data_9RB4 # _entry.id 9RB4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.414 _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 9RB4 pdb_00009rb4 10.2210/pdb9rb4/pdb WWPDB D_1292148023 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2026-06-03 _pdbx_audit_revision_history.part_number ? # _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 ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9RB4 _pdbx_database_status.recvd_initial_deposition_date 2025-05-21 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible N # loop_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 2 e.ennifar@unistra.fr Eric Ennifar ? 'principal investigator/group leader' 0000-0002-5076-846X 3 Ronald.Micura@uibk.ac.at Ronald Micura ? 'principal investigator/group leader' 0000-0003-2661-6105 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Ennifar, E.' 1 ? 'Micura, R.' 2 ? # 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.pdbx_database_id_patent _citation.unpublished_flag ? ? ? ? ? ? ? ? ? ? primary 'To Be Published' ? 0353 ? ? ? ? ? ? ? 'Ecoli Sarcin Ricin Loop (SLR) including a Kappa-Xanthosine base pair' ? ? ? ? ? ? ? ? ? ? ? ? ? DK ? ? 1 'Acta Crystallogr., Sect. D: Biol. Crystallogr.' ABCRE6 0766 0907-4449 ? ? 75 ? 861 877 'Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix' 2019 ? 10.1107/S2059798319011471 31588918 ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ennifar, E.' 1 ? primary 'Micura, R.' 2 ? 1 'Liebschner, D.' 3 0000-0003-3921-3209 1 'Afonine, P.V.' 4 0000-0002-5052-991X 1 'Baker, M.L.' 5 ? 1 'Bunkoczi, G.' 6 ? 1 'Chen, V.B.' 7 0000-0003-2492-979X 1 'Croll, T.I.' 8 ? 1 'Hintze, B.' 9 0000-0002-4871-2096 1 'Hung, L.W.' 10 0000-0001-6690-8458 1 'Jain, S.' 11 ? 1 'McCoy, A.J.' 12 ? 1 'Moriarty, N.W.' 13 0000-0001-8857-9464 1 'Oeffner, R.D.' 14 0000-0003-3107-2202 1 'Poon, B.K.' 15 0000-0001-9633-6067 1 'Prisant, M.G.' 16 ? 1 'Read, R.J.' 17 0000-0001-8273-0047 1 'Richardson, J.S.' 18 0000-0002-3311-2944 1 'Richardson, D.C.' 19 ? 1 'Sammito, M.D.' 20 0000-0002-8346-9247 1 'Sobolev, O.V.' 21 0000-0002-0623-3214 1 'Stockwell, D.H.' 22 ? 1 'Terwilliger, T.C.' 23 0000-0001-6384-0320 1 'Urzhumtsev, A.G.' 24 ? 1 'Videau, L.L.' 25 ? 1 'Williams, C.J.' 26 ? 1 'Adams, P.D.' 27 0000-0001-9333-8219 # 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)' 8743.270 1 ? ? ? ? 2 non-polymer syn GLYCEROL 92.094 3 ? ? ? ? 3 water nat water 18.015 152 ? ? ? ? # _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(A1JD2)CCUAGUACGAGAGGACCGG(HYJ)GUG' _entity_poly.pdbx_seq_one_letter_code_can UGCXCCUAGUACGAGAGGACCGGGGUG _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 A1JD2 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 HYJ 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 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _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 A1JD2 non-polymer . '[(2~{R},3~{S},4~{R},5~{S})-5-[2,4-bis(azanyl)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxyphosphinic acid' ? 'C9 H15 N4 O6 P' 306.212 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 HYJ 'L-RNA linking' n ;9-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-2-oxidanyl-1~{H}-purin-6-one ; ? 'C10 H13 N4 O9 P' 364.205 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 A1JD2 4 2650 2650 A1JD2 KAP 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 HYJ 24 2670 2670 HYJ XAN 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_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 A1JD2 ? ? A1JD2 ? ? 'SUBJECT OF INVESTIGATION' ? 2 HYJ ? ? HYJ ? ? 