0.017249 0.000000 0.003578 0.000000 0.044377 0.000000 0.000000 0.000000 0.017468 0.000000 0.000000 0.000000 Correll, C.C. Swinger, K. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 101.72 90.00 57.974 22.534 58.465 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 UK RNA RNARFU 2122 1355-8382 9 355 363 10.1261/rna.2147803 12592009 Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution 2003 10.2210/pdb1msy/pdb pdb_00001msy 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 100 1 CCD 2000-07-06 CUSTOM-MADE Si-111 double crystal monochromator SINGLE WAVELENGTH M x-ray 1 0.97764 1.0 19-ID APS 0.97764 SYNCHROTRON APS BEAMLINE 19-ID GUAA tetraloop mutant 8705.215 SARCIN/RICIN DOMAIN FROM 23 S RRNA A2660U, G2661A 1 syn polymer 18.015 water 109 nat water no no UGCUCCUAGUACGUAAGGACCGGAGUG UGCUCCUAGUACGUAAGGACCGGAGUG 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 1 2.15 42.73 VAPOR DIFFUSION, HANGING DROP 7.0 ammonium sulfate, potassium MOPS, magnesium chloride, manganese chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K 292 (NH4)2SO4 1 potassium MOPS 1 MgCl2 1 MnCl2 1 (NH4)2SO4 2 MgCl2 2 MnCl2 2 1.954 A 2647 A 2673 -43.734 A_U2647:G2673_A 1 -3.602 -1.590 -0.263 0.316 4.665 28 A 2648 A 2672 -2.953 A_G2648:U2672_A 2 -7.747 -2.367 0.107 -0.597 9.595 1 19 A 2649 A 2671 -2.310 A_C2649:G2671_A 3 -15.927 0.087 0.021 -0.169 4.923 1 20 A 2650 A 2670 6.329 A_U2650:A2670_A 4 -16.454 0.109 0.249 -0.111 1.460 1 19 A 2651 A 2669 3.271 A_C2651:G2669_A 5 -17.745 0.186 -0.072 -0.103 -4.322 1 19 A 2652 A 2668 0.533 A_C2652:G2668_A 6 -8.628 0.285 0.257 -0.107 -0.399 A 2653 A 2667 -15.307 A_U2653:C2667_A 7 -12.063 5.745 -0.252 -2.187 8.420 4 24 A 2656 A 2665 -106.047 A_U2656:A2665_A 8 -17.415 4.035 -0.496 -1.616 -1.133 9 11 A 2657 A 2664 -0.455 A_A2657:G2664_A 9 2.564 -6.873 -0.064 -4.208 6.738 1 19 A 2658 A 2663 1.141 A_C2658:G2663_A 10 -3.956 0.121 -0.289 -0.106 -0.984 10 A 2659 A 2662 -11.757 A_G2659:A2662_A 11 -18.469 6.786 1.187 -4.822 2.465 35.815 A A 2647 2648 11.104 A A 2673 2672 3.218 6.766 2.964 -1.315 AA_U2647G2648:U2672G2673_AA 1 -5.289 8.680 34.803 -2.995 -5.490 3.014 41.997 A A 2648 2649 5.288 A A 2672 2671 3.127 3.784 -0.235 -1.261 AA_G2648C2649:G2671U2672_AA 2 -2.093 2.925 41.783 -2.129 0.123 2.877 34.239 A A 2649 2650 12.418 A A 2671 2670 3.246 7.258 0.788 -1.420 AA_C2649U2650:A2670G2671_AA 3 -0.330 0.565 33.482 -3.494 -1.388 2.997 33.816 A A 2650 2651 6.807 A A 2670 2669 3.232 3.948 -0.448 -1.599 AA_U2650C2651:G2669A2670_AA 4 2.117 -3.649 33.526 -3.358 1.097 2.823 30.731 A A 2651 2652 15.287 A A 2669 2668 3.372 8.010 -0.133 -1.725 AA_C2651C2652:G2668G2669_AA 5 -1.242 2.371 29.668 -4.771 0.016 3.129 52.506 A A 2652 2653 4.765 A A 2668 2667 3.362 4.203 -1.098 -1.100 