data_5D99 # _entry.id 5D99 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 5D99 pdb_00005d99 10.2210/pdb5d99/pdb WWPDB D_1000212876 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2016-04-13 2 'Structure model' 1 1 2017-03-15 3 'Structure model' 1 2 2017-09-27 4 'Structure model' 1 3 2019-12-11 5 'Structure model' 1 4 2019-12-25 6 'Structure model' 1 5 2024-03-06 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 2 'Structure model' 'Experimental preparation' 3 2 'Structure model' Other 4 2 'Structure model' 'Structure summary' 5 3 'Structure model' 'Author supporting evidence' 6 4 'Structure model' 'Author supporting evidence' 7 5 'Structure model' 'Database references' 8 6 'Structure model' 'Data collection' 9 6 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' pdbx_audit_support 2 4 'Structure model' pdbx_audit_support 3 5 'Structure model' citation 4 5 'Structure model' citation_author 5 6 'Structure model' chem_comp_atom 6 6 'Structure model' chem_comp_bond 7 6 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_pdbx_audit_support.funding_organization' 2 4 'Structure model' '_pdbx_audit_support.funding_organization' 3 5 'Structure model' '_citation.country' 4 5 'Structure model' '_citation.journal_abbrev' 5 5 'Structure model' '_citation.journal_id_ASTM' 6 5 'Structure model' '_citation.journal_id_ISSN' 7 5 'Structure model' '_citation.page_last' 8 5 'Structure model' '_citation.pdbx_database_id_PubMed' 9 5 'Structure model' '_citation.title' 10 5 'Structure model' '_citation_author.name' 11 6 'Structure model' '_database_2.pdbx_DOI' 12 6 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5D99 _pdbx_database_status.recvd_initial_deposition_date 2015-08-18 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.details ;3dw4 contains the original structure that was determined by molecular replacement. The current deposition is a redetermination of that structure by direct methods.THIS ENTRY 5D99 REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R3DW4SF ; _pdbx_database_related.db_id 3DW4 _pdbx_database_related.content_type re-refinement # _audit_author.name 'Mooers, B.H.M.' _audit_author.pdbx_ordinal 1 _audit_author.identifier_ORCID ? # loop_ _citation.abstract _citation.abstract_id_CAS _citation.book_id_ISBN _citation.book_publisher _citation.book_publisher_city _citation.book_title _citation.coordinate_linkage _citation.country _citation.database_id_Medline _citation.details _citation.id _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_full _citation.journal_issue _citation.journal_volume _citation.language _citation.page_first _citation.page_last _citation.title _citation.year _citation.database_id_CSD _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.unpublished_flag ? ? ? ? ? ? ? ? ? ? primary 'Acta Crystallogr D Struct Biol' ? ? 2059-7983 ? ? 72 ? 477 487 'Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry.' 2016 ? 10.1107/S2059798316001224 27050127 ? ? ? ? ? ? ? ? UK ? ? original_data_1 RNA RNARFU 2122 1469-9001 ? ? 15 ? 707 715 'A fast selenium derivatization strategy for crystallization and phasing of RNA structures.' 2009 ? 