'SUBJECT OF INVESTIGATION' ? # 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 1 GOL GOL A . C 2 GOL 1 2702 2 GOL GOL A . D 2 GOL 1 2703 3 GOL GOL A . E 3 HOH 1 2801 8 HOH HOH A . E 3 HOH 2 2802 37 HOH HOH A . E 3 HOH 3 2803 67 HOH HOH A . E 3 HOH 4 2804 77 HOH HOH A . E 3 HOH 5 2805 119 HOH HOH A . E 3 HOH 6 2806 38 HOH HOH A . E 3 HOH 7 2807 60 HOH HOH A . E 3 HOH 8 2808 94 HOH HOH A . E 3 HOH 9 2809 55 HOH HOH A . E 3 HOH 10 2810 91 HOH HOH A . E 3 HOH 11 2811 85 HOH HOH A . E 3 HOH 12 2812 101 HOH HOH A . E 3 HOH 13 2813 84 HOH HOH A . E 3 HOH 14 2814 32 HOH HOH A . E 3 HOH 15 2815 134 HOH HOH A . E 3 HOH 16 2816 86 HOH HOH A . E 3 HOH 17 2817 13 HOH HOH A . E 3 HOH 18 2818 48 HOH HOH A . E 3 HOH 19 2819 47 HOH HOH A . E 3 HOH 20 2820 148 HOH HOH A . E 3 HOH 21 2821 42 HOH HOH A . E 3 HOH 22 2822 65 HOH HOH A . E 3 HOH 23 2823 80 HOH HOH A . E 3 HOH 24 2824 110 HOH HOH A . E 3 HOH 25 2825 68 HOH HOH A . E 3 HOH 26 2826 39 HOH HOH A . E 3 HOH 27 2827 161 HOH HOH A . E 3 HOH 28 2828 11 HOH HOH A . E 3 HOH 29 2829 12 HOH HOH A . E 3 HOH 30 2830 28 HOH HOH A . E 3 HOH 31 2831 120 HOH HOH A . E 3 HOH 32 2832 72 HOH HOH A . E 3 HOH 33 2833 5 HOH HOH A . E 3 HOH 34 2834 96 HOH HOH A . E 3 HOH 35 2835 95 HOH HOH A . E 3 HOH 36 2836 23 HOH HOH A . E 3 HOH 37 2837 15 HOH HOH A . E 3 HOH 38 2838 93 HOH HOH A . E 3 HOH 39 2839 7 HOH HOH A . E 3 HOH 40 2840 125 HOH HOH A . E 3 HOH 41 2841 27 HOH HOH A . E 3 HOH 42 2842 138 HOH HOH A . E 3 HOH 43 2843 18 HOH HOH A . E 3 HOH 44 2844 31 HOH HOH A . E 3 HOH 45 2845 45 HOH HOH A . E 3 HOH 46 2846 50 HOH HOH A . E 3 HOH 47 2847 57 HOH HOH A . E 3 HOH 48 2848 75 HOH HOH A . E 3 HOH 49 2849 92 HOH HOH A . E 3 HOH 50 2850 146 HOH HOH A . E 3 HOH 51 2851 41 HOH HOH A . E 3 HOH 52 2852 104 HOH HOH A . E 3 HOH 53 2853 107 HOH HOH A . E 3 HOH 54 2854 114 HOH HOH A . E 3 HOH 55 2855 29 HOH HOH A . E 3 HOH 56 2856 26 HOH HOH A . E 3 HOH 57 2857 17 HOH HOH A . E 3 HOH 58 2858 61 HOH HOH A . E 3 HOH 59 2859 123 HOH HOH A . E 3 HOH 60 2860 63 HOH HOH A . E 3 HOH 61 2861 46 HOH HOH A . E 3 HOH 62 2862 97 HOH HOH A . E 3 HOH 63 2863 1 HOH HOH A . E 3 HOH 64 2864 115 HOH HOH A . E 3 HOH 65 2865 3 HOH HOH A . E 3 HOH 66 2866 144 HOH HOH A . E 3 HOH 67 2867 9 HOH HOH A . E 3 HOH 68 2868 89 HOH HOH A . E 3 HOH 69 2869 111 HOH HOH A . E 3 HOH 70 2870 36 HOH HOH A . E 3 HOH 71 2871 87 HOH HOH A . E 3 HOH 72 2872 2 HOH HOH A . E 3 HOH 73 2873 44 HOH HOH A . E 3 HOH 74 2874 22 HOH HOH A . E 3 HOH 75 2875 113 HOH HOH A . E 3 HOH 76 2876 103 HOH HOH A . E 3 HOH 77 2877 106 HOH HOH A . E 3 HOH 78 2878 71 HOH HOH A . E 3 HOH 79 2879 51 HOH HOH A . E 3 HOH 80 2880 157 HOH HOH A . E 3 HOH 81 2881 10 HOH HOH A . E 3 HOH 82 2882 49 HOH HOH A . E 3 HOH 83 2883 147 HOH HOH A . E 3 HOH 84 2884 6 HOH HOH A . E 3 HOH 85 2885 19 HOH HOH A . E 3 HOH 86 2886 20 HOH HOH A . E 3 HOH 87 2887 109 HOH HOH A . E 3 HOH 88 2888 74 HOH HOH A . E 3 HOH 89 2889 52 HOH HOH A . E 3 HOH 90 2890 56 HOH HOH A . E 3 HOH 91 2891 64 HOH HOH A . E 3 HOH 92 2892 35 HOH HOH A . E 3 HOH 93 2893 54 HOH HOH A . E 3 HOH 94 2894 34 HOH HOH A . E 3 HOH 95 2895 79 HOH HOH A . E 3 HOH 96 2896 99 HOH HOH A . E 3 HOH 97 2897 78 HOH HOH A . E 3 HOH 98 2898 33 HOH HOH A . E 3 HOH 99 2899 24 HOH HOH A . E 3 HOH 100 2900 21 HOH HOH A . E 3 HOH 101 2901 40 HOH HOH A . E 3 HOH 102 2902 116 HOH HOH A . E 3 HOH 103 2903 98 HOH HOH A . E 3 HOH 104 2904 4 HOH HOH A . E 3 HOH 105 2905 69 HOH HOH A . E 3 HOH 106 2906 62 HOH HOH A . E 3 HOH 107 2907 76 HOH HOH A . E 3 HOH 108 2908 143 HOH HOH A . E 3 HOH 109 2909 117 HOH HOH A . E 3 HOH 110 2910 105 HOH HOH A . E 3 HOH 111 2911 14 HOH HOH A . E 3 HOH 112 2912 70 HOH HOH A . E 3 HOH 113 2913 81 HOH HOH A . E 3 HOH 114 2914 126 HOH HOH A . E 3 HOH 115 2915 130 HOH HOH A . E 3 HOH 116 2916 141 HOH HOH A . E 3 HOH 117 2917 59 HOH HOH A . E 3 HOH 118 2918 122 HOH HOH A . E 3 HOH 119 2919 43 HOH HOH A . E 3 HOH 120 2920 25 HOH HOH A . E 3 HOH 