AA_C2652U2653:C2667G2668_AA 6 6.243 -7.078 52.001 -1.518 1.648 6.429 31.607 A A 2653 2656 -8.790 A A 2667 2665 6.407 -4.755 0.497 -0.569 AA_U2653U2656:A2665C2667_AA 7 4.388 -8.111 30.954 0.703 0.699 3.823 -14.587 A A 2656 2657 14.680 A A 2665 2664 3.557 -3.677 5.495 -1.210 AA_U2656A2657:G2664A2665_AA 8 -1.906 -7.611 -13.990 8.486 19.712 3.143 60.686 A A 2657 2658 4.913 A A 2664 2663 3.217 4.959 -0.284 -0.971 AA_A2657C2658:G2663G2664_AA 9 -1.816 1.799 60.478 -1.195 0.195 3.076 45.623 A A 2658 2659 19.734 A A 2663 2662 3.386 15.028 -3.036 -1.156 AA_C2658G2659:A2662G2663_AA 10 -3.711 4.873 43.049 -2.834 3.583 software chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Data collection Refinement description Data collection Database references Refinement description 1 0 2003-02-25 1 1 2008-04-28 1 2 2011-07-13 1 3 2019-07-24 1 4 2024-02-14 _software.classification _software.name _database_2.pdbx_DOI _database_2.pdbx_database_accession WT Sarcin/Ricin domain from E. Coli 23 S rRNA Ribotoxin Restrictocin and a 31- Mer SRD RNA inhibitor Ribotoxin Restrictocin and a 29-Mer SRD RNA analog Ribotoxin Restrictocin and a 29-Mer SRD RNA analog WT Sarcin/Ricin domain from E. Coli 23 S rRNA COMPOUND A CRYSTALLOGRAPHIC TWO-FOLD AXIS PASSES THROUGH THE TERMINAL GU WOBBLEBASE PAIR. EACH MOLECULE ABOUT THE 2-FOLD CONTRIBUTES ONE NUCLEOTIDE TO THE WOBBLE PAIR AND THE NUCLEOTIDE THAT COULD FORM THE INTRAMOLECULAR CLOSING PAIR IS DISORDERED. NOTE THAT THE OCCUPANCIES FOR THESE NUCLEOTIDES IS 0.5. RCSB Y RCSB 2002-09-19 REL REL HOH water A2660U and G2661U double mutant of the SRL domain from E.coli rRNA sample 483D PDB experimental model HOH 3001 2 HOH HOH 3001 A HOH 3002 2 HOH HOH 3002 A HOH 3003 2 HOH HOH 3003 A HOH 3004 2 HOH HOH 3004 A HOH 3005 2 HOH HOH 3005 A HOH 3006 2 HOH HOH 3006 A HOH 3007 2 HOH HOH 3007 A HOH 3008 2 HOH HOH 3008 A HOH 3009 2 HOH HOH 3009 A HOH 3010 2 HOH HOH 3010 A HOH 3011 2 HOH HOH 3011 A HOH 3012 2 HOH HOH 3012 A HOH 3013 2 HOH HOH 3013 A HOH 3014 2 HOH HOH 3014 A HOH 3015 2 HOH HOH 3015 A HOH 3016 2 HOH HOH 3016 A HOH 3017 2 HOH HOH 3017 A HOH 3018 2 HOH HOH 3018 A HOH 3019 2 HOH HOH 3019 A HOH 3020 2 HOH HOH 3020 A HOH 3021 2 HOH HOH 3021 A HOH 3022 2 HOH HOH 3022 A HOH 3023 2 HOH HOH 3023 A HOH 3024 2 HOH HOH 3024 A HOH 3025 2 HOH HOH 3025 A HOH 3026 2 HOH HOH 3026 A HOH 3027 2 HOH HOH 3027 A HOH 3028 2 HOH HOH 3028 A HOH 3029 2 HOH HOH 3029 A HOH 3030 2 HOH HOH 3030 A HOH 3031 2 HOH HOH 3031 A HOH 3032 2 HOH HOH 3032 A HOH 3033 2 HOH HOH 3033 A HOH 3034 2 HOH HOH 3034 A HOH 3035 2 HOH HOH 3035 A HOH 3036 2 HOH HOH 3036 A HOH 3037 2 HOH HOH 3037 A HOH 3038 2 HOH HOH 3038 A HOH 3039 2 HOH HOH 3039 A HOH 3040 2 HOH HOH 3040 A HOH 3041 2 HOH HOH 3041 A HOH 3042 2 HOH HOH 3042 A HOH 3043 2 HOH