10.1261/rna.1499309 19228585 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mooers, B.H.' 1 ? original_data_1 'Olieric, V.' 2 ? original_data_1 'Rieder, U.' 3 ? original_data_1 'Lang, K.' 4 ? original_data_1 'Serganov, A.' 5 ? original_data_1 'Schulze-Briese, C.' 6 ? original_data_1 'Micura, R.' 7 ? original_data_1 'Dumas, P.' 8 ? original_data_1 'Ennifar, E.' 9 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'RNA (27-MER) hairpin from sarcin-ricin domain of E. coli 23S rRNA' 8758.282 1 ? ? ? ? 2 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 3 water nat water 18.015 172 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'UGC(OMU)CCUAGUACGAGAGGACCGGAGUG' _entity_poly.pdbx_seq_one_letter_code_can UGCUCCUAGUACGAGAGGACCGGAGUG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 GLYCEROL GOL 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 G n 1 3 C n 1 4 OMU n 1 5 C n 1 6 C n 1 7 U n 1 8 A n 1 9 G n 1 10 U n 1 11 A n 1 12 C n 1 13 G n 1 14 A n 1 15 G n 1 16 A n 1 17 G n 1 18 G n 1 19 A n 1 20 C n 1 21 C n 1 22 G n 1 23 G n 1 24 A n 1 25 G n 1 26 U n 1 27 G n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 27 _pdbx_entity_src_syn.organism_scientific 'Enterobacteria phage L1' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 268588 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 HOH non-polymer . WATER ? 'H2 O' 18.015 OMU 'RNA linking' n ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; ? 'C10 H15 N2 O9 P' 338.208 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 U 1 2647 2647 U U A . n A 1 2 G 2 2648 2648 G G A . n A 1 3 C 3 2649 2649 C C A . n A 1 4 OMU 4 2650 2650 OMU OMU A . n A 1 5 C 5 2651 2651 C C A . n A 1 6 C 6 2652 2652 C C A . n A 1 7 U 7 2653 2653 U U A . n A 1 8 A 8 2654 2654 A A A . n A 1 9 G 9 2655 2655 G G A . n A 1 10 U 10 2656 2656 U U A . n A 1 11 A 11 2657 2657 A A A . n A 1 12 C 12 2658 2658 C C A . n A 1 13 G 13 2659 2659 G G A . n A 1 14 A 14 2660 2660 A A A . n A 1 15 G 15 2661 2661 G G A . n A 1 16 A 16 2662 2662 A A A . n A 1 17 G 17 2663 2663 G G A . n A 1 18 G 18 2664 2664 G G A . n A 1 19 A 19 2665 2665 A A A . n A 1 20 C 20 2666 2666 C C A . n A 1 21 C 21 2667 2667 C C A . n A 1 22 G 22 2668 2668 G G A . n A 1 23 G 23 2669 2669 G G A . n A 1 24 A 24 2670 2670 A A A . n A 1 25 G 25 2671 2671 G G A . n A 1 26 U 26 2672 2672 U U A . n A 1 27 G 27 2673 2673 G G A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 GOL 1 2701 2701 GOL GOL A . C 3 HOH 1 2801 2801 HOH HOH A . C 3 HOH 2 2802 2802 HOH HOH A . C 3 HOH 3 2803 2803 HOH HOH A . C 3 HOH 4 2804 2804 HOH HOH A . C 3 HOH 5 2805 2805 HOH HOH A . C 3 HOH 6 2806 2806 HOH HOH A . C 3 HOH 7 2807 2807 HOH HOH A . C 3 HOH 8 2808 2816 HOH HOH A . C 3 HOH 9 2809 2808 HOH HOH A . C 3 HOH 10 2810 2812 HOH HOH A . C 3 HOH 11 2811 2809 HOH HOH A . C 3 HOH 12 2812 2810 HOH HOH A . C 3 HOH 13 2813 2813 HOH HOH A . C 3 HOH 14 2814 2814 HOH HOH A . C 3 HOH 15 2815 2811 HOH HOH A . C 3 HOH 16 2816 2815 HOH HOH A . C 3 HOH 17 2817 2832 HOH HOH A . C 3 HOH 18 2818 2817 HOH HOH A . C 3 HOH 19 2819 2820 HOH HOH A . C 3 HOH 20 2820 2819 HOH HOH A . C 3 HOH 21 2821 2828 HOH HOH A . C 3 HOH 22 2822 2818 HOH HOH A . C 3 HOH 23 2823 2833 HOH HOH A . C 3 HOH 24 2824 2822 HOH HOH A . C 3 HOH 25 2825 