121 2921 16 HOH HOH A . E 3 HOH 122 2922 30 HOH HOH A . E 3 HOH 123 2923 90 HOH HOH A . E 3 HOH 124 2924 100 HOH HOH A . E 3 HOH 125 2925 131 HOH HOH A . E 3 HOH 126 2926 128 HOH HOH A . E 3 HOH 127 2927 158 HOH HOH A . E 3 HOH 128 2928 88 HOH HOH A . E 3 HOH 129 2929 132 HOH HOH A . E 3 HOH 130 2930 66 HOH HOH A . E 3 HOH 131 2931 153 HOH HOH A . E 3 HOH 132 2932 58 HOH HOH A . E 3 HOH 133 2933 142 HOH HOH A . E 3 HOH 134 2934 129 HOH HOH A . E 3 HOH 135 2935 149 HOH HOH A . E 3 HOH 136 2936 118 HOH HOH A . E 3 HOH 137 2937 73 HOH HOH A . E 3 HOH 138 2938 150 HOH HOH A . E 3 HOH 139 2939 112 HOH HOH A . E 3 HOH 140 2940 162 HOH HOH A . E 3 HOH 141 2941 159 HOH HOH A . E 3 HOH 142 2942 121 HOH HOH A . E 3 HOH 143 2943 82 HOH HOH A . E 3 HOH 144 2944 83 HOH HOH A . E 3 HOH 145 2945 133 HOH HOH A . E 3 HOH 146 2946 140 HOH HOH A . E 3 HOH 147 2947 160 HOH HOH A . E 3 HOH 148 2948 102 HOH HOH A . E 3 HOH 149 2949 135 HOH HOH A . E 3 HOH 150 2950 108 HOH HOH A . E 3 HOH 151 2951 163 HOH HOH A . E 3 HOH 152 2952 139 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_reference_DOI _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(1.21.2_5419: ???)' ? 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . ? 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? STARANISO ? ? ? . ? 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . ? 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 9RB4 _cell.details ? _cell.formula_units_Z ? _cell.length_a 29.665 _cell.length_a_esd ? _cell.length_b 29.665 _cell.length_b_esd ? _cell.length_c 76.547 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 4 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9RB4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' _symmetry.pdbx_full_space_group_name_H-M ? # _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 9RB4 _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 1.93 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 36.14 _exptl_crystal.description ? _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 ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '1 volume [3.1M AS, 50mM KMops pH7.0, 10mM MgCl2, 10mM MnCl2] + 2 volumes [RNA 2.5mg/ml, 1mM EDTA pH8.0, 10mM Tris pH 8.0]' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _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.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER R 4M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2023-09-18 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _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 0.826561 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'SLS BEAMLINE X06DA' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.826561 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline X06DA _diffrn_source.pdbx_synchrotron_site SLS # _reflns.B_iso_Wilson_estimate 8.82 _reflns.entry_id 9RB4 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 0.938 _reflns.d_resolution_low 27.66 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 520196 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 93.4 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 12.9 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 16.5 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # _reflns_shell.d_res_high 0.938 _reflns_shell.d_res_low 0.974 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 13500 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.584 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_percent_possible_ellipsoidal ? _reflns_shell.pdbx_percent_possible_spherical ? _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns_shell.pdbx_percent_possible_spherical_anomalous ? _reflns_shell.pdbx_redundancy_anomalous ? _reflns_shell.pdbx_CC_half_anomalous ? _reflns_shell.pdbx_absDiff_over_sigma_anomalous ? _reflns_shell.pdbx_percent_possible_anomalous ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 9RB4 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.00 _refine.ls_d_res_low 27.66 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 35587 _refine.ls_number_reflns_R_free 1776 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.93 _refine.ls_percent_reflns_R_free 4.99 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1174 _refine.ls_R_factor_R_free 0.1339 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1165 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.correlation_coeff_I_to_Fcsqd_work ? _refine.correlation_coeff_I_to_Fcsqd_free ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.38 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.10 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 12.34 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.08 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 1.00 _refine_hist.d_res_low 27.66 _refine_hist.number_atoms_solvent 152 _refine_hist.number_atoms_total 750 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 580 _refine_hist.pdbx_number_atoms_ligand 18 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_Zscore _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.008 ? 836 ? f_bond_d ? ? ? 'X-RAY DIFFRACTION' ? 1.604 ? 1302 ? f_angle_d ? ? ? 'X-RAY DIFFRACTION' ? 22.870 ? 511 ? f_dihedral_angle_d ? ? ? 'X-RAY DIFFRACTION' ? 0.055 ? 165 ? f_chiral_restr ? ? ? 'X-RAY DIFFRACTION' ? 0.033 ? 37 ? f_plane_restr ? ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.correlation_coeff_Fo_to_Fc _refine_ls_shell.correlation_coeff_Fo_to_Fc_free _refine_ls_shell.correlation_coeff_I_to_Fcsqd_work _refine_ls_shell.correlation_coeff_I_to_Fcsqd_free _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 1.00 1.03 . . 136 2565 99.00 . . . . 0.1950 . . . . . . . . . . . . . . . 0.2312 'X-RAY DIFFRACTION' 1.03 1.06 . . 136 2593 100.00 . . . . 0.1557 . . . . . . . . . . . . . . . 0.2011 'X-RAY DIFFRACTION' 1.06 1.09 . . 138 2613 100.00 . . . . 0.1321 . . . . . . . . . . . . . . . 0.1621 'X-RAY DIFFRACTION' 1.09 1.13 . . 135 2577 100.00 . . . . 0.1281 . . . . . . . . . . . . . . . 0.1585 'X-RAY DIFFRACTION' 1.13 1.18 . . 138 2606 100.00 . . . . 0.1182 . . . . . . . . . . . . . . . 0.1202 'X-RAY DIFFRACTION' 1.18 1.23 . . 137 2608 100.00 . . . . 0.1113 . . . . . . . . . . . . . . . 0.1302 'X-RAY DIFFRACTION' 1.23 1.29 . . 136 2579 100.00 . . . . 0.1104 . . . . . . . . . . . . . . . 0.1395 'X-RAY DIFFRACTION' 1.29 1.38 . . 136 2591 100.00 . . . . 0.1124 . . . . . . . . . . . . . . . 0.1159 'X-RAY DIFFRACTION' 1.38 1.48 . . 138 2616 100.00 . . . . 0.1187 . . . . . . . . . . . . . . . 0.1300 'X-RAY DIFFRACTION' 1.48 1.63 . . 137 2599 100.00 . . . . 0.1088 . . . . . . . . . . . . . . . 0.1146 'X-RAY DIFFRACTION' 1.63 1.87 . . 138 2612 100.00 . . . . 0.1018 . . . . . . . . . . . . . . . 0.0950 'X-RAY DIFFRACTION' 1.87 2.35 . . 137 2615 100.00 . . . . 0.1251 . . . . . . . . . . . . . . . 0.1344 'X-RAY DIFFRACTION' 2.35 27.66 . . 134 2637 100.00 . . . . 0.1115 . . . . . . . . . . . . . . . 0.1463 # _struct.entry_id 9RB4 _struct.title 'Ecoli Sarcin Ricin Loop (SLR) including a Kappa-Xanthosine base pair' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 9RB4 _struct_keywords.text 'RNA, modification' _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 2 ? D N N 2 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 9RB4 _struct_ref.pdbx_db_accession 9RB4 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 9RB4 _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 9RB4 _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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 570 ? 