0.034095 0.000000 0.000000 0.000000 0.034095 0.000000 0.000000 0.000000 0.011141 0.00000 0.00000 0.00000 Kondo, J. Dock-Bregeon, A.C. Willkomm, D.K. Hartmann, R.K. Westhof, E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.000 90.000 90.000 29.330 29.330 89.760 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 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 O N 115 N P N 116 N O N 117 N O N 118 N O N 119 N C N 120 R C N 121 N O N 122 S C N 123 N O N 124 R C N 125 N O N 126 R C N 127 N N N 128 N C N 129 N O N 130 N N N 131 N C N 132 N O N 133 N C N 134 N C 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 145 N H N 146 N H N 147 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 sing N 119 N sing N 120 N doub 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 sing N 143 N sing N 144 N doub N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N doub N 151 N sing N 152 N sing DK Acta Crystallogr.,Sect.F 1744-3091 69 634 639 10.1107/S1744309113013018 23722840 Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet 2013 10.2210/pdb4jrt/pdb pdb_00004jrt 100 1 CCD 2009-07-04 SINGLE WAVELENGTH M x-ray 1 1.0723 1.0 ID23-1 ESRF 1.0723 SYNCHROTRON ESRF BEAMLINE ID23-1 3979.408 RNA (5'-R(P*GP*GP*GP*UP*GP*GP*UP*GP*CP*GP*GP*G)-3') 1 syn polymer 3723.264 RNA (5'-R(P*CP*CP*UP*GP*CP*AP*CP*UP*GP*CP*CP*C)-3') 1 syn polymer 18.015 water 23 nat water no no GGGUGGUGCGGG GGGUGGUGCGGG A polyribonucleotide no no CCUGCACUGCCC CCUGCACUGCCC B 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 1 2.51 50.92 VAPOR DIFFUSION 7.0 Sodium Cacodylate, Lithium acetate, PEG3350, pH 7.0, vapor diffusion, temperature 310K 310 -6.256 1 19 A 1 B 24 -4.942 A_G1:C24_B 1 -7.088 0.311 0.352 0.130 1.802 1 19 A 2 B 23 8.360 A_G2:C23_B 2 -0.871 0.124 0.342 0.258 -8.634 1 19 A 3 B 22 4.737 A_G3:C22_B 3 -6.756 -0.252 0.013 -0.105 -0.350 1 28 A 4 B 21 3.016 A_U4:G21_B 4 -1.225 2.211 0.259 -0.288 -11.055 1 28 A 5 B 20 5.705 A_G5:U20_B 5 -15.663 -2.354 -0.568 -0.629 -12.358 1 19 A 6 B 19 6.328 A_G6:C19_B 6 -9.003 -0.423 -0.273 -0.136 -0.278 1 20 A 7 B 18 2.464 A_U7:A18_B 7 -5.301 -0.258 0.149 0.081 3.812 1 19 A 8 B 17 6.436 A_G8:C17_B 8 -11.757 -0.237 0.108 0.048 6.588 1 19 A 9 B 16 -2.766 A_C9:G16_B 9 -11.386 0.480 -0.332 -0.342 -2.968 1 28 A 10 B 15 1.587 A_G10:U15_B 10 -16.347 -1.798 0.159 -0.575 -10.692 1 19 A 11 B 14 4.768 A_G11:C14_B 11 -14.068 -0.573 -0.134 0.061 -13.977 1 19 A 12 B 13 6.827 A_G12:C13_B 12 -13.044 -0.498 -0.739 -0.066 3.077 33.290 A A 1 2 -0.398 B B 24 23 3.101 -0.228 0.421 -1.847 AA_G1G2:C23C24_BB 1 -2.351 4.108 33.209 -3.187 -1.106 1.819 36.379 A A 2 3 32.991 B B 23 22 3.198 19.560 -0.047 -1.704 AA_G2G3:C22C23_BB 2 2.154 -3.633 30.750 -5.010 0.326 2.721 39.581 A A 3 4 11.658 B B 22 21 2.992 7.845 0.209 -1.154 AA_G3U4:G21C22_BB 3 0.738 -1.096 38.819 -2.515 -0.233 1.236 23.166 A A 4 5 39.709 B B 21 20 3.232 14.449 1.029 -2.284 AA_U4G5:U20G21_BB 4 7.174 -19.714 16.681 -9.689 -0.575 2.885 38.140 A A 5 6 12.334 