1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Cabello-Villegas, J. Winkler, M.E. Nikonowicz, E.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 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 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C 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 H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 R C N 49 N O N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 58 N C 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 H N 72 N H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 R C N 84 N O N 85 R C Y 86 N N Y 87 N C Y 88 N N Y 89 N C N 90 N C N 91 N O N 92 N N N 93 N C N 94 N N N 95 N N Y 96 N C 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 H N 109 N H N 110 N H N 111 N O N 112 N P N 113 N O N 114 N O N 115 N O N 116 N C N 117 R C N 118 N O N 119 S C N 120 N O N 121 R C N 122 N O N 123 R C N 124 N N N 125 N C N 126 N O N 127 N N N 128 N C N 129 N O N 130 N C N 131 N C 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 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 N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N doub 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 sing N 65 N sing N 66 N doub N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub 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 N 97 N sing N 98 N sing N 99 N sing Y 100 N sing Y 101 N sing Y 102 N doub N 103 N sing Y 104 N sing N 105 N sing Y 106 N doub N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N doub 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 sing 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 sing N 146 N doub N 147 N sing N 148 N doub N 149 N sing N 150 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 319 1015 1034 10.1016/S0022-2836(02)00382-0 12079344 Solution conformations of unmodified and A(37)N(6)-dimethylallyl modified anticodon stem-loops of Escherichia coli tRNA(Phe). 2002 10.2210/pdb1j4y/pdb pdb_00001j4y 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 5466.324 anticodon stem-loop of tRNA(Phe) 1 syn polymer no no GGGGAUUGAAAAUCCCC GGGGAUUGAAAAUCCCC A polyribonucleotide n n n n n n n n n n n n n n n n n -13.752 1 19 A 1 A 17 -3.272 A_G1:C17_A 1 -4.119 -0.459 -1.274 -0.531 -2.803 1 19 A 2 A 16 -1.740 A_G2:C16_A 2 12.085 -0.017 -0.218 -0.196 -23.359 1 19 A 3 A 15 -4.287 A_G3:C15_A 3 -3.786 0.133 -0.534 0.044 -8.709 1 19 A 4 A 14 -0.609 A_G4:C14_A 4 -7.071 0.407 -0.775 -0.002 -17.666 1 20 A 5 A 13 2.716 A_A5:U13_A 5 -21.510 0.121 -1.016 -0.025 -23.210 1 20 A 6 A 12 1.557 A_U6:A12_A 6 -15.197 0.613 0.688 -0.102 -26.473 1 A 7 A 11 45.988 A_U7:A11_A 7 20.618 2.382 1.678 -0.149 2.419 24.703 A A 1 2 21.535 A A 17 16 3.004 8.951 -0.876 -1.378 AA_G1G2:C16C17_AA 1 -4.695 11.295 22.570 -5.588 0.805 1.150 53.610 A A 2 3 55.101 A A 16 15 4.178 43.413 0.684 -1.813 AA_G2G3:C15C16_AA 2 0.462 -0.586 32.243 -4.891 -0.728 1.990 33.500 A A 3 4 38.615 A A 15 14 3.423 20.645 1.339 -1.449 AA_G3G4:C14C15_AA 3 4.681 -8.755 26.114 -5.701 -1.601 3.139 31.059 A A 4 5 23.831 A A 14 13 3.887 12.378 1.685 -1.617 AA_G4A5:U13C14_AA 4 4.365 -8.405 28.211 -5.702 -2.202 3.477 29.057 A A 5 6 -0.425 A A 13 12 3.663 -0.212 0.439 -1.954 AA_A5U6:A12U13_AA 5 -6.839 13.755 28.257 -3.844 -2.538 3.940 52.301 A A 6 7 -51.612 A A 12 11 5.195 -39.272 1.011 -1.701 AA_U6U7:A11A12_AA 6 -18.502 24.316 29.902 2.864 -3.406 database_2 pdbx_nmr_exptl_sample_conditions pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Experimental preparation Data collection 1 0 2002-07-17 1 1 2008-04-26 1 2 2011-07-13 1 3 2022-02-23 1 4 2023-12-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_software.name 1KKA contains the ensemble RCSB Y RCSB 2001-12-12 REL REL T7 RNA polymerase in vitro transcription sample The structure was determined using 1H, 13C, 15N and 31P heteronuclear NMR spectroscopy. 