1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Huber, P.W. Rife, J.P. Moore, P.B. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking UK J.Mol.Biol. JMOBAK 0070 0022-2836 312 823 832 10.1006/jmbi.2001.4966 11575935 The structure of helix III in Xenopus oocyte 5 S rRNA: an RNA stem containing a two-nucleotide bulge. 2001 10.2210/pdb1jur/pdb pdb_00001jur 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 Helix III domain of Xenopus Oocyte 5 S rRNA 7135.346 5'-R(*GP*GP*CP*CP*UP*GP*AP*GP*GP*AP*GP*AP*CP*UP*CP*AP*GP*AP*AP*GP*CP*C)-3' 1 syn polymer no no GGCCUGAGGAGACUCAGAAGCC GGCCUGAGGAGACUCAGAAGCC A polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n 8.114 1 19 A 1 A 22 -3.470 A_G1:C22_A 1 -9.493 0.329 -0.342 -0.055 -4.325 1 19 A 2 A 21 -3.046 A_G2:C21_A 2 -14.804 -0.695 -0.242 -0.273 -23.600 1 19 A 3 A 20 -2.833 A_C3:G20_A 3 0.310 0.285 0.469 -0.029 11.307 1 19 A 4 A 17 -7.731 A_C4:G17_A 4 -25.487 -0.669 0.117 -0.118 0.125 1 20 A 5 A 16 -1.550 A_U5:A16_A 5 -12.452 0.102 0.476 -0.118 6.567 1 19 A 6 A 15 -2.873 A_G6:C15_A 6 -11.669 -0.089 0.124 -0.095 -11.360 1 20 A 7 A 14 -9.361 A_A7:U14_A 7 -0.845 -0.461 -0.163 -0.059 32.027 1 19 A 8 A 13 -5.391 A_G8:C13_A 8 32.131 0.602 1.001 -0.026 41.164 A 9 A 12 26.482 A_G9:A12_A 9 44.043 6.009 0.769 -3.461 0.838 28.069 A A 1 2 43.940 A A 22 21 3.541 19.150 -0.287 -2.525 AA_G1G2:C21C22_AA 1 -6.590 15.121 19.537 -8.796 -0.644 3.043 39.766 A A 2 3 20.403 A A 21 20 3.848 13.606 -0.030 -1.762 AA_G2C3:G20C21_AA 2 -2.960 4.439 37.341 -4.312 -0.330 1.894 76.129 A A 3 4 20.906 A A 20 17 4.332 24.596 3.352 -1.377 AA_C3C4:G17G20_AA 3 -36.277 30.834 63.873 -1.900 -3.874 3.629 34.511 A A 4 5 -1.041 A A 17 16 3.601 -0.614 -0.322 -1.766 AA_C4U5:A16G17_AA 4 -6.573 11.144 33.893 -2.870 -0.594 3.342 30.394 A A 5 6 -4.534 A A 16 15 3.177 -2.373 -0.271 -2.146 AA_U5G6:C15A16_AA 5 -1.877 3.586 30.247 -3.618 0.142 2.954 30.171 A A 6 7 11.648 A A 15 14 3.466 6.024 -0.791 -2.285 AA_G6A7:U14C15_AA 6 -0.012 0.024 29.578 -5.605 1.518 2.565 34.311 A A 7 8 -20.777 A A 14 13 2.171 -11.774 0.139 -2.076 AA_A7G8:C13U14_AA 7 -11.636 20.534 30.159 -2.089 -1.648 1.256 41.723 A A 8 9 29.512 A A 13 12 2.481 20.170 0.871 -1.793 AA_G8G9:A12C13_AA 8 -4.302 6.295 36.469 -3.821 -1.501 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 2002-01-16 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 RCSB Y RCSB 2001-08-26 REL REL The stem of this hairpin occurs naturally in Xenopus Oocytes. sample This structure was determined using standard 2D homonuclear techniques. structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the lowest energy 30 9 2D NOESY 2D NOESY DQF-COSY 2D_13C_separated_HMQC 2D_31P_separated_COSY 100 mM KCl 6.5 ambient 10 K 100 mM KCl 6.5 ambient 30 K In addition to the experimentally derived distance constraints and