2823 HOH HOH A . C 3 HOH 26 2826 2821 HOH HOH A . C 3 HOH 27 2827 2825 HOH HOH A . C 3 HOH 28 2828 2824 HOH HOH A . C 3 HOH 29 2829 2827 HOH HOH A . C 3 HOH 30 2830 2826 HOH HOH A . C 3 HOH 31 2831 2829 HOH HOH A . C 3 HOH 32 2832 2831 HOH HOH A . C 3 HOH 33 2833 2830 HOH HOH A . C 3 HOH 34 2834 2834 HOH HOH A . C 3 HOH 35 2835 2835 HOH HOH A . C 3 HOH 36 2836 2836 HOH HOH A . C 3 HOH 37 2837 2842 HOH HOH A . C 3 HOH 38 2838 2837 HOH HOH A . C 3 HOH 39 2839 2838 HOH HOH A . C 3 HOH 40 2840 2840 HOH HOH A . C 3 HOH 41 2841 2839 HOH HOH A . C 3 HOH 42 2842 2843 HOH HOH A . C 3 HOH 43 2843 2841 HOH HOH A . C 3 HOH 44 2844 2844 HOH HOH A . C 3 HOH 45 2845 2848 HOH HOH A . C 3 HOH 46 2846 2847 HOH HOH A . C 3 HOH 47 2847 2846 HOH HOH A . C 3 HOH 48 2848 2852 HOH HOH A . C 3 HOH 49 2849 2849 HOH HOH A . C 3 HOH 50 2850 2851 HOH HOH A . C 3 HOH 51 2851 2845 HOH HOH A . C 3 HOH 52 2852 2862 HOH HOH A . C 3 HOH 53 2853 2855 HOH HOH A . C 3 HOH 54 2854 2864 HOH HOH A . C 3 HOH 55 2855 2853 HOH HOH A . C 3 HOH 56 2856 2857 HOH HOH A . C 3 HOH 57 2857 2854 HOH HOH A . C 3 HOH 58 2858 2859 HOH HOH A . C 3 HOH 59 2859 2856 HOH HOH A . C 3 HOH 60 2860 2858 HOH HOH A . C 3 HOH 61 2861 2861 HOH HOH A . C 3 HOH 62 2862 2850 HOH HOH A . C 3 HOH 63 2863 2860 HOH HOH A . C 3 HOH 64 2864 2863 HOH HOH A . C 3 HOH 65 2865 2873 HOH HOH A . C 3 HOH 66 2866 2865 HOH HOH A . C 3 HOH 67 2867 2866 HOH HOH A . C 3 HOH 68 2868 2869 HOH HOH A . C 3 HOH 69 2869 2867 HOH HOH A . C 3 HOH 70 2870 2871 HOH HOH A . C 3 HOH 71 2871 2868 HOH HOH A . C 3 HOH 72 2872 2875 HOH HOH A . C 3 HOH 73 2873 2877 HOH HOH A . C 3 HOH 74 2874 2872 HOH HOH A . C 3 HOH 75 2875 2870 HOH HOH A . C 3 HOH 76 2876 2874 HOH HOH A . C 3 HOH 77 2877 2876 HOH HOH A . C 3 HOH 78 2878 2878 HOH HOH A . C 3 HOH 79 2879 2880 HOH HOH A . C 3 HOH 80 2880 2885 HOH HOH A . C 3 HOH 81 2881 2882 HOH HOH A . C 3 HOH 82 2882 2881 HOH HOH A . C 3 HOH 83 2883 2879 HOH HOH A . C 3 HOH 84 2884 2883 HOH HOH A . C 3 HOH 85 2885 2884 HOH HOH A . C 3 HOH 86 2886 2896 HOH HOH A . C 3 HOH 87 2887 2886 HOH HOH A . C 3 HOH 88 2888 2887 HOH HOH A . C 3 HOH 89 2889 2894 HOH HOH A . C 3 HOH 90 2890 2888 HOH HOH A . C 3 HOH 91 2891 2889 HOH HOH A . C 3 HOH 92 2892 2892 HOH HOH A . C 3 HOH 93 2893 2891 HOH HOH A . C 3 HOH 94 2894 2890 HOH HOH A . C 3 HOH 95 2895 2893 HOH HOH A . C 3 HOH 96 2896 2904 HOH HOH A . C 3 HOH 97 2897 2897 HOH HOH A . C 3 HOH 98 2898 2895 HOH HOH A . C 3 HOH 99 2899 2901 HOH HOH A . C 3 HOH 100 2900 2900 HOH HOH A . C 3 HOH 101 2901 2899 HOH HOH A . C 3 HOH 102 2902 2903 HOH HOH A . C 3 HOH 103 2903 2902 HOH HOH A . C 3 HOH 104 2904 2898 HOH HOH A . C 3 HOH 105 2905 2905 HOH HOH A . C 3 HOH 106 2906 2906 HOH HOH A . C 3 HOH 107 2907 2909 HOH HOH A . C 3 HOH 108 2908 2907 HOH HOH A . C 3 HOH 109 2909 2908 HOH HOH A . C 3 HOH 110 2910 2910 HOH HOH A . C 3 HOH 111 2911 2911 HOH HOH A . C 3 HOH 112 2912 2912 HOH HOH A . C 3 HOH 113 2913 2914 HOH HOH A . C 3 HOH 114 2914 2913 HOH HOH A . C 3 HOH 115 2915 2916 HOH HOH A . C 3 HOH 116 2916 2917 HOH HOH A . C 3 HOH 117 2917 2918 HOH HOH A . C 3 HOH 118 2918 2921 HOH HOH A . C 3 HOH 119 2919 2920 HOH HOH A . C 3 HOH 120 2920 2919 HOH HOH A . C 3 HOH 121 2921 2922 