HOH 3043 A HOH 3044 2 HOH HOH 3044 A HOH 3045 2 HOH HOH 3045 A HOH 3046 2 HOH HOH 3046 A HOH 3047 2 HOH HOH 3047 A HOH 3048 2 HOH HOH 3048 A HOH 3049 2 HOH HOH 3049 A HOH 3050 2 HOH HOH 3050 A HOH 3051 2 HOH HOH 3051 A HOH 3052 2 HOH HOH 3052 A HOH 3053 2 HOH HOH 3053 A HOH 3054 2 HOH HOH 3054 A HOH 3055 2 HOH HOH 3055 A HOH 3056 2 HOH HOH 3056 A HOH 3057 2 HOH HOH 3057 A HOH 3058 2 HOH HOH 3058 A HOH 3059 2 HOH HOH 3059 A HOH 3060 2 HOH HOH 3060 A HOH 3061 2 HOH HOH 3061 A HOH 3062 2 HOH HOH 3062 A HOH 3063 2 HOH HOH 3063 A HOH 3064 2 HOH HOH 3064 A HOH 3065 2 HOH HOH 3065 A HOH 3066 2 HOH HOH 3066 A HOH 3067 2 HOH HOH 3067 A HOH 3068 2 HOH HOH 3068 A HOH 3069 2 HOH HOH 3069 A HOH 3070 2 HOH HOH 3070 A HOH 3071 2 HOH HOH 3071 A HOH 3072 2 HOH HOH 3072 A HOH 3073 2 HOH HOH 3073 A HOH 3074 2 HOH HOH 3074 A HOH 3075 2 HOH HOH 3075 A HOH 3076 2 HOH HOH 3076 A HOH 3077 2 HOH HOH 3077 A HOH 3078 2 HOH HOH 3078 A HOH 3079 2 HOH HOH 3079 A HOH 3080 2 HOH HOH 3080 A HOH 3081 2 HOH HOH 3081 A HOH 3082 2 HOH HOH 3082 A HOH 3083 2 HOH HOH 3083 A HOH 3084 2 HOH HOH 3084 A HOH 3086 2 HOH HOH 3086 A HOH 3087 2 HOH HOH 3087 A HOH 3088 2 HOH HOH 3088 A HOH 3089 2 HOH HOH 3089 A HOH 3090 2 HOH HOH 3090 A HOH 3091 2 HOH HOH 3091 A HOH 3092 2 HOH HOH 3092 A HOH 3093 2 HOH HOH 3093 A HOH 3094 2 HOH HOH 3094 A HOH 3095 2 HOH HOH 3095 A HOH 3096 2 HOH HOH 3096 A HOH 3098 2 HOH HOH 3098 A HOH 3099 2 HOH HOH 3099 A HOH 3100 2 HOH HOH 3100 A HOH 3101 2 HOH HOH 3101 A HOH 3102 2 HOH HOH 3102 A HOH 3103 2 HOH HOH 3103 A HOH 3104 2 HOH HOH 3104 A HOH 3105 2 HOH HOH 3105 A HOH 3107 2 HOH HOH 3107 A HOH 3108 2 HOH HOH 3108 A HOH 3109 2 HOH HOH 3109 A HOH 3110 2 HOH HOH 3110 A HOH 3111 2 HOH HOH 3111 A HOH 3112 2 HOH HOH 3112 A URI 2647 n 1 U 2647 A GUA 2648 n 2 G 2648 A CYT 2649 n 3 C 2649 A URI 2650 n 4 U 2650 A CYT 2651 n 5 C 2651 A CYT 2652 n 6 C 2652 A URI 2653 n 7 U 2653 A ADE 2654 n 8 A 2654 A GUA 2655 n 9 G 2655 A URI 2656 n 10 U 2656 A ADE 2657 n 11 A 2657 A CYT 2658 n 12 C 2658 A GUA 2659 n 13 G 2659 A URI 2660 n 14 U 2660 A ADE 2661 n 15 A 2661 A ADE 2662 n 16 A 2662 A GUA 2663 n 17 G 2663 A GUA 2664 n 18 G 2664 A ADE 2665 n 19 A 2665 A CYT 2666 n 20 C 2666 A CYT 2667 n 21 C 2667 A GUA 2668 n 22 G 2668 A GUA 2669 n 23 G 2669 A ADE 2670 n 24 A 2670 A GUA 2671 n 25 G 2671 A URI 2672 n 26 U 2672 A GUA 2673 n 27 G 2673 A 0.1383 0.1637 0.1366 0.164 0.1784 0.207 1082 1419 10.8 11.0 10030 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 U 2647 A U 1 1 A G 2673 A G 27 1 A HOH 3002 B HOH 1 A HOH 3004 B HOH 1 A HOH 3068 B HOH 1 3.38 0.50 129.30 132.68 A A A N1 C2 N3 A A A 2657 2657 2657 N 1 -8.69 1.10 112.00 103.31 A A A N9 C1' C2' G G G 2659 2659 2659 N 1 3.08 0.50 111.90 114.98 A A A C2 N3 C4 G G G 2659 2659 2659 N 1 3.09 0.50 111.50 114.59 A A A C5 C6 N1 G G G 2659 2659 2659 N 1 -8.42 1.20 119.70 111.28 A A A C3' O3' P A A G 2662 2662 2663 A Y 1 7.41 1.20 110.70 118.11 A A A O5' P OP1 G G G 2663 2663 2663 B B N 1 -4.15 0.60 128.60 124.45 A A A C5 C6 O6 G G G 2664 2664 2664 N 1 -4.33 0.60 119.90 115.57 A A A N1 C6 O6 G G G 2673 2673 2673 N ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ? 