dihedral angle constraints, the structures were computed using 22 non-experimental constraints to ensure Watson-Crick Base pairing and tetraloop formation. torsion angle dynamics 1 closest to the average 2mM Helix III hairpin; 5mM Cacodylate buffer (pH 6.5); 100 mM KCl 90% H2O/10% D2O 2mM Helix III hairpin; 5mM Cacodylate buffer (pH 6.5); 100 mM KCl 100% D2O Varian collection VNMR Biosym processing Felix 95 Brunger structure solution X-PLOR 3.851 Brunger refinement X-PLOR 3.851 500 Varian UNITY 600 Varian UNITYPLUS 800 Varian INOVA 500 GE OMEGA G 1 n 1 G 1 A G 2 n 2 G 2 A C 3 n 3 C 3 A C 4 n 4 C 4 A U 5 n 5 U 5 A G 6 n 6 G 6 A A 7 n 7 A 7 A G 8 n 8 G 8 A G 9 n 9 G 9 A A 10 n 10 A 10 A G 11 n 11 G 11 A A 12 n 12 A 12 A C 13 n 13 C 13 A U 14 n 14 U 14 A C 15 n 15 C 15 A A 16 n 16 A 16 A G 17 n 17 G 17 A A 18 n 18 A 18 A A 19 n 19 A 19 A G 20 n 20 G 20 A C 21 n 21 C 21 A C 22 n 22 C 22 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 G 1 0.077 SIDE CHAIN 1 A C 3 0.071 SIDE CHAIN 1 A G 8 0.064 SIDE CHAIN 1 A G 9 0.101 SIDE CHAIN 1 A A 10 0.085 SIDE CHAIN 1 A G 11 0.068 SIDE CHAIN 1 A A 12 0.125 SIDE CHAIN 1 A C 13 0.120 SIDE CHAIN 1 A G 17 0.092 SIDE CHAIN 1 A A 18 0.091 SIDE CHAIN 1 A G 20 0.095 SIDE CHAIN 1 A C 22 0.060 SIDE CHAIN 2 A G 1 0.080 SIDE CHAIN 2 A G 9 0.069 SIDE CHAIN 2 A A 10 0.082 SIDE CHAIN 2 A G 11 0.065 SIDE CHAIN 2 A A 12 0.097 SIDE CHAIN 2 A C 13 0.148 SIDE CHAIN 2 A G 17 0.083 SIDE CHAIN 2 A A 19 0.087 SIDE CHAIN 2 A G 20 0.100 SIDE CHAIN 3 A C 3 0.084 SIDE CHAIN 3 A A 7 0.076 SIDE CHAIN 3 A G 8 0.091 SIDE CHAIN 3 A G 9 0.082 SIDE CHAIN 3 A A 10 0.067 SIDE CHAIN 3 A A 12 0.120 SIDE CHAIN 3 A C 13 0.191 SIDE CHAIN 3 A G 17 0.090 SIDE CHAIN 3 A A 18 0.110 SIDE CHAIN 3 A G 20 0.119 SIDE CHAIN 3 A C 22 0.073 SIDE CHAIN 4 A G 1 0.074 SIDE CHAIN 4 A G 9 0.092 SIDE CHAIN 4 A A 10 0.093 SIDE CHAIN 4 A G 11 0.088 SIDE CHAIN 4 A A 12 0.085 SIDE CHAIN 4 A C 13 0.131 SIDE CHAIN 4 A A 16 0.070 SIDE CHAIN 4 A A 18 0.132 SIDE CHAIN 4 A G 20 0.147 SIDE CHAIN 5 A G 1 0.077 SIDE CHAIN 5 A G 6 0.080 SIDE CHAIN 5 A A 7 0.079 SIDE CHAIN 5 A A 10 0.072 SIDE CHAIN 5 A A 12 0.071 SIDE CHAIN 5 A C 13 0.143 SIDE CHAIN 5 A U 14 0.098 SIDE CHAIN 5 A A 18 0.135 SIDE CHAIN 5 A A 19 0.112 SIDE CHAIN 5 A G 20 0.127 SIDE CHAIN 5 A C 22 0.064 SIDE CHAIN 6 A U 5 0.061 SIDE CHAIN 6 A A 7 0.062 SIDE CHAIN 6 A G 9 0.084 SIDE CHAIN 6 A A 10 0.073 SIDE CHAIN 6 A A 12 0.091 SIDE CHAIN 6 A C 13 0.148 SIDE CHAIN 6 A G 17 0.095 SIDE CHAIN 6 A G 20 0.143 SIDE CHAIN 6 A C 21 0.074 SIDE CHAIN 7 A G 9 0.123 SIDE CHAIN 7 A A 10 0.055 SIDE CHAIN 7 A G 11 0.066 SIDE CHAIN 7 A A 12 0.094 SIDE CHAIN 7 A C 13 0.145 SIDE CHAIN 7 A U 14 0.066 SIDE CHAIN 7 A G 17 0.083 SIDE CHAIN 7 A G 20 0.105 SIDE CHAIN 7 A C 21 0.077 SIDE CHAIN 7 A C 22 0.077 SIDE CHAIN 8 A G 1 0.077 SIDE CHAIN 8 A G 