HOH HOH A . C 3 HOH 122 2922 2924 HOH HOH A . C 3 HOH 123 2923 2923 HOH HOH A . C 3 HOH 124 2924 2930 HOH HOH A . C 3 HOH 125 2925 2925 HOH HOH A . C 3 HOH 126 2926 2927 HOH HOH A . C 3 HOH 127 2927 2929 HOH HOH A . C 3 HOH 128 2928 2928 HOH HOH A . C 3 HOH 129 2929 2926 HOH HOH A . C 3 HOH 130 2930 2932 HOH HOH A . C 3 HOH 131 2931 2931 HOH HOH A . C 3 HOH 132 2932 2915 HOH HOH A . C 3 HOH 133 2933 2934 HOH HOH A . C 3 HOH 134 2934 2933 HOH HOH A . C 3 HOH 135 2935 2935 HOH HOH A . C 3 HOH 136 2936 2936 HOH HOH A . C 3 HOH 137 2937 2937 HOH HOH A . C 3 HOH 138 2938 2938 HOH HOH A . C 3 HOH 139 2939 2939 HOH HOH A . C 3 HOH 140 2940 2941 HOH HOH A . C 3 HOH 141 2941 2942 HOH HOH A . C 3 HOH 142 2942 2940 HOH HOH A . C 3 HOH 143 2943 2943 HOH HOH A . C 3 HOH 144 2944 2945 HOH HOH A . C 3 HOH 145 2945 2944 HOH HOH A . C 3 HOH 146 2946 2946 HOH HOH A . C 3 HOH 147 2947 2947 HOH HOH A . C 3 HOH 148 2948 2948 HOH HOH A . C 3 HOH 149 2949 2949 HOH HOH A . C 3 HOH 150 2950 2950 HOH HOH A . C 3 HOH 151 2951 2951 HOH HOH A . C 3 HOH 152 2952 2952 HOH HOH A . C 3 HOH 153 2953 2953 HOH HOH A . C 3 HOH 154 2954 2954 HOH HOH A . C 3 HOH 155 2955 2956 HOH HOH A . C 3 HOH 156 2956 2955 HOH HOH A . C 3 HOH 157 2957 2957 HOH HOH A . C 3 HOH 158 2958 2958 HOH HOH A . C 3 HOH 159 2959 2959 HOH HOH A . C 3 HOH 160 2960 2960 HOH HOH A . C 3 HOH 161 2961 2961 HOH HOH A . C 3 HOH 162 2962 2962 HOH HOH A . C 3 HOH 163 2963 2963 HOH HOH A . C 3 HOH 164 2964 2965 HOH HOH A . C 3 HOH 165 2965 2966 HOH HOH A . C 3 HOH 166 2966 2964 HOH HOH A . C 3 HOH 167 2967 2967 HOH HOH A . C 3 HOH 168 2968 2968 HOH HOH A . C 3 HOH 169 2969 2969 HOH HOH A . C 3 HOH 170 2970 2970 HOH HOH A . C 3 HOH 171 2971 2971 HOH HOH A . C 3 HOH 172 2972 2972 HOH HOH A . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.10_2142 1 ? phasing ? ? ? ? ? ? ? ? ? ? ? Sir2014 ? ? ? . 2 # _cell.entry_id 5D99 _cell.length_a 29.630 _cell.length_b 29.630 _cell.length_c 76.330 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D99 _symmetry.space_group_name_H-M 'P 43' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 5D99 _exptl.crystals_number ? _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 1.91 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 35.70 _exptl_crystal.description 'AUTHOR USED THE SF DATA FROM ENTRY 3DW4.' _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _diffrn.ambient_environment ? _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 5D99 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 38814 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.952 _refine.ls_d_res_high 0.970 _refine.ls_percent_reflns_obs 99.94 _refine.ls_R_factor_obs 0.1054 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1046 _refine.ls_R_factor_R_free 0.1199 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.23 _refine.ls_number_reflns_R_free 2029 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'AB INITIO PHASING' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details 'Random selection' _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.06 _refine.pdbx_overall_phase_error 10.59 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 580 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 172 _refine_hist.number_atoms_total 758 _refine_hist.d_res_high 0.970 _refine_hist.d_res_low 20.952 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.006 ? ? 