0.207 0.164 0.1637 0.1637 1.41 29.0 6236 1419 14372 14372 8182 11.0 97.9 RANDOM 1 FREE R 0.0 0.0 MOLECULAR REPLACEMENT 483D 2 0.00 662.50 1.41 29.0 109 691 0 582 0 0.010 0.028 0.0195 0.009 0.006 0.079 1.40 40.0 1MSY 14372 14372 0.0 -3.0 0.072 0.072 1 21.8 6.3 97.9 0.323 1.40 1.42 2.3 0.323 80.0 refinement SHELXL-97 data scaling SCALEPACK refinement CNS data reduction DENZO phasing CNS GUAA tetraloop mutant of Sarcin/Ricin domain from E. Coli 23 S rRNA 1 N N 2 N N hydrog U-G MISPAIR A U 2647 A O4 U 1 1_555 A G 2673 A N1 G 27 1_555 hydrog TYPE_28_PAIR A G 2648 A N1 G 2 1_555 A U 2672 A O2 U 26 1_555 hydrog TYPE_28_PAIR A G 2648 A O6 G 2 1_555 A U 2672 A N3 U 26 1_555 hydrog WATSON-CRICK A C 2649 A N3 C 3 1_555 A G 2671 A N1 G 25 1_555 hydrog WATSON-CRICK A C 2649 A N4 C 3 1_555 A G 2671 A O6 G 25 1_555 hydrog WATSON-CRICK A C 2649 A O2 C 3 1_555 A G 2671 A N2 G 25 1_555 hydrog WATSON-CRICK A U 2650 A N3 U 4 1_555 A A 2670 A N1 A 24 1_555 hydrog WATSON-CRICK A U 2650 A O4 U 4 1_555 A A 2670 A N6 A 24 1_555 hydrog WATSON-CRICK A C 2651 A N3 C 5 1_555 A G 2669 A N1 G 23 1_555 hydrog WATSON-CRICK A C 2651 A N4 C 5 1_555 A G 2669 A O6 G 23 1_555 hydrog WATSON-CRICK A C 2651 A O2 C 5 1_555 A G 2669 A N2 G 23 1_555 hydrog WATSON-CRICK A C 2652 A N3 C 6 1_555 A G 2668 A N1 G 22 1_555 hydrog WATSON-CRICK A C 2652 A N4 C 6 1_555 A G 2668 A O6 G 22 1_555 hydrog WATSON-CRICK A C 2652 A O2 C 6 1_555 A G 2668 A N2 G 22 1_555 hydrog U-C MISPAIR A U 2653 A O2 U 7 1_555 A C 2667 A N4 C 21 1_555 hydrog G-U MISPAIR A G 2655 A N2 G 9 1_555 A U 2656 A O4 U 10 1_555 hydrog REVERSED HOOGSTEEN A U 2656 A N3 U 10 1_555 A A 2665 A N7 A 19 1_555 hydrog REVERSED HOOGSTEEN A U 2656 A O2 U 10 1_555 A A 2665 A N6 A 19 1_555 hydrog TYPE_11_PAIR A A 2657 A N6 A 11 1_555 A G 2664 A N3 G 18 1_555 hydrog TYPE_11_PAIR A A 2657 A N7 A 11 1_555 A G 2664 A N2 G 18 1_555 hydrog WATSON-CRICK A C 2658 A N3 C 12 1_555 A G 2663 A N1 G 17 1_555 hydrog WATSON-CRICK A C 2658 A N4 C 12 1_555 A G 2663 A O6 G 17 1_555 hydrog WATSON-CRICK A C 2658 A O2 C 12 1_555 A G 2663 A N2 G 17 1_555 hydrog G-A MISPAIR A G 2659 A N2 G 13 1_555 A A 2662 A N7 A 16 1_555 RNA A-minor motif, sarcin/ricin loop, RNA structure, RNA tertiary contacts, RNA motifs, conformational change, RNA-protein recognition, hydration, RNA 1MSY PDB 1 1MSY 2647 2673 1MSY 2647 2673 1MSY A 1 1 27 5 C 1 2 1