1 MORE -3 ? 1 'SSA (A^2)' 4900 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _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 one ? A C 3 "O3'" ? ? ? 1_555 A A1JD2 4 P ? ? A C 2649 A A1JD2 2650 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale one ? A A1JD2 4 "O3'" ? ? ? 1_555 A C 5 P ? ? A A1JD2 2650 A C 2651 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale3 covale both ? A G 23 "O3'" A ? ? 1_555 A HYJ 24 P A ? A G 2669 A HYJ 2670 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale4 covale both ? A G 23 "O3'" B ? ? 1_555 A HYJ 24 P B ? A G 2669 A HYJ 2670 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale5 covale one ? A HYJ 24 "O3'" A ? ? 1_555 A G 25 P ? ? A HYJ 2670 A G 2671 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale6 covale one ? A HYJ 24 "O3'" B ? ? 1_555 A G 25 P ? ? A HYJ 2670 A G 2671 1_555 ? ? ? ? ? ? ? 1.606 ? ? hydrog1 hydrog ? ? A G 2 N1 A ? ? 1_555 A U 26 O2 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog2 hydrog ? ? A G 2 N1 B ? ? 1_555 A U 26 O2 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A G 2 O6 A ? ? 1_555 A U 26 N3 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog4 hydrog ? ? A G 2 O6 B ? ? 1_555 A U 26 N3 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog5 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 23 N1 A ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 23 N1 B ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 23 O6 A ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 23 O6 B ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 23 N2 A ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 23 N2 B ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 7 O2 A ? ? 1_555 A C 21 N4 ? ? A U 2653 A C 2667 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog18 hydrog ? ? A U 7 O2 B ? ? 1_555 A C 21 N4 ? ? A U 2653 A C 2667 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog19 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 19 N7 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog20 hydrog ? ? A U 10 O2 ? ? ? 1_555 A A 19 N6 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog21 hydrog ? ? A A 11 N6 ? ? ? 1_555 A G 18 N3 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog22 hydrog ? ? A A 11 N7 ? ? ? 1_555 A G 18 N2 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog23 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 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 ? ? # _pdbx_entry_details.entry_id 9RB4 _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O5'" A G 2655 ? A P A G 2655 ? A OP1 A G 2655 ? A 118.26 110.70 7.56 1.20 N 2 1 "O5'" A G 2655 ? A P A G 2655 ? A OP2 A G 2655 ? A 98.08 105.70 -7.62 0.90 N 3 1 "O3'" A G 2669 ? B P A HYJ 2670 ? B OP1 A HYJ 2670 ? B 91.72 105.20 -13.48 2.20 Y # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y,x,z+3/4 3 y,-x,z+1/4 4 -x,-y,z+1/2 # _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 2952 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.17 _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 A1JD2 C1 C Y N 38 A1JD2 "C1'" C N S 39 A1JD2 C2 C Y N 40 A1JD2 "C2'" C N R 41 A1JD2 "C3'" C N S 42 A1JD2 C4 C Y N 43 A1JD2 "C4'" C N R 44 A1JD2 "C5'" C N N 45 A1JD2 C6 C Y N 46 A1JD2 N3 N Y N 47 A1JD2 N5 N Y N 48 A1JD2 N75 N N N 49 A1JD2 N78 N N N 50 A1JD2 "O2'" O N N 51 A1JD2 "O3'" O N N 52 A1JD2 "O4'" O N N 53 A1JD2 "O5'" O N N 54 A1JD2 OP1 O N N 55 A1JD2 OP2 O N N 56 A1JD2 P P N N 57 A1JD2 "H1'" H N N 58 A1JD2 "H2'" H N N 59 A1JD2 "H3'" H N N 60 A1JD2 "H4'" H N N 61 A1JD2 "H5'1" H N N 62 A1JD2 "H5'2" H N N 63 A1JD2 H6 H N N 64 A1JD2 H751 H N N 65 A1JD2 H752 H N N 66 A1JD2 H782 H N N 67 A1JD2 H781 H N N 68 A1JD2 "HO2'" H N N 69 A1JD2 H1 H N N 70 A1JD2 H2 H N N 71 A1JD2 H3 H N N 72 C OP3 O N N 73 C P P N N 74 C OP1 O N N 75 C OP2 O N N 76 C "O5'" O N N 77 C "C5'" C N N 78 C "C4'" C N R 79 C "O4'" O N N 80 C "C3'" C N S 81 C "O3'" O N N 82 C "C2'" C N R 83 C "O2'" O N N 84 C "C1'" C N R 85 C N1 N N N 86 C C2 C N N 87 C O2 O N N 88 C N3 N N N 89 C C4 C N N 90 C N4 N N N 91 C C5 C N N 92 C C6 C N N 93 C HOP3 H N N 94 C HOP2 H N N 95 C "H5'" H N N 96 C "H5''" H N N 97 C "H4'" H N N 98 C "H3'" H N N 99 C "HO3'" H N N 100 C "H2'" H N N 101 C "HO2'" H N N 102 C "H1'" H N N 103 C H41 H N N 104 C H42 H N N 105 C H5 H N N 106 C H6 H N N 107 G OP3 O N N 108 G P P N N 109 G OP1 O N N 110 G OP2 O N N 111 G "O5'" O N N 112 G "C5'" C N N 113 G "C4'" C N R 114 G "O4'" O N N 115 G "C3'" C N S 116 G "O3'" O N N 117 G "C2'" C N R 118 G "O2'" O N N 119 G "C1'" C N R 120 G N9 N Y N 121 G C8 C Y N 122 G N7 N Y N 123 G C5 C Y N 124 G C6 C N N 125 G O6 O N N 126 G N1 N N N 127 G C2 C N N 128 G N2 N N N 129 G N3 N N N 130 G C4 C Y N 131 G HOP3 H N N 132 G HOP2 H N N 133 G "H5'" H N N 134 G "H5''" H N N 135 G "H4'" H N N 136 G "H3'" H N N 137 G "HO3'" H N N 138 G "H2'" H N N 139 G "HO2'" H N N 140 G "H1'" H N N 141 G H8 H N N 142 G H1 H N N 143 G H21 H N N 144 G H22 H N N 145 GOL C1 C N N 146 GOL O1 O N N 147 GOL C2 C N N 148 GOL O2 O N N 149 GOL C3 C N N 150 GOL O3 O N N 151 GOL H11 H N N 152 GOL H12 H N N 153 GOL HO1 H N N 154 GOL H2 H N N 155 GOL HO2 H N N 156 GOL H31 H N N 157 GOL H32 H N N 158 GOL HO3 H N N 159 HOH O O N N 160 HOH H1 H N N 161 HOH H2 H N N 162 HYJ N9 N Y N 163 HYJ C4 C Y N 164 HYJ N3 N N N 165 HYJ C2 C N N 166 HYJ O2 O N N 167 HYJ N1 N N N 168 HYJ C6 C N N 169 HYJ O6 O N N 170 HYJ C5 C Y N 171 HYJ N7 N Y N 172 HYJ C8 C Y N 173 HYJ "C1'" C N R 174 HYJ "C2'" C N R 175 HYJ "C3'" C N S 176 HYJ "C4'" C N R 177 HYJ "C5'" C N N 178 HYJ "O2'" O N N 179 HYJ "O3'" O N N 180 HYJ "O4'" O N N 181 HYJ "O5'" O N N 182 HYJ OP1 O N N 183 HYJ OP2 O N N 184 HYJ P P N N 185 HYJ HO2 H N N 186 HYJ H1 H N N 187 HYJ H8 H N N 188 HYJ "H1'" H N N 189 HYJ "H2'" H N N 190 HYJ "H3'" H N N 191 HYJ "H4'" H N N 192 HYJ "H5'2" H N N 193 HYJ "H5'1" H N N 194 HYJ "HO2'" H N N 195 HYJ H2 H N N 196 HYJ H3 H N N 197 HYJ OP3 O N N 198 HYJ H6 H N N 199 U OP3 O N N 200 U P P N N 201 U OP1 O N N 202 U OP2 O N N 203 U "O5'" O N N 204 U "C5'" C N N 205 U "C4'" C N R 206 U "O4'" O N N 207 U "C3'" C N S 208 U "O3'" O N N 209 U "C2'" C N R 210 U "O2'" O N N 211 U "C1'" C N R 212 U N1 N N N 213 U C2 C N N 214 U O2 O N N 215 U N3 N N N 216 U C4 C N N 217 U O4 O N N 218 U C5 C N N 219 U C6 C N N 220 U HOP3 H N N 221 U HOP2 H N N 222 U "H5'" H N N 223 U "H5''" H N N 224 U "H4'" H N N 225 U "H3'" H N N 226 U "HO3'" H N N 227 U "H2'" H N N 228 U "HO2'" H N N 229 U "H1'" H N N 230 U H3 H N N 231 U H5 H N N 232 U H6 H N N 233 # 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 A1JD2 N78 C4 sing N N 40 A1JD2 C4 N5 doub Y N 41 A1JD2 C4 N3 sing Y N 42 A1JD2 N5 C6 sing Y N 43 A1JD2 N3 C2 doub Y N 44 A1JD2 C6 C1 doub Y N 45 A1JD2 OP2 P doub N N 46 A1JD2 C2 C1 sing Y N 47 A1JD2 C2 N75 sing N N 48 A1JD2 C1 "C1'" sing N N 49 A1JD2 P "O5'" sing N N 50 A1JD2 P OP1 sing N N 51 A1JD2 "O4'" "C1'" sing N N 52 A1JD2 "O4'" "C4'" sing N N 53 A1JD2 "C1'" "C2'" sing N N 54 A1JD2 "C5'" "O5'" sing N N 55 A1JD2 "C5'" "C4'" sing N N 56 A1JD2 "C4'" "C3'" sing N N 57 A1JD2 "C3'" "C2'" sing N N 58 A1JD2 "C3'" "O3'" sing N N 59 A1JD2 "C2'" "O2'" sing N N 60 A1JD2 "C1'" "H1'" sing N N 61 A1JD2 "C2'" "H2'" sing N N 62 A1JD2 "C3'" "H3'" sing N N 63 A1JD2 "C4'" "H4'" sing N N 64 A1JD2 "C5'" "H5'1" sing N N 65 A1JD2 "C5'" "H5'2" sing N N 66 A1JD2 C6 H6 sing N N 67 A1JD2 N75 H751 sing N N 68 A1JD2 N75 H752 sing N N 69 A1JD2 N78 H782 sing N N 70 A1JD2 N78 H781 