758 'X-RAY DIFFRACTION' ? f_angle_d 1.224 ? ? 1184 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 15.737 ? ? 376 'X-RAY DIFFRACTION' ? f_chiral_restr 0.050 ? ? 153 'X-RAY DIFFRACTION' ? f_plane_restr 0.020 ? ? 31 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all 'X-RAY DIFFRACTION' . 0.9700 0.9943 2644 0.1808 99.00 0.1912 . . 141 . . 'X-RAY DIFFRACTION' . 0.9943 1.0212 2650 0.1519 100.00 0.1635 . . 138 . . 'X-RAY DIFFRACTION' . 1.0212 1.0512 2603 0.1273 100.00 0.1302 . . 151 . . 'X-RAY DIFFRACTION' . 1.0512 1.0852 2614 0.1129 100.00 0.1250 . . 136 . . 'X-RAY DIFFRACTION' . 1.0852 1.1239 2609 0.1060 100.00 0.1160 . . 152 . . 'X-RAY DIFFRACTION' . 1.1239 1.1689 2618 0.1000 100.00 0.1188 . . 131 . . 'X-RAY DIFFRACTION' . 1.1689 1.2221 2597 0.0949 100.00 0.1092 . . 158 . . 'X-RAY DIFFRACTION' . 1.2221 1.2866 2671 0.0914 100.00 0.1066 . . 136 . . 'X-RAY DIFFRACTION' . 1.2866 1.3672 2595 0.0981 100.00 0.1118 . . 163 . . 'X-RAY DIFFRACTION' . 1.3672 1.4727 2640 0.1038 100.00 0.1280 . . 131 . . 'X-RAY DIFFRACTION' . 1.4727 1.6208 2628 0.0988 100.00 0.1123 . . 146 . . 'X-RAY DIFFRACTION' . 1.6208 1.8553 2629 0.0956 100.00 0.1099 . . 147 . . 'X-RAY DIFFRACTION' . 1.8553 2.3369 2622 0.1132 100.00 0.1230 . . 150 . . 'X-RAY DIFFRACTION' . 2.3369 20.9565 2665 0.1019 100.00 0.1215 . . 149 . . # _struct.entry_id 5D99 _struct.title '3DW4 redetermined by direct methods starting from random phase angles' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 5D99 _struct_keywords.text 'ab initio direct methods structure determination, hairpin RNA, RNA' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_ref.db_code 5D99 _struct_ref.db_name PDB _struct_ref.details ? _struct_ref.entity_id 1 _struct_ref.id 1 _struct_ref.seq_align ? _struct_ref.seq_dif ? _struct_ref.pdbx_db_accession 5D99 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_align_end ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5D99 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 27 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 5D99 _struct_ref_seq.db_align_beg 2647 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 2673 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2647 _struct_ref_seq.pdbx_auth_seq_align_end 2673 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A C 3 "O3'" ? ? ? 1_555 A OMU 4 P ? ? A C 2649 A OMU 2650 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale2 covale both ? A OMU 4 "O3'" ? ? ? 1_555 A C 5 P ? ? A OMU 2650 A C 2651 1_555 ? ? ? ? ? ? ? 1.599 ? ? hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 26 O2 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog2 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 26 N3 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 25 N1 A ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 25 O6 A ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 25 N2 A ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A OMU 4 N3 ? ? ? 1_555 A A 24 N1 A ? A OMU 2650 A A 2670 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A OMU 4 O4 ? ? ? 