B B 20 19 3.292 7.968 -0.492 -1.859 AA_G5G6:C19U20_BB 5 -6.438 9.967 36.788 -3.815 -0.030 2.620 32.508 A A 6 7 11.982 B B 19 18 2.883 6.652 -0.572 -1.236 AA_G6U7:A18C19_BB 6 -3.275 5.899 31.673 -3.201 0.534 2.361 33.626 A A 7 8 24.826 B B 18 17 3.178 13.933 0.165 -1.354 AA_U7G8:C17A18_BB 7 2.912 -5.189 30.544 -4.367 0.139 2.706 34.262 A A 8 9 20.628 B B 17 16 3.279 11.892 -0.114 -1.039 AA_G8C9:G16C17_BB 8 3.549 -6.156 31.998 -3.537 0.724 1.647 31.020 A A 9 10 32.496 B B 16 15 3.231 16.486 1.158 -1.855 AA_C9G10:U15G16_BB 9 -3.257 6.420 26.169 -6.048 -2.675 3.132 36.019 A A 10 11 8.557 B B 15 14 3.391 5.273 -0.173 -1.603 AA_G10G11:C14U15_BB 10 -0.648 1.052 35.638 -3.344 0.187 3.097 35.071 A A 11 12 14.912 B B 14 13 3.557 8.841 0.616 -1.642 AA_G11G12:C13C14_BB 11 6.683 -11.272 33.326 -4.110 0.025 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model repository Initial release Database references Data collection Database references Refinement description 1 0 2013-06-05 1 1 2013-07-03 1 2 2023-11-08 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y PDBJ 2013-03-21 REL REL HOH water in vitro transcription sample in vitro transcription sample HOH (A 111) AND HOH (A 112) ARE CLOSED TO SYMMETRY-RELATED RNA MOLECULE. 353D PDB ENTRY 353D PDB experimental model HOH 2 3 HOH HOH 101 A HOH 5 3 HOH HOH 102 A HOH 6 3 HOH HOH 103 A HOH 7 3 HOH HOH 104 A HOH 8 3 HOH HOH 105 A HOH 10 3 HOH HOH 106 A HOH 11 3 HOH HOH 107 A HOH 12 3 HOH HOH 108 A HOH 20 3 HOH HOH 109 A HOH 23 3 HOH HOH 110 A HOH 24 3 HOH HOH 111 A HOH 26 3 HOH HOH 112 A HOH 28 3 HOH HOH 113 A HOH 25 3 HOH HOH 114 A HOH 1 3 HOH HOH 101 B HOH 3 3 HOH HOH 102 B HOH 4 3 HOH HOH 103 B HOH 9 3 HOH HOH 104 B HOH 13 3 HOH HOH 105 B HOH 19 3 HOH HOH 106 B HOH 21 3 HOH HOH 107 B HOH 22 3 HOH HOH 108 B HOH 27 3 HOH HOH 109 B G 1 n 1 G 1 A G 2 n 2 G 2 A G 3 n 3 G 3 A U 4 n 4 U 4 A G 5 n 5 G 5 A G 6 n 6 G 6 A U 7 n 7 U 7 A G 8 n 8 G 8 A C 9 n 9 C 9 A G 10 n 10 G 10 A G 11 n 11 G 11 A G 12 n 12 G 12 A C 13 n 1 C 13 B C 14 n 2 C 14 B U 15 n 3 U 15 B G 16 n 4 G 16 B C 17 n 5 C 17 B A 18 n 6 A 18 B C 19 n 7 C 19 B U 20 n 8 U 20 B G 21 n 9 G 21 B C 22 n 10 C 22 B C 23 n 11 C 23 B C 24 n 12 C 24 B author_and_software_defined_assembly PISA 2 dimeric 1250 -9 4610 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 P OP3 G G 1 1 -0.078 0.012 1.607 1.529 N 1 B B P OP3 C C 13 13 -0.078 0.012 1.607 1.529 N CNS_TOPPAR:dna-rna_rep.param CNS_TOPPAR:water_rep.param CNS_TOPPAR:ion.param ccc_xplor.param 113.100 76.1548 41.680 21.0200 0.0000 0.0000 21.0200 0.0000 -42.0400 0.2275 0.1848 2.6000 20.7 220 2330 9.4000 99.4000 1.000 1.000 1 0.000 MOLECULAR REPLACEMENT PDB ENTRY 353D 41.7378 2.6000 20.7 23 540 0 517 0 0.006 1.195 0.000 1.500 1.526 2.000 0.000 2.000 2.268 2.500 0.4593 0.3756 2.6900 22 211 233 10 100.0000 0.3398 0.3873 2.8000 25 198 223 10 100.0000 0.4286 0.3556 2.9300 26 225 251 10 100.0000 0.3369 0.2959 3.0800 15 203 218 10 100.0000 0.2870 0.2167 3.2800 23 223 246 10 100.0000 