sing N N 71 A1JD2 "O2'" "HO2'" sing N N 72 A1JD2 "O3'" H1 sing N N 73 A1JD2 OP1 H2 sing N N 74 A1JD2 P H3 sing N N 75 C OP3 P sing N N 76 C OP3 HOP3 sing N N 77 C P OP1 doub N N 78 C P OP2 sing N N 79 C P "O5'" sing N N 80 C OP2 HOP2 sing N N 81 C "O5'" "C5'" sing N N 82 C "C5'" "C4'" sing N N 83 C "C5'" "H5'" sing N N 84 C "C5'" "H5''" sing N N 85 C "C4'" "O4'" sing N N 86 C "C4'" "C3'" sing N N 87 C "C4'" "H4'" sing N N 88 C "O4'" "C1'" sing N N 89 C "C3'" "O3'" sing N N 90 C "C3'" "C2'" sing N N 91 C "C3'" "H3'" sing N N 92 C "O3'" "HO3'" sing N N 93 C "C2'" "O2'" sing N N 94 C "C2'" "C1'" sing N N 95 C "C2'" "H2'" sing N N 96 C "O2'" "HO2'" sing N N 97 C "C1'" N1 sing N N 98 C "C1'" "H1'" sing N N 99 C N1 C2 sing N N 100 C N1 C6 sing N N 101 C C2 O2 doub N N 102 C C2 N3 sing N N 103 C N3 C4 doub N N 104 C C4 N4 sing N N 105 C C4 C5 sing N N 106 C N4 H41 sing N N 107 C N4 H42 sing N N 108 C C5 C6 doub N N 109 C C5 H5 sing N N 110 C C6 H6 sing N N 111 G OP3 P sing N N 112 G OP3 HOP3 sing N N 113 G P OP1 doub N N 114 G P OP2 sing N N 115 G P "O5'" sing N N 116 G OP2 HOP2 sing N N 117 G "O5'" "C5'" sing N N 118 G "C5'" "C4'" sing N N 119 G "C5'" "H5'" sing N N 120 G "C5'" "H5''" sing N N 121 G "C4'" "O4'" sing N N 122 G "C4'" "C3'" sing N N 123 G "C4'" "H4'" sing N N 124 G "O4'" "C1'" sing N N 125 G "C3'" "O3'" sing N N 126 G "C3'" "C2'" sing N N 127 G "C3'" "H3'" sing N N 128 G "O3'" "HO3'" sing N N 129 G "C2'" "O2'" sing N N 130 G "C2'" "C1'" sing N N 131 G "C2'" "H2'" sing N N 132 G "O2'" "HO2'" sing N N 133 G "C1'" N9 sing N N 134 G "C1'" "H1'" sing N N 135 G N9 C8 sing Y N 136 G N9 C4 sing Y N 137 G C8 N7 doub Y N 138 G C8 H8 sing N N 139 G N7 C5 sing Y N 140 G C5 C6 sing N N 141 G C5 C4 doub Y N 142 G C6 O6 doub N N 143 G C6 N1 sing N N 144 G N1 C2 sing N N 145 G N1 H1 sing N N 146 G C2 N2 sing N N 147 G C2 N3 doub N N 148 G N2 H21 sing N N 149 G N2 H22 sing N N 150 G N3 C4 sing N N 151 GOL C1 O1 sing N N 152 GOL C1 C2 sing N N 153 GOL C1 H11 sing N N 154 GOL C1 H12 sing N N 155 GOL O1 HO1 sing N N 156 GOL C2 O2 sing N N 157 GOL C2 C3 sing N N 158 GOL C2 H2 sing N N 159 GOL O2 HO2 sing N N 160 GOL C3 O3 sing N N 161 GOL C3 H31 sing N N 162 GOL C3 H32 sing N N 163 GOL O3 HO3 sing N N 164 HOH O H1 sing N N 165 HOH O H2 sing N N 166 HYJ O2 C2 sing N N 167 HYJ C2 N1 sing N N 168 HYJ C2 N3 doub N N 169 HYJ N1 C6 sing N N 170 HYJ N3 C4 sing N N 171 HYJ C6 O6 doub N N 172 HYJ C6 C5 sing N N 173 HYJ C4 C5 doub Y N 174 HYJ C4 N9 sing Y N 175 HYJ C5 N7 sing Y N 176 HYJ "C1'" N9 sing N N 177 HYJ "C1'" "O4'" sing N N 178 HYJ "C1'" "C2'" sing N N 179 HYJ N9 C8 sing Y N 180 HYJ "O4'" "C4'" sing N N 181 HYJ N7 C8 doub Y N 182 HYJ "O2'" "C2'" sing N N 183 HYJ "C2'" "C3'" sing N N 184 HYJ "C4'" "C5'" sing N N 185 HYJ "C4'" "C3'" sing N N 186 HYJ "C5'" "O5'" sing N N 187 HYJ "O5'" P sing N N 188 HYJ "C3'" "O3'" sing N N 189 HYJ P OP2 doub N N 190 HYJ P OP1 sing N N 191 HYJ O2 HO2 sing N N 192 HYJ N1 H1 sing N N 193 HYJ C8 H8 sing N N 194 HYJ "C1'" "H1'" sing N N 195 HYJ "C2'" "H2'" sing N N 196 HYJ "C3'" "H3'" sing N N 197 HYJ "C4'" "H4'" sing N N 198 HYJ "C5'" "H5'2" sing N N 199 HYJ "C5'" "H5'1" sing N N 200 HYJ "O2'" "HO2'" sing N N 201 HYJ "O3'" H2 sing N N 202 HYJ OP1 H3 sing N N 203 HYJ P OP3 sing N N 204 HYJ OP3 H6 sing N N 205 U OP3 P sing N N 206 U OP3 HOP3 sing N N 207 U P OP1 doub N N 208 U P OP2 sing N N 209 U P "O5'" sing N N 210 U OP2 HOP2 sing N N 211 U "O5'" "C5'" sing N N 212 U "C5'" "C4'" sing N N 213 U "C5'" "H5'" sing N N 214 U "C5'" "H5''" sing N N 215 U "C4'" "O4'" sing N N 216 U "C4'" "C3'" sing N N 217 U "C4'" "H4'" sing N N 218 U "O4'" "C1'" sing N N 219 U "C3'" "O3'" sing N N 220 U "C3'" "C2'" sing N N 221 U "C3'" "H3'" sing N N 222 U "O3'" "HO3'" sing