1_555 A A 24 N6 A ? A OMU 2650 A A 2670 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 23 N1 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 23 O6 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 23 N2 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 7 O2 ? ? ? 1_555 A C 21 N4 ? ? A U 2653 A C 2667 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog15 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 19 N7 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog16 hydrog ? ? A U 10 O2 ? ? ? 1_555 A A 19 N6 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog17 hydrog ? ? A A 11 N6 ? ? ? 1_555 A G 18 N3 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog18 hydrog ? ? A A 11 N7 ? ? ? 1_555 A G 18 N2 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog19 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 13 N2 ? ? ? 1_555 A A 16 N7 ? ? A G 2659 A A 2662 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id GOL _struct_site.pdbx_auth_seq_id 2701 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 9 _struct_site.details 'binding site for residue GOL A 2701' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 9 U A 1 ? U A 2647 . ? 1_655 ? 2 AC1 9 U A 7 ? U A 2653 . ? 1_555 ? 3 AC1 9 A A 8 ? A A 2654 . ? 1_555 ? 4 AC1 9 U A 10 ? U A 2656 . ? 1_555 ? 5 AC1 9 A A 14 ? A A 2660 . ? 1_545 ? 6 AC1 9 C A 20 ? C A 2666 . ? 1_555 ? 7 AC1 9 HOH C . ? HOH A 2828 . ? 1_555 ? 8 AC1 9 HOH C . ? HOH A 2922 . ? 1_655 ? 9 AC1 9 HOH C . ? HOH A 2970 . ? 1_655 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 "HO2'" A U 2653 ? ? HO2 A GOL 2701 ? ? 1.29 2 1 O A HOH 2828 ? ? O A HOH 2900 ? ? 2.14 3 1 OP2 A A 2670 ? A O A HOH 2801 ? ? 2.15 # _pdbx_database_remark.id 0 _pdbx_database_remark.text ;This entry 5D99 reflects an alternative modeling of the structural data in r3dw4SF original data determined by Author: V.Olieric,U.Rieder,K.Lang,A.Serganov,C.Schulze-Briese,R.Micura,P.Dumas,E.Ennifar ; # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id A _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 2972 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.05 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 GOL C1 C N N 111 GOL O1 O N N 112 GOL C2 C N N 113 GOL O2 O N N 114 GOL C3 C N N 115 GOL O3 O N N 116 GOL H11 H N N 117 GOL H12 H N N 118 GOL HO1 H N N 119 GOL H2 H N N 120 GOL HO2 H N N 121 GOL H31 H N N 122 GOL H32 H N N 123 GOL HO3 H N N 124 HOH O O N N 125 HOH H1 H N N 126 HOH H2 H N N 127 OMU N1 N N N 128 OMU C2 C N N 129 OMU N3 N N N 130 OMU C4 C N N 131 OMU C5 C N N 132 OMU C6 C N N 133 OMU O2 O N N 134 OMU O4 O N N 135 OMU "C1'" C N R 136 OMU "C2'" C N R 137 OMU "O2'" O N N 138 OMU CM2 C N N 139 OMU "C3'" C N R 140 OMU "C4'" C N R 141 OMU "O3'" O N N 142 OMU "O4'" O N N 143 OMU "C5'" C N N 144 OMU "O5'" O N N 145 OMU P P N N 146 OMU OP1 O N N 147 OMU OP2 O N N 148 OMU OP3 O N N 149 OMU HN3 H N N 150 OMU H5 H N N 151 OMU H6 H N N 152 OMU "H1'" H N N 153 OMU "H2'" H N N 154 OMU HM21 H N N 155 OMU HM22 H N N 156 OMU HM23 H N N 157 OMU "H3'" H N N 158 OMU "H4'" H N N 159 OMU "HO3'" H N N 160 OMU "H5'" H N N 161 OMU "H5''" H N N 162 OMU HOP2 H