' C1' N1 DT DT DT 16 16 16 N 1 -3.66 0.60 122.90 119.24 A A A C6 C5 C7 DT DT DT 16 16 16 N 1 2.90 0.30 108.30 111.20 A A A O4' C1' N9 DA DA DA 20 20 20 N 1 2.27 0.30 108.30 110.57 A A A O4' C1' N9 DA DA DA 22 22 22 N 1 2.23 0.30 108.30 110.53 A A A O4' C1' N9 DA DA DA 23 23 23 N 1 2.16 0.30 108.30 110.46 A A A O4' C1' N9 DG DG DG 25 25 25 N 1 3.79 0.30 108.30 112.09 A A A O4' C1' N9 DG DG DG 27 27 27 N 2 1.97 0.30 108.30 110.27 A A A O4' C1' N1 DC DC DC 1 1 1 N 2 2.37 0.30 108.30 110.67 A A A O4' C1' N1 DT DT DT 2 2 2 N 2 2.14 0.30 108.30 110.44 A A A O4' C1' N1 DC DC DC 3 3 3 N 2 3.34 0.30 108.30 111.64 A A A O4' C1' N1 DT DT DT 4 4 4 N 2 -3.67 0.60 122.90 119.23 A A A C6 C5 C7 DT DT DT 4 4 4 N 2 1.85 0.30 108.30 110.15 A A A O4' C1' N1 DC DC DC 5 5 5 N 2 4.34 0.30 108.30 112.64 A A A O4' C1' N1 DC DC DC 6 6 6 N 2 2.89 0.30 108.30 111.19 A A A O4' C1' N1 DT DT DT 7 7 7 N 2 2.61 0.30 108.30 110.91 A A A O4' C1' N9 DG DG DG 9 9 9 N 2 1.87 0.30 108.30 110.17 A A A O4' C1' N1 DT DT DT 10 10 10 N 2 4.33 0.30 108.30 112.63 A A A O4' C1' N9 DA DA DA 11 11 11 N 2 2.69 0.30 108.30 110.99 A A A O4' C1' N1 DT DT DT 12 12 12 N 2 2.76 0.30 108.30 111.06 A A A O4' C1' N1 DT DT DT 13 13 13 N 2 5.59 0.30 108.30 113.89 A A A O4' C1' N1 DT DT DT 14 14 14 N 2 -5.70 0.60 122.90 117.20 A A A C6 C5 C7 DT DT DT 14 14 14 N 2 8.66 0.30 108.30 116.96 A A A O4' C1' N1 DC DC DC 15 15 15 N 2 4.05 0.60 118.90 122.95 A A A N1 C2 O2 DC DC DC 15 15 15 N 2 -3.66 0.60 122.90 119.24 A A A C6 C5 C7 DT DT DT 16 16 16 N 2 2.05 0.30 108.30 110.35 A A A O4' C1' N1 DT DT DT 17 17 17 N 2 3.02 0.30 108.30 111.32 A A A O4' C1' N9 DA DA DA 20 20 20 N 2 2.04 0.30 108.30 110.34 A A A O4' C1' N9 DA DA DA 21 21 21 N 2 3.21 0.30 108.30 111.51 A A A O4' C1' N9 DA DA DA 22 22 22 N 2 3.70 0.30 108.30 112.00 A A A O4' C1' N9 DA DA DA 23 23 23 N 2 3.91 0.30 108.30 112.21 A A A O4' C1' N9 DG DG DG 27 27 27 N 3 1.83 0.30 108.30 110.13 A A A O4' C1' N1 DC DC DC 1 1 1 N 3 2.83 0.30 108.30 111.13 A A A O4' C1' N1 DT DT DT 2 2 2 N 3 3.82 0.30 108.30 112.12 A A A O4' C1' N1 DT DT DT 4 4 4 N 3 3.80 0.30 108.30 112.10 A A A O4' C1' N1 DC DC DC 6 6 6 N 3 3.50 0.30 108.30 111.80 A A A O4' C1' N1 DT DT DT 7 7 7 N 3 3.09 0.30 108.30 111.39 A A A O4' C1' N9 DG DG DG 9 9 9 N 3 5.38 0.30 108.30 113.68 A A A O4' C1' N9 DA DA DA 11 11 11 N 3 2.53 0.30 108.30 110.83 A A A O4' C1' N1 DT DT DT 12 12 12 N 3 -3.66 0.60 122.90 119.24 A A A