0.008579 0.004953 0.000000 0.000000 0.009907 0.000000 0.000000 0.000000 0.017263 0.000000 0.000000 0.000000 Wedekind, J.E. Jenkins, J.L. Krucinska, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.000 90.000 120.000 116.558 116.558 57.926 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 H2 O 18.015 WATER non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer O4 S -2 96.063 SULFATE ION non-polymer 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 H N 113 N H N 114 N MG N 115 N S N 116 N O N 117 N O N 118 N O N 119 N O N 120 N O N 121 N P N 122 N O N 123 N O N 124 N O N 125 N C N 126 R C N 127 N O N 128 S C N 129 N O N 130 R C N 131 N O N 132 R C N 133 N N N 134 N C N 135 N O N 136 N N N 137 N C N 138 N O N 139 N C N 140 N C N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 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 doub N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N doub 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 sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N sing N 151 N sing N 152 N doub N 153 N sing N 154 N doub N 155 N sing N 156 N sing US J.Biol.Chem. JBCHA3 0071 0021-9258 286 24626 24637 10.1074/jbc.M111.230375 21592962 Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation. 2011 US J.Biol.Chem. JBCHA3 0071 0021-9258 284 11012 11016 19261617 The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain. 2010 10.2210/pdb3q51/pdb pdb_00003q51 100 1 Rh coated flat mirror, toroidal focusing mirror CCD 2010-04-16 MARMOSAIC 325 mm CCD Si(111) SINGLE WAVELENGTH M x-ray 1 0.98 1.0 BL9-2 SSRL 0.98 SYNCHROTRON SSRL BEAMLINE BL9-2 10599.417 PREQ1 RIBOSWITCH 1 syn polymer 96.063 SULFATE ION 1 syn non-polymer 24.305 MAGNESIUM ION 1 syn non-polymer 18.015 water 4 nat water no no CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG A polyribonucleotide 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 n n n n 1 5.358 77.044 VAPOR DIFFUSION, HANGING DROP 6.0 1.5 M Li2SO4, 0.2 M MES pH 6.0, 0.02 M Magnesium sulfate, and 0.002 M spermine-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K 295 4.695 1 19 A 1 A 20 -5.939 A_C1:G20_A 1 -8.608 0.077 -0.141 -0.093 1.934 1 20 A 2 A 19 -1.308 A_U2:A19_A 2 -14.773 -0.224 0.185 -0.253 -10.408 1 19 A 3 A 18 -1.279 A_G3:C18_A 3 -9.593 0.159 -0.151 -0.107 -5.524 1 19 A 4 A 17 -3.067 A_G4:C17_A 4 -10.804 -0.161 0.215 -0.296 -11.988 1 19 A 5 A 16 -5.436 A_G5:C16_A 5 -14.052 0.258 -0.302 -0.131 -29.189 3 23 A 6 A 28 -72.010 A_U6:A28_A 6 -11.392 -0.380 0.761 3.134 -15.354 A 14 A 29 -12.132 A_A14:A29_A 7 -21.281 2.721 0.733 1.767 -4.611 1 19 A 11 A 30 -5.057 A_G11:C30_A 8 -20.129 -0.362 0.365 -0.527 18.766 6 10 A 8 A 31 -66.607 A_G8:A31_A 9 10.836 3.512 -0.561 -4.088 3.139 10 A 10 A 32 -23.985 A_A10:A32_A 10 -10.715 6.458 0.059 -4.602 1.935 1 19 A 33 A 9 -3.727 A_G33:C9_A 11 -4.286 0.234 0.246 -0.400 2.934 35.007 A A 1 2 9.822 A A 20 19 3.261 5.882 0.738 -1.732 AA_C1U2:A19G20_AA 1 -0.049 0.083 34.524 -3.723 -1.234 2.451 36.644 A A 2 3 23.219 A A 19 18 3.365 14.219 -0.359 -1.643 AA_U2G3:C18A19_AA 2 3.362 -5.491 33.698 -4.426 0.999 2.913 26.086 A A 3 4 8.075 A A 18 17 3.169 3.633 0.362 -1.548 AA_G3G4:C17C18_AA 3 -0.911 2.026 25.820 -4.356 -1.034 3.188 40.786 A A 4 5 