N N 163 OMU HOP3 H N N 164 U OP3 O N N 165 U P P N N 166 U OP1 O N N 167 U OP2 O N N 168 U "O5'" O N N 169 U "C5'" C N N 170 U "C4'" C N R 171 U "O4'" O N N 172 U "C3'" C N S 173 U "O3'" O N N 174 U "C2'" C N R 175 U "O2'" O N N 176 U "C1'" C N R 177 U N1 N N N 178 U C2 C N N 179 U O2 O N N 180 U N3 N N N 181 U C4 C N N 182 U O4 O N N 183 U C5 C N N 184 U C6 C N N 185 U HOP3 H N N 186 U HOP2 H N N 187 U "H5'" H N N 188 U "H5''" H N N 189 U "H4'" H N N 190 U "H3'" H N N 191 U "HO3'" H N N 192 U "H2'" H N N 193 U "HO2'" H N N 194 U "H1'" H N N 195 U H3 H N N 196 U H5 H N N 197 U H6 H N N 198 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 GOL C1 O1 sing N N 116 GOL C1 C2 sing N N 117 GOL C1 H11 sing N N 118 GOL C1 H12 sing N N 119 GOL O1 HO1 sing N N 120 GOL C2 O2 sing N N 121 GOL C2 C3 sing N N 122 GOL C2 H2 sing N N 123 GOL O2 HO2 sing N N 124 GOL C3 O3 sing N N 125 GOL C3 H31 sing N N 126 GOL C3 H32 sing N N 127 GOL O3 HO3 sing N N 128 HOH O H1 sing N N 129 HOH O H2 sing N N 130 OMU N1 C2 sing N N 131 OMU N1 C6 sing N N 132 OMU N1 "C1'" sing N N 133 OMU C2 N3 sing N N 134 OMU C2 O2 doub N N 135 OMU N3 C4 sing N N 136 OMU N3 HN3 sing N N 137 OMU C4 C5 sing N N 138 OMU C4 O4 doub N N 139 OMU C5 C6 doub N N 140 OMU C5 H5 sing N N 141 OMU C6 H6 sing N N 142 OMU "C1'" "C2'" sing N N 143 OMU "C1'" "O4'" sing N N 144 OMU "C1'" "H1'" sing N N 145 OMU "C2'" "O2'" sing N N 146 OMU "C2'" "C3'" sing N N 147 OMU "C2'" "H2'" sing N N 148 OMU "O2'" CM2 sing N N 149 OMU CM2 HM21 sing N N 150 OMU CM2 HM22 sing N N 151 OMU CM2 HM23 sing N N 152 OMU "C3'" "C4'" sing N N 153 OMU "C3'" "O3'" sing N N 154 OMU "C3'" "H3'" sing N N 155 OMU "C4'" "O4'" sing N N 156 OMU "C4'" "C5'" sing N N 157 OMU "C4'" "H4'" sing N N 158 OMU "O3'" "HO3'" sing N N 159 OMU "C5'" "O5'" sing N N 160 OMU "C5'" "H5'" sing N N 161 OMU "C5'" "H5''" sing N N 162 OMU "O5'" P sing N N 163 OMU P OP1 doub N N 164 OMU P OP2 sing N N 165 OMU P OP3 sing N N 166 OMU OP2 HOP2 sing N N 167 OMU OP3 HOP3 sing N N 168 U OP3 P sing N N 169 U OP3 HOP3 sing N N 170 U P OP1 doub N N 171 U P OP2 sing N N 172 U P "O5'" sing N N 173 U OP2 HOP2 sing N N 174 U "O5'" "C5'" sing N N 175 U "C5'" "C4'" sing N N 176 U "C5'" "H5'" sing N N 177 U "C5'" "H5''" sing N N 178 U "C4'" "O4'" sing N N 179 U "C4'" "C3'" sing N N 180 U "C4'" "H4'" sing N N 181 U "O4'" "C1'" sing N N 182 U "C3'" "O3'" sing N N 183 U "C3'" "C2'" sing N N 184 U "C3'" "H3'" sing N N 185 U "O3'" "HO3'" sing N N 186 U "C2'" "O2'" sing N N 187 U "C2'" "C1'" sing N N 188 U "C2'" "H2'" sing N N 189 U "O2'" "HO2'" sing N N 190 U "C1'" N1 sing N N 191 U "C1'" "H1'" sing N N 192 U N1 C2 sing N N 193 U N1 C6 sing N N 194 U C2 O2 doub N N 195 U C2 N3 sing N N 196 U N3 C4 sing N N 197 U N3 H3 sing N N 198 U C4 O4 doub N N 199 U C4 C5 sing N N 200 U C5 C6 doub N N 201 U C5 H5 sing N N 202 U C6 H6 sing N N 203 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5D99 'double helix' 5D99 'a-form double helix' 5D99 tetraloop 5D99 'mismatched base pair' 5D99 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 2 1_555 A U 26 1_555 -2.359 -0.531 0.229 4.781 -13.132 1.516 1 A_G2648:U2672_A A 2648 ? A 2672 ? 