C6 C5 C7 DT DT DT 12 12 12 N 3 5.17 0.30 108.30 113.47 A A A O4' C1' N1 DT DT DT 14 14 14 N 3 -4.81 0.60 122.90 118.09 A A A C6 C5 C7 DT DT DT 14 14 14 N 3 7.70 0.30 108.30 116.00 A A A O4' C1' N1 DC DC DC 15 15 15 N 3 3.72 0.60 118.90 122.62 A A A N1 C2 O2 DC DC DC 15 15 15 N 3 2.80 0.30 108.30 111.10 A A A O4' C1' N1 DT DT DT 16 16 16 N 3 1.84 0.30 108.30 110.14 A A A O4' C1' N1 DT DT DT 17 17 17 N 3 2.80 0.30 108.30 111.10 A A A O4' C1' N9 DA DA DA 20 20 20 N 3 2.82 0.30 108.30 111.12 A A A O4' C1' N9 DA DA DA 22 22 22 N 3 3.05 0.30 108.30 111.35 A A A O4' C1' N9 DA DA DA 23 23 23 N 3 1.97 0.30 108.30 110.27 A A A O4' C1' N9 DG DG DG 25 25 25 N 3 3.29 0.30 108.30 111.59 A A A O4' C1' N9 DG DG DG 27 27 27 N 4 2.92 0.30 108.30 111.22 A A A O4' C1' N1 DT DT DT 2 2 2 N 4 2.18 0.30 108.30 110.48 A A A O4' C1' N1 DC DC DC 3 3 3 N 4 3.75 0.30 108.30 112.05 A A A O4' C1' N1 DT DT DT 4 4 4 N 4 3.34 0.30 108.30 111.64 A A A O4' C1' N1 DC DC DC 5 5 5 N 4 3.15 0.30 108.30 111.45 A A A O4' C1' N1 DC DC DC 6 6 6 N 4 3.26 0.30 108.30 111.56 A A A O4' C1' N1 DT DT DT 7 7 7 N 4 3.61 0.30 108.30 111.91 A A A O4' C1' N9 DG DG DG 9 9 9 N 4 4.47 0.30 108.30 112.77 A A A O4' C1' N9 DA DA DA 11 11 11 N 4 1.95 0.30 108.30 110.25 A A A O4' C1' N1 DT DT DT 12 12 12 N 4 -3.72 0.60 122.90 119.18 A A A C6 C5 C7 DT DT DT 12 12 12 N 4 5.57 0.30 108.30 113.87 A A A O4' C1' N1 DT DT DT 14 14 14 N 4 -5.24 0.60 122.90 117.66 A A A C6 C5 C7 DT DT DT 14 14 14 N 4 8.11 0.30 108.30 116.41 A A A O4' C1' N1 DC DC DC 15 15 15 N 4 3.74 0.60 118.90 122.64 A A A N1 C2 O2 DC DC DC 15 15 15 N 4 3.06 0.30 108.30 111.36 A A A O4' C1' N9 DA DA DA 20 20 20 N 4 2.31 0.30 108.30 110.61 A A A O4' C1' N9 DA DA DA 21 21 21 N 4 2.43 0.30 108.30 110.73 A A A O4' C1' N9 DA DA DA 22 22 22 N 4 2.75 0.30 108.30 111.05 A A A O4' C1' N9 DA DA DA 23 23 23 N 4 2.32 0.30 108.30 110.62 A A A O4' C1' N9 DG DG DG 25 25 25 N 4 3.63 0.30 108.30 111.93 A A A O4' C1' N9 DG DG DG 27 27 27 N 5 2.61 0.30 108.30 110.91 A A A O4' C1' N1 DT DT DT 2 2 2 N 5 3.81 0.30 108.30 112.11 A A A O4' C1' N1 DT DT DT 4 4 4 N 5 3.35 0.30 108.30 111.65 A A A O4' C1' N1 DC DC DC 6 6 6 N 5 3.41 0.30 108.30 111.71 A A A O4' C1' N1 DT DT DT 7 7 7 N 5 2.70 0.30 108.30 111.00 A A A O4' C1' N1 DT DT DT 8 8 8 N 5 3.37 0.30 108.30 111.67 A A A O4' C1' N9 DG DG DG 9 9 9 N 5 4.71 0.30 108.30 113.01 A A A O4' C1' N9 DA DA DA 11 11 11 N 5 2.54 0.30 108.30 110.84 A A