10.098 A A 17 16 3.509 6.993 0.184 -1.665 AA_G4G5:C16C17_AA 4 4.300 -6.209 39.986 -3.187 0.227 -1.767 24.501 A A 5 6 -9.937 A A 16 28 1.634 -3.999 -6.395 -0.647 AA_G5U6:A28C16_AA 5 12.600 -31.312 20.675 -1.551 14.984 -1.615 176.600 A A 6 14 -51.465 A A 28 29 -2.805 -102.421 -0.244 -2.699 AA_U6A14:A29A28_AA 6 -139.238 69.965 123.176 -1.681 0.572 -3.221 -45.227 A A 14 11 7.358 A A 29 30 -3.316 -5.645 0.246 0.647 AA_A14G11:C30A29_AA 7 1.185 1.545 -44.876 -1.347 0.214 1.307 -174.828 A A 11 8 4.626 A A 30 31 3.165 -9.168 -2.608 3.093 AA_G11G8:A31C30_AA 8 -170.348 -85.946 -113.227 -1.512 -1.973 4.841 -160.792 A A 8 10 -21.788 A A 31 32 -1.892 39.513 -6.056 2.785 AA_G8A10:A32A31_AA 9 155.637 85.821 -17.086 -1.728 -1.826 1.407 -179.845 A A 10 33 -46.832 A A 32 9 1.738 93.644 1.482 3.079 AA_A10G33:C9A32_AA 10 -153.314 -76.673 -127.279 -1.732 0.427 audit_author chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_site repository Initial release Version format compliance Database references Structure summary Data collection Database references Derived calculations Refinement description 1 0 2011-05-18 1 1 2011-07-13 1 2 2013-06-12 1 3 2018-01-24 1 4 2023-09-13 _audit_author.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Crystal structure of PreQ1 riboswitch with PreQ0 metabolite bound RCSB Y RCSB 2010-12-26 REL REL SO4 SULFATE ION MG MAGNESIUM ION HOH water The RNA strand was chemically synthesized based on the sequence of a class I, Type 1 PreQ1 riboswitch aptamer from T. tengcongensis sample 3GCA PDB experimental model SO4 103 2 SO4 SO4 103 A MG 105 3 MG MG 105 A HOH 200 4 HOH HOH 200 A HOH 201 4 HOH HOH 201 A HOH 202 4 HOH HOH 202 A HOH 203 4 HOH HOH 203 A C 1 n 1 C 1 A U 2 n 2 U 2 A G 3 n 3 G 3 A G 4 n 4 G 4 A G 5 n 5 G 5 A U 6 n 6 U 6 A C 7 n 7 C 7 A G 8 n 8 G 8 A C 9 n 9 C 9 A A 10 n 10 A 10 A G 11 n 11 G 11 A U 12 n 12 U 12 A n 13 13 A A 14 n 14 A 14 A C 15 n 15 C 15 A C 16 n 16 C 16 A C 17 n 17 C 17 A C 18 n 18 C 18 A A 19 n 19 A 19 A G 20 n 20 G 20 A U 21 n 21 U 21 A U 22 n 22 U 22 A A 23 n 23 A 23 A A 24 n 24 A 24 A C 25 n 25 C 25 A A 26 n 26 A 26 A A 27 n 27 A 27 A A 28 n 28 A 28 A A 29 n 29 A 29 A C 30 n 30 C 30 A A 31 n 31 A 31 A A 32 n 32 A 32 A G 33 n 33 G 33 A author_and_software_defined_assembly PISA 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 A 13 A A 13 1 Y 104.740 56.6848 34.720 10.6047 0.0000 -0.0000 10.6047 0.0000 -21.2094 0.2722 0.2260 0.2306 2.8500 27.8400 561 5639 9.9500 97.5800 1.000 0.500 0.4000 copied R-free set from 3GCA 1 THROUGHOUT 0.000 FOURIER SYNTHESIS 0.7200 1.0000 3GCA FLAT BULK SOLVENT MODEL 50.2930 0.2630 0.40 2.8500 27.8400 4 690 6 680 0 0.006 764 0.844 1186 0.056 159 0.008 32 19.382 377 0.3643 0.3714 3.1366 129 1210 1339 4 95.0000 0.3131 0.2379 3.5897 136 1243 1379 4 98.0000 0.2707 0.2294 4.5195 143 1279 1422 4 99.0000 0.2403 0.1907 27.8410 153 1346 1499 4 98.0000 70.4 2.85 50.000 3Q51 5771 0 -3 0.075 1.292 1 14.800 7.200 99.200 0.357 2.850 2.950 558 0.875 1 8.400 100.00 0.249 2.950 3.070 564 0.960 1 8.400 99.800 0.178 3.070 3.210 562 1.237 1 8.300 100.00 0.118 3.210 3.380 563 1.845 1 7.700 100.00 0.099 3.380 3.590 570 1.455 1 7.500 99.800 0.085 3.590 3.870 577 1.529 1 7.000 99.800 0.074 3.870 4.260 567 1.422 