0.2602 0.2351 3.5300 19 198 217 10 100.0000 0.1995 0.1689 3.8800 18 222 240 10 100.0000 0.1901 0.1314 4.4500 26 214 240 10 99.2000 0.1971 0.1256 5.6000 22 212 234 10 100.0000 0.1843 0.1612 100.0000 24 204 228 10 94.6000 2.6 20.7 4JRT 2330 1 phasing Jorge Navaza ccp4@ccp4.ac.uk Fortran_77 http://www.ccp4.ac.uk/ AMoRE program refinement Axel T. Brunger axel.brunger@yale.edu Fortran_77 http://cns-online.org/ CNS package data extraction PDB deposit@deposit.rcsb.org April 22, 2011 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.11 data reduction CrystalClear data scaling CrystalClear Crystal structure of an A-form RNA duplex containing three GU base pairs 1 N N 2 N N 3 N N 3 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 24 B N3 C 12 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 24 B O2 C 12 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 24 B N4 C 12 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 B C 23 B N3 C 11 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 B C 23 B O2 C 11 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 B C 23 B N4 C 11 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 B C 22 B N3 C 10 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 B C 22 B O2 C 10 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 B C 22 B N4 C 10 1_555 hydrog TYPE_28_PAIR A U 4 A N3 U 4 1_555 B G 21 B O6 G 9 1_555 hydrog TYPE_28_PAIR A U 4 A O2 U 4 1_555 B G 21 B N1 G 9 1_555 hydrog TYPE_28_PAIR A G 5 A N1 G 5 1_555 B U 20 B O2 U 8 1_555 hydrog TYPE_28_PAIR A G 5 A O6 G 5 1_555 B U 20 B N3 U 8 1_555 hydrog WATSON-CRICK A G 6 A N1 G 6 1_555 B C 19 B N3 C 7 1_555 hydrog WATSON-CRICK A G 6 A N2 G 6 1_555 B C 19 B O2 C 7 1_555 hydrog WATSON-CRICK A G 6 A O6 G 6 1_555 B C 19 B N4 C 7 1_555 hydrog WATSON-CRICK A U 7 A N3 U 7 1_555 B A 18 B N1 A 6 1_555 hydrog WATSON-CRICK A U 7 A O4 U 7 1_555 B A 18 B N6 A 6 1_555 hydrog WATSON-CRICK A G 8 A N1 G 8 1_555 B C 17 B N3 C 5 1_555 hydrog WATSON-CRICK A G 8 A N2 G 8 1_555 B C 17 B O2 C 5 1_555 hydrog WATSON-CRICK A G 8 A O6 G 8 1_555 B C 17 B N4 C 5 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 B G 16 B N1 G 4 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 B G 16 B O6 G 4 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 B G 16 B N2 G 4 1_555 hydrog TYPE_28_PAIR A G 10 A N1 G 10 1_555 B U 15 B O2 U 3 1_555 hydrog TYPE_28_PAIR A G 10 A O6 G 10 1_555 B U 15 B N3 U 3 1_555 hydrog WATSON-CRICK A G 11 A N1 G 11 1_555 B C 14 B N3 C 2 1_555 hydrog WATSON-CRICK A G 11 A N2 G 11 1_555 B C 14 B O2 C 2 1_555 hydrog WATSON-CRICK A G 11 A O6 G 11 1_555 B C 14 B N4 C 2 1_555 hydrog WATSON-CRICK A G 12 A N1 G 12 1_555 B C 13 B N3 C 1 1_555 hydrog WATSON-CRICK A G 12 A N2 G 12 1_555 B C 13 B O2 C 1 1_555 hydrog WATSON-CRICK A G 12 A O6 G 12 1_555 B C 13 B N4 C 1 1_555 RNA A-form RNA, ribose-zipper motif, GU base pair, RNA 4JRT PDB 1 4JRT 4JRT PDB 2 4JRT 1 12 4JRT 1 12 4JRT A 1 1 12 13 24 4JRT 13 24 4JRT B 2 1 12 78 P 43