2 0.058 SIDE CHAIN 8 A C 3 0.099 SIDE CHAIN 8 A C 4 0.076 SIDE CHAIN 8 A G 9 0.055 SIDE CHAIN 8 A A 10 0.079 SIDE CHAIN 8 A G 11 0.055 SIDE CHAIN 8 A C 13 0.156 SIDE CHAIN 8 A G 17 0.071 SIDE CHAIN 8 A A 18 0.067 SIDE CHAIN 8 A A 19 0.060 SIDE CHAIN 8 A C 22 0.072 SIDE CHAIN 9 A G 8 0.136 SIDE CHAIN 9 A G 9 0.097 SIDE CHAIN 9 A A 10 0.092 SIDE CHAIN 9 A A 12 0.115 SIDE CHAIN 9 A C 13 0.092 SIDE CHAIN 9 A A 18 0.061 SIDE CHAIN 9 A G 20 0.149 SIDE CHAIN 9 A C 21 0.066 SIDE CHAIN 1 -9.49 0.70 101.30 91.81 A A A C3' C2' C1' A A A 12 12 12 N 1 7.85 1.30 114.00 121.85 A A A N9 C1' C2' A A A 12 12 12 N 1 7.20 0.70 108.50 115.70 A A A O4' C1' N9 A A A 16 16 16 N 1 9.16 1.20 119.70 128.86 A A A C3' O3' P A A A 18 18 19 Y 1 4.68 0.70 108.50 113.18 A A A O4' C1' N9 A A A 19 19 19 N 2 -9.30 0.70 101.30 92.00 A A A C3' C2' C1' A A A 12 12 12 N 2 -3.41 0.40 120.30 116.89 A A A C6 N1 C2 C C C 13 13 13 N 2 8.43 0.70 108.50 116.93 A A A O4' C1' N9 A A A 16 16 16 N 2 6.45 0.90 109.80 116.25 A A A C5' C4' O4' G G G 17 17 17 N 3 10.90 1.60 113.70 124.60 A A A C2' C3' O3' C C C 3 3 3 N 3 10.86 1.60 113.70 124.56 A A A C2' C3' O3' A A A 12 12 12 N 3 -8.97 0.70 101.30 92.33 A A A C3' C2' C1' A A A 12 12 12 N 3 8.71 1.30 114.00 122.71 A A A N9 C1' C2' A A A 12 12 12 N 3 -3.06 0.40 120.30 117.24 A A A C6 N1 C2 C C C 13 13 13 N 3 7.99 0.70 108.50 116.49 A A A O4' C1' N9 A A A 16 16 16 N 3 4.27 0.70 108.50 112.77 A A A O4' C1' N9 G G G 17 17 17 N 4 9.79 1.60 113.70 123.49 A A A C2' C3' O3' A A A 10 10 10 N 4 -9.37 0.70 101.30 91.93 A A A C3' C2' C1' A A A 12 12 12 N 4 8.15 0.70 108.50 116.65 A A A O4' C1' N9 A A A 16 16 16 N 5 -9.00 0.70 101.30 92.30 A A A C3' C2' C1' A A A 12 12 12 N 5 7.86 1.30 114.00 121.86 A A A N9 C1' C2' A A A 12 12 12 N 5 -2.53 0.40 120.30 117.77 A A A C6 N1 C2 C C C 13 13 13 N 5 6.92 0.70 108.50 115.42 A A A O4' C1' N9 A A A 16 16 16 N 5 3.02 0.50 113.80 116.82 A A A N7 C8 N9 A A A 16 16 16 N 5 5.43 0.70 108.50 113.93 A A A O4' C1' N9 A A A 18 18 18 N 5 4.81 0.70 108.50 113.31 A A A O4' C1' N9 A A A 19 19 19 N 6 4.56 0.70 108.50 113.06 A A A O4' C1' N9 G G G 1 1 1 N 6 -9.47 0.70 101.30 91.83 A A A C3' C2' C1' A A A 12 12 12 N 6 4.47 0.70 108.50 112.97 A A A O4' C1' N9 A A A 12 12 12 N 6 -3.11 0.40 120.30 117.19 A A A C6 N1 C2 C C C 13 13 13 N 6 7.15 0.70 108.50 115.65 A A A O4' C1' N9 A A A 16 16 16 N 6 3.10 0.50 113.80 116.90 A A A N7 C8 N9 A A A 16 16 16 N 7 9.73 1.60 113.70 123.43 A A A C2' C3' O3' A A A 12 12 12 N 7 -8.94 0.70 101.30 92.36 A A A C3' C2' C1' A A A 12 12 12 N 7 -3.13 0.40 120.30 117.17 A A A C6 N1 C2 C C C 13 13 13 N 7 7.84 0.70 108.50 116.34 A A A O4' C1' N9 A A A 16 16 16 N 8 -4.63 0.70 109.70 105.07 A A A C1' O4' C4' G G G 1 1 1 N 8 5.49 0.70 108.50 113.99 A A A O4' C1' N9 G G G 1 1 1 N 8 -8.20 0.70 101.30 93.10 A A A C3' C2' C1' A