28 1 1 A C 3 1_555 A G 25 1_555 0.454 -0.106 0.085 10.739 -18.030 1.912 2 A_C2649:G2671_A A 2649 ? A 2671 ? 19 1 1 A OMU 4 1_555 A A 24 1_555 -0.209 -0.014 0.128 3.714 -16.853 1.012 3 A_OMU2650:A2670_A A 2650 ? A 2670 ? 20 1 1 A C 5 1_555 A G 23 1_555 0.276 -0.144 -0.009 5.783 -17.099 1.991 4 A_C2651:G2669_A A 2651 ? A 2669 ? 19 1 1 A C 6 1_555 A G 22 1_555 0.297 -0.158 0.010 -1.382 -12.984 -2.342 5 A_C2652:G2668_A A 2652 ? A 2668 ? 19 1 1 A U 7 1_555 A C 21 1_555 5.725 -2.191 -0.203 -3.543 -12.587 -13.705 6 A_U2653:C2667_A A 2653 ? A 2667 ? ? ? 1 A U 10 1_555 A A 19 1_555 4.094 -1.724 -0.803 8.710 -20.706 -104.319 7 A_U2656:A2665_A A 2656 ? A 2665 ? 24 4 1 A A 11 1_555 A G 18 1_555 -6.839 -4.315 -0.106 -2.010 3.592 -3.617 8 A_A2657:G2664_A A 2657 ? A 2664 ? 11 10 1 A C 12 1_555 A G 17 1_555 0.157 -0.086 -0.176 7.313 -2.452 0.569 9 A_C2658:G2663_A A 2658 ? A 2663 ? 19 1 1 A G 13 1_555 A A 16 1_555 7.212 -5.277 0.738 17.948 -5.713 -19.382 10 A_G2659:A2662_A A 2659 ? A 2662 ? ? ? # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 2 1_555 A U 26 1_555 A C 3 1_555 A G 25 1_555 -0.007 -1.216 3.100 -1.073 2.421 42.691 -1.895 -0.091 3.029 3.322 1.472 42.769 1 AA_G2648C2649:G2671U2672_AA A 2648 ? A 2672 ? A 2649 ? A 2671 ? 1 A C 3 1_555 A G 25 1_555 A OMU 4 1_555 A A 24 1_555 -0.580 -1.832 3.154 -2.709 11.767 29.472 -5.215 0.627 2.314 22.002 5.065 31.799 2 AA_C2649OMU2650:A2670G2671_AA A 2649 ? A 2671 ? A 2650 ? A 2670 ? 1 A OMU 4 1_555 A A 24 1_555 A C 5 1_555 A G 23 1_555 0.331 -0.997 3.182 -0.848 2.999 35.117 -2.073 -0.667 3.080 4.958 1.403 35.250 3 AA_OMU2650C2651:G2669A2670_AA A 2650 ? A 2670 ? A 2651 ? A 2669 ? 1 A C 5 1_555 A G 23 1_555 A C 6 1_555 A G 22 1_555 -0.641 -1.885 3.360 -0.291 8.493 32.141 -4.659 1.074 2.790 15.015 0.515 33.217 4 AA_C2651C2652:G2668G2669_AA A 2651 ? A 2669 ? A 2652 ? A 2668 ? 1 A C 6 1_555 A G 22 1_555 A U 7 1_555 A C 21 1_555 -0.472 -0.958 3.518 6.980 9.025 54.730 -1.569 0.926 3.258 9.698 -7.501 55.816 5 AA_C2652U2653:C2667G2668_AA A 2652 ? A 2668 ? A 2653 ? A 2667 ? 1 A U 7 1_555 A C 21 1_555 A U 10 1_555 A A 19 1_555 0.412 -0.845 6.270 4.576 -3.614 32.356 -0.293 0.792 6.322 -6.420 -8.129 32.864 6 AA_U2653U2656:A2665C2667_AA A 2653 ? A 2667 ? A 2656 ? A 2665 ? 1 A U 10 1_555 A A 19 1_555 A A 11 1_555 A G 18 1_555 5.236 -1.319 3.602 -2.023 -2.295 -11.862 9.606 21.522 4.104 10.868 -9.580 -12.249 7 AA_U2656A2657:G2664A2665_AA A 2656 ? A 2665 ? A 2657 ? A 2664 ? 1 A A 11 1_555 A G 18 1_555 A C 12 1_555 A G 17 1_555 0.211 -1.212 3.159 -2.280 3.708 59.982 -1.384 -0.318 3.078 3.703 2.278 60.125 8 AA_A2657C2658:G2663G2664_AA A 2657 ? A 2664 ? A 2658 ? A 2663 ? 1 A C 12 1_555 A G 17 1_555 A G 13 1_555 A A 16 1_555 -2.811 -1.424 2.935 -7.887 5.788 49.564 -2.057 2.771 3.145 6.828 9.304 50.460 9 AA_C2658G2659:A2662G2663_AA A 2658 ? A 2663 ? A 2659 ? A 2662 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)' 'United States' 'R01 AI088011' 1 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' 'P20 GM103640' 2 # _atom_sites.entry_id 5D99 _atom_sites.fract_transf_matrix[1][1] 0.033750 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.033750 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.013101 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_