1 3D_15N-separated_NOESY 3D_13C-separated_NOESY DQF-COSY HNN-COSY 10 mM KPi, 10mM NaCl 6.8 1 atm 298 K 10 mM KPi, 10mM NaCl 6.8 1 atm 288 K 294 NOE distance constraints, 36 base pair constraints, 70 torsion angle constraints. Global fold without torsion angle constraints. Refinement with torsion angle constraints. simulated annealing 2mM ACSL-Phe, 15N, 13C 10 mM Potassium Phosphate, 10mM NaCl, 0.02mM EDTA. 90% H2O-10% D2O or 100% D2O. Brunger, A. refinement X-PLOR 3.861 MSI-Biosym data analysis Felix 98 Brunger structure solution X-PLOR 3.1 500 Bruker AMX G 1 n 1 G 1 A G 2 n 2 G 2 A G 3 n 3 G 3 A G 4 n 4 G 4 A A 5 n 5 A 5 A U 6 n 6 U 6 A U 7 n 7 U 7 A G 8 n 8 G 8 A A 9 n 9 A 9 A A 10 n 10 A 10 A A 11 n 11 A 11 A A 12 n 12 A 12 A U 13 n 13 U 13 A C 14 n 14 C 14 A C 15 n 15 C 15 A C 16 n 16 C 16 A C 17 n 17 C 17 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 4.47 0.50 113.10 117.57 A A A N7 C8 N9 G G G 1 1 1 N 1 -2.59 0.40 106.40 103.81 A A A C8 N9 C4 G G G 1 1 1 N 1 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 2 2 2 N 1 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 2 2 2 N 1 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 3 3 3 N 1 -2.70 0.40 106.40 103.70 A A A C8 N9 C4 G G G 3 3 3 N 1 4.51 0.50 113.10 117.61 A A A N7 C8 N9 G G G 4 4 4 N 1 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 4 4 4 N 1 3.72 0.50 113.80 117.52 A A A N7 C8 N9 A A A 5 5 5 N 1 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 8 8 8 N 1 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 8 8 8 N 1 3.74 0.50 113.80 117.54 A A A N7 C8 N9 A A A 9 9 9 N 1 3.55 0.50 113.80 117.35 A A A N7 C8 N9 A A A 10 10 10 N 1 3.76 0.50 113.80 117.56 A A A N7 C8 N9 A A A 11 11 11 N 1 3.78 0.50 113.80 117.58 A A A N7 C8 N9 A A A 12 12 12 N Solution Structure of the Unmodified Anticodon Stem-loop from E. coli tRNA(Phe) 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 17 A N3 C 17 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 17 A O2 C 17 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 17 A N4 C 17 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 16 A N3 C 16 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 16 A O2 C 16 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 16 A N4 C 16 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 17 A N3 C 17 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 17 A O2 C 17 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 17 A N4 C 17 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 A C 15 A N3 C 15 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 A C 15 A O2 C 15 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 A C 15 A N4 C 15 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 A C 14 A N3 C 14 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 A C 14 A O2 C 14 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 A C 14 A N4 C 14 1_555 hydrog WATSON-CRICK A A 5 A N1 A 5 1_555 A U 13 A N3 U 13 1_555 hydrog WATSON-CRICK A A 5 A N6 A 5 1_555 A U 13 A O4 U 13 1_555 hydrog WATSON-CRICK A U 6 A N3 U 6 1_555 A A 12 A N1 A 12 1_555 hydrog WATSON-CRICK A U 6 A O4 U 6 1_555 A A 12 A N6 A 12 1_555 hydrog U-A PAIR A U 7 A O2 U 7 1_555 A A 10 A N6 A 10 1_555 hydrog U-A PAIR A U 7 A N3 U 7 1_555 A A 11 A N1 A 11 1_555 RNA RNA stem-loop, trinucleotide loop, hairpin, RNA 1J4Y PDB 1 1J4Y 1 17 1J4Y 1 17 1J4Y A 1 1 17