N N 223 U "C2'" "O2'" sing N N 224 U "C2'" "C1'" sing N N 225 U "C2'" "H2'" sing N N 226 U "O2'" "HO2'" sing N N 227 U "C1'" N1 sing N N 228 U "C1'" "H1'" sing N N 229 U N1 C2 sing N N 230 U N1 C6 sing N N 231 U C2 O2 doub N N 232 U C2 N3 sing N N 233 U N3 C4 sing N N 234 U N3 H3 sing N N 235 U C4 O4 doub N N 236 U C4 C5 sing N N 237 U C5 C6 doub N N 238 U C5 H5 sing N N 239 U C6 H6 sing N N 240 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9RB4 'double helix' 9RB4 'a-form double helix' 9RB4 tetraloop 9RB4 'mismatched base pair' 9RB4 '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 -2.305 -0.596 0.142 3.073 -10.830 -0.831 1 A_G2648:U2672_A A 2648 ? A 2672 ? 28 1 1 A C 3 1_555 A G 25 1_555 0.119 -0.113 0.198 4.933 -13.546 -2.737 2 A_C2649:G2671_A A 2649 ? A 2671 ? 19 1 1 A C 5 1_555 A G 23 1_555 0.305 0.069 0.278 7.537 -17.970 2.341 3 A_C2651:G2669_A A 2651 ? A 2669 ? 19 1 1 A C 6 1_555 A G 22 1_555 0.358 -0.155 -0.004 -1.148 -12.196 -1.683 4 A_C2652:G2668_A A 2652 ? A 2668 ? 19 1 1 A U 7 1_555 A C 21 1_555 5.923 -2.241 -0.501 -4.029 -13.827 -13.747 5 A_U2653:C2667_A A 2653 ? A 2667 ? ? ? 1 A U 10 1_555 A A 19 1_555 4.159 -1.919 -0.801 6.518 -19.611 -101.923 6 A_U2656:A2665_A A 2656 ? A 2665 ? 24 4 1 A A 11 1_555 A G 18 1_555 -6.824 -4.285 -0.174 -2.435 4.141 -1.765 7 A_A2657:G2664_A A 2657 ? A 2664 ? 11 9 1 A C 12 1_555 A G 17 1_555 0.139 -0.106 -0.146 7.684 -2.171 0.243 8 A_C2658:G2663_A A 2658 ? A 2663 ? 19 1 1 A G 13 1_555 A A 16 1_555 7.240 -5.243 0.691 17.477 -5.880 -19.932 9 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 -0.234 -0.902 3.169 -1.516 3.954 46.525 -1.454 0.174 3.092 4.993 1.915 46.707 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 C 5 1_555 A G 23 1_555 0.328 -4.089 5.965 1.665 10.928 57.998 -5.121 -0.186 5.193 11.160 -1.701 58.952 2 AA_C2649C2651:G2669G2671_AA A 2649 ? A 2671 ? 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 -0.651 -1.929 3.472 -0.287 5.961 32.628 -4.393 1.093 3.086 10.501 0.506 33.155 3 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 -0.661 -1.158 3.514 7.839 8.364 54.240 -1.756 1.189 3.201 9.060 -8.492 55.349 4 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 0.741 -1.211 6.263 6.198 -3.411 31.578 -0.994 0.815 6.382 -6.172 -11.213 32.341 5 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 5.073 -1.197 3.590 -1.915 -0.988 -10.916 7.991 22.649 4.287 5.130 -9.940 -11.126 6 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 -0.086 -1.121 3.164 -3.219 3.514 58.810 -1.311 -0.071 3.099 3.572 3.273 58.986 7 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 -2.651 -1.295 3.045 -7.246 6.032 50.647 -1.888 2.576 3.208 6.981 8.387 51.461 8 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 'Centre National de la Recherche Scientifique (CNRS)' France ? 1 'Austrian Research Promotion Agency' Austria ? 2 'Austrian Science Fund' Austria 10.55776/F80 3 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3DVZ _pdbx_initial_refinement_model.details ? # _space_group.name_H-M_alt 'P 43' _space_group.name_Hall 'P 4cw' _space_group.IT_number 78 _space_group.crystal_system tetragonal _space_group.id 1 # _atom_sites.entry_id 9RB4 _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.033710 _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] 0.033710 _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] 0.013064 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? H ? ? 0.53795 0.34799 0.11320 ? 10.08003 29.74760 2.57510 ? 0.0 ;3-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 ? ? 15.80542 1.70748 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O1- ? ? 4.31557 2.79156 1.86576 ? 8.03600 32.36470 0.29580 ? 0.0 ;3-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_ # loop_ #