A A 12 12 12 N 8 8.00 1.30 114.00 122.00 A A A N9 C1' C2' A A A 12 12 12 N 8 -3.65 0.40 120.30 116.65 A A A C6 N1 C2 C C C 13 13 13 N 8 8.42 0.70 108.50 116.92 A A A O4' C1' N9 A A A 16 16 16 N 8 5.44 0.70 108.50 113.94 A A A O4' C1' N9 G G G 17 17 17 N 9 5.21 0.70 108.50 113.71 A A A O4' C1' N9 G G G 1 1 1 N 9 -2.54 0.40 120.30 117.76 A A A C6 N1 C2 C C C 4 4 4 N 9 9.73 1.60 113.70 123.43 A A A C2' C3' O3' A A A 12 12 12 N 9 -8.38 0.70 101.30 92.92 A A A C3' C2' C1' A A A 12 12 12 N 9 -2.77 0.40 105.80 103.03 A A A C8 N9 C4 A A A 12 12 12 N 9 4.40 0.70 108.50 112.90 A A A O4' C1' N1 U U U 14 14 14 N 9 7.30 0.70 108.50 115.80 A A A O4' C1' N9 A A A 16 16 16 N 1 A A C8 N9 A A 16 16 -0.056 0.008 1.373 1.317 N 2 A A C8 N9 A A 16 16 -0.055 0.008 1.373 1.318 N 3 A A C8 N9 A A 16 16 -0.056 0.008 1.373 1.317 N 4 A A C8 N9 A A 16 16 -0.055 0.008 1.373 1.318 N 5 A A C8 N9 A A 16 16 -0.057 0.008 1.373 1.316 N 6 A A C8 N9 A A 16 16 -0.056 0.008 1.373 1.317 N 7 A A C8 N9 A A 16 16 -0.054 0.008 1.373 1.319 N 8 A A C8 N9 A A 16 16 -0.055 0.008 1.373 1.318 N 9 A A C8 N9 A A 16 16 -0.051 0.008 1.373 1.322 N Solution Structure of Helix III in Xenopus Oocyte 5S rRNA. 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 22 A N3 C 22 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 22 A O2 C 22 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 22 A N4 C 22 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 21 A N3 C 21 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 21 A O2 C 21 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 21 A N4 C 21 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 20 A N1 G 20 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 20 A O6 G 20 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 20 A N2 G 20 1_555 hydrog WATSON-CRICK A C 4 A N3 C 4 1_555 A G 17 A N1 G 17 1_555 hydrog WATSON-CRICK A C 4 A N4 C 4 1_555 A G 17 A O6 G 17 1_555 hydrog WATSON-CRICK A C 4 A O2 C 4 1_555 A G 17 A N2 G 17 1_555 hydrog C-A MISPAIR A C 4 A O2 C 4 1_555 A A 19 A N6 A 19 1_555 hydrog WATSON-CRICK A U 5 A N3 U 5 1_555 A A 16 A N1 A 16 1_555 hydrog WATSON-CRICK A U 5 A O4 U 5 1_555 A A 16 A N6 A 16 1_555 hydrog WATSON-CRICK A G 6 A N1 G 6 1_555 A C 15 A N3 C 15 1_555 hydrog WATSON-CRICK A G 6 A N2 G 6 1_555 A C 15 A O2 C 15 1_555 hydrog WATSON-CRICK A G 6 A O6 G 6 1_555 A C 15 A N4 C 15 1_555 hydrog WATSON-CRICK A A 7 A N1 A 7 1_555 A U 14 A N3 U 14 1_555 hydrog WATSON-CRICK A A 7 A N6 A 7 1_555 A U 14 A O4 U 14 1_555 hydrog WATSON-CRICK A G 8 A N1 G 8 1_555 A C 13 A N3 C 13 1_555 hydrog WATSON-CRICK A G 8 A N2 G 8 1_555 A C 13 A O2 C 13 1_555 hydrog WATSON-CRICK A G 8 A O6 G 8 1_555 A C 13 A N4 C 13 1_555 hydrog G-A MISPAIR A G 9 A N3 G 9 1_555 A A 12 A N6 A 12 1_555 RNA RNA, 5 S rRNA, bulge 1JUR PDB 1 1JUR 1 22 1JUR 1 22 1JUR A 1 1 22