A O4' C1' N1 DT DT DT 12 12 12 N 5 -3.65 0.60 122.90 119.25 A A A C6 C5 C7 DT DT DT 12 12 12 N 5 2.55 0.30 108.30 110.85 A A A O4' C1' N1 DT DT DT 13 13 13 N 5 5.54 0.30 108.30 113.84 A A A O4' C1' N1 DT DT DT 14 14 14 N 5 -5.28 0.60 122.90 117.62 A A A C6 C5 C7 DT DT DT 14 14 14 N 5 9.77 0.30 108.30 118.07 A A A O4' C1' N1 DC DC DC 15 15 15 N 5 3.93 0.60 118.90 122.83 A A A N1 C2 O2 DC DC DC 15 15 15 N 5 2.09 0.30 108.30 110.39 A A A O4' C1' N1 DT DT DT 17 17 17 N 5 2.79 0.30 108.30 111.09 A A A O4' C1' N9 DA DA DA 20 20 20 N 5 2.48 0.30 108.30 110.78 A A A O4' C1' N9 DA DA DA 22 22 22 N 5 2.85 0.30 108.30 111.15 A A A O4' C1' N9 DA DA DA 23 23 23 N 5 3.56 0.30 108.30 111.86 A A A O4' C1' N9 DG DG DG 27 27 27 N minimized average NMR Structure of Putative 3'Terminator for B. Anthracis pagA Gene Noncoding Strand 1 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 27 A N1 DG 27 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 27 A O6 DG 27 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 27 A N2 DG 27 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 A DA 26 A N1 DA 26 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 A DA 26 A N6 DA 26 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 A DG 25 A N1 DG 25 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 A DG 25 A O6 DG 25 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 A DG 25 A N2 DG 25 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 A DA 24 A N1 DA 24 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 A DA 24 A N6 DA 24 1_555 hydrog DC-DA MISPAIR A DC 5 A N3 DC 5 1_555 A DA 23 A N6 DA 23 1_555 hydrog DC-DA MISPAIR A DC 6 A N3 DC 6 1_555 A DA 22 A N6 DA 22 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 A DA 20 A N1 DA 20 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 A DA 20 A N6 DA 20 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 A DC 19 A N3 DC 19 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 A DC 19 A O2 DC 19 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 A DC 19 A N4 DC 19 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 A DA 18 A N1 DA 18 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 A DA 18 A N6 DA 18 1_555 hydrog WATSON-CRICK A DA 11 A N1 DA 11 1_555 A DT 17 A N3 DT 17 1_555 hydrog WATSON-CRICK A DA 11 A N6 DA 11 1_555 A DT 17 A O4 DT 17 1_555 DNA B-Form DNA Hairpin, DNA 1NGU PDB 1 1NGU 1 27 1NGU 1 27 1NGU A 1 1 27