1 6.800 99.600 0.058 4.260 4.870 595 1.258 1 6.300 99.800 0.048 4.870 6.140 592 1.234 1 5.600 99.500 0.056 6.140 50.000 623 1.034 1 5.600 94.400 data scaling Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ SCALEPACK program refinement Paul D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package 1.6.4_486 data extraction PDB deposit@deposit.rcsb.org June 10, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.10 data collection HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing PHENIX 1.6.4_486 Structural analysis of a class I PreQ1 riboswitch aptamer in the metabolite-free state. 1 N N 2 N N 3 N N 4 N N hydrog WATSON-CRICK A C 1 A N3 C 1 1_555 A G 20 A N1 G 20 1_555 hydrog WATSON-CRICK A C 1 A N4 C 1 1_555 A G 20 A O6 G 20 1_555 hydrog WATSON-CRICK A C 1 A O2 C 1 1_555 A G 20 A N2 G 20 1_555 hydrog WATSON-CRICK A U 2 A N3 U 2 1_555 A A 19 A N1 A 19 1_555 hydrog WATSON-CRICK A U 2 A O4 U 2 1_555 A A 19 A N6 A 19 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 A C 18 A N3 C 18 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 A C 18 A O2 C 18 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 A C 18 A N4 C 18 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 A C 17 A N3 C 17 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 A C 17 A O2 C 17 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 A C 17 A N4 C 17 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 16 A N3 C 16 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 16 A O2 C 16 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 16 A N4 C 16 1_555 hydrog TYPE_10_PAIR A G 5 A N2 G 5 1_555 A A 27 A N1 A 27 1_555 hydrog TYPE_10_PAIR A G 5 A N3 G 5 1_555 A A 27 A N6 A 27 1_555 hydrog U-A PAIR A U 6 A O4 U 6 1_555 A A 14 A N6 A 14 1_555 hydrog HOOGSTEEN A U 6 A N3 U 6 1_555 A A 28 A N7 A 28 1_555 hydrog HOOGSTEEN A U 6 A O4 U 6 1_555 A A 28 A N6 A 28 1_555 hydrog C-G PAIR A C 7 A N4 C 7 1_555 A G 11 A N7 G 11 1_555 hydrog C-C MISPAIR A C 7 A O2 C 7 1_555 A C 30 A N4 C 30 1_555 hydrog TYPE_10_PAIR A G 8 A N2 G 8 1_555 A A 31 A N1 A 31 1_555 hydrog TYPE_10_PAIR A G 8 A N3 G 8 1_555 A A 31 A N6 A 31 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 A G 33 A N1 G 33 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 A G 33 A O6 G 33 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 A G 33 A N2 G 33 1_555 hydrog A-A MISPAIR A A 10 A N3 A 10 1_555 A A 32 A N6 A 32 1_555 hydrog WATSON-CRICK A G 11 A N1 G 11 1_555 A C 30 A N3 C 30 1_555 hydrog WATSON-CRICK A G 11 A N2 G 11 1_555 A C 30 A O2 C 30 1_555 hydrog WATSON-CRICK A G 11 A O6 G 11 1_555 A C 30 A N4 C 30 1_555 hydrog A-A MISPAIR A A 14 A N1 A 14 1_555 A A 29 A N6 A 29 1_555 hydrog C-A MISPAIR A C 16 A O2 C 16 1_555 A A 28 A N6 A 28 1_555 hydrog C-A MISPAIR A C 17 A O2 C 17 1_555 A A 26 A N6 A 26 1_555 hydrog G-U MISPAIR A G 20 A N2 G 20 1_555 A U 21 A O4 U 21 1_555 RNA PREQ1, PREQ0, RNA, RIBOSOMAL BINDING SITE, APTAMER, METABOLITE, Pseudoknot, H-type, RIBOSWITCH 3Q51 PDB 1 3Q51 CUGGGUCGCAGUAACCCCAGUUAACAAAACAAG 1 33 3Q51 1 33 3Q51 A 1 1 33 BINDING SITE FOR RESIDUE SO4 A 103 A SO4 103 Software 1 BINDING SITE FOR RESIDUE MG A 105 A MG 105 Software 1 A C 18 A C 18 1 1_555 A G 5 A G 5 1 1_555 182 P 63 2 2