data_3DW6 # _entry.id 3DW6 # _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 3DW6 pdb_00003dw6 10.2210/pdb3dw6/pdb NDB UR0164 ? ? RCSB RCSB048564 ? ? WWPDB D_1000048564 ? ? # 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 2009-03-24 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 # _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' 'Non-polymer description' 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' 5 3 'Structure model' 'Derived calculations' # 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' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_conn 5 3 'Structure model' struct_site # 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' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 3DW6 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-07-21 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1q9a 'Crystal structure of the sarcin/ricin domain from E.coli 23S rRNA at 1.04 resolution' unspecified PDB 3DVZ . unspecified PDB 3DW4 . unspecified PDB 3DW5 . unspecified PDB 3DW7 . unspecified PDB 483D . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Olieric, V.' 1 'Rieder, U.' 2 'Lang, K.' 3 'Serganov, A.' 4 'Schulze-Briese, C.' 5 'Micura, R.' 6 'Dumas, P.' 7 'Ennifar, E.' 8 # _citation.id primary _citation.title 'A fast selenium derivatization strategy for crystallization and phasing of RNA structures.' _citation.journal_abbrev Rna _citation.journal_volume 15 _citation.page_first 707 _citation.page_last 715 _citation.year 2009 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19228585 _citation.pdbx_database_id_DOI 10.1261/rna.1499309 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Olieric, V.' 1 ? primary 'Rieder, U.' 2 ? primary 'Lang, K.' 3 ? primary 'Serganov, A.' 4 ? primary 'Schulze-Briese, C.' 5 ? primary 'Micura, R.' 6 ? primary 'Dumas, P.' 7 ? primary 'Ennifar, E.' 8 ? # 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 'Sarcin/Ricin Domain from E. Coli 23 S rRNA' 8821.241 1 ? ? ? ? 2 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 3 water nat water 18.015 184 ? ? ? ? # _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(UMS)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 UMS 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 # 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 UMS 'DNA linking' n "2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE" ? 'C10 H15 N2 O8 P Se' 401.168 # 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 UMS 4 2650 2650 UMS UMS 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 1 1 GOL GOL A . C 3 HOH 1 2674 1 HOH HOH A . C 3 HOH 2 2675 2 HOH HOH A . C 3 HOH 3 2676 3 HOH HOH A . C 3 HOH 4 2677 4 HOH HOH A . C 3 HOH 5 2678 5 HOH HOH A . C 3 HOH 6 2679 6 HOH HOH A . C 3 HOH 7 2680 7 HOH HOH A . C 3 HOH 8 2681 8 HOH HOH A . C 3 HOH 9 2682 9 HOH HOH A . C 3 HOH 10 2683 10 HOH HOH A . C 3 HOH 11 2684 11 HOH HOH A . C 3 HOH 12 2685 12 HOH HOH A . C 3 HOH 13 2686 13 HOH HOH A . C 3 HOH 14 2687 14 HOH HOH A . C 3 HOH 15 2688 15 HOH HOH A . C 3 HOH 16 2689 16 HOH HOH A . C 3 HOH 17 2690 17 HOH HOH A . C 3 HOH 18 2691 18 HOH HOH A . C 3 HOH 19 2692 19 HOH HOH A . C 3 HOH 20 2693 20 HOH HOH A . C 3 HOH 21 2694 21 HOH HOH A . C 3 HOH 22 2695 22 HOH HOH A . C 3 HOH 23 2696 23 HOH HOH A . C 3 HOH 24 2697 24 HOH HOH A . C 3 HOH 25 2698 25 HOH HOH A . C 3 HOH 26 2699 26 HOH HOH A . C 3 HOH 27 2700 27 HOH HOH A . C 3 HOH 28 2701 28 HOH HOH A . C 3 HOH 29 2702 29 HOH HOH A . C 3 HOH 30 2703 30 HOH HOH A . C 3 HOH 31 2704 31 HOH HOH A . C 3 HOH 32 2705 32 HOH HOH A . C 3 HOH 33 2706 33 HOH HOH A . C 3 HOH 34 2707 34 HOH HOH A . C 3 HOH 35 2708 35 HOH HOH A . C 3 HOH 36 2709 36 HOH HOH A . C 3 HOH 37 2710 37 HOH HOH A . C 3 HOH 38 2711 38 HOH HOH A . C 3 HOH 39 2712 39 HOH HOH A . C 3 HOH 40 2713 40 HOH HOH A . C 3 HOH 41 2714 41 HOH HOH A . C 3 HOH 42 2715 42 HOH HOH A . C 3 HOH 43 2716 43 HOH HOH A . C 3 HOH 44 2717 44 HOH HOH A . C 3 HOH 45 2718 45 HOH HOH A . C 3 HOH 46 2719 46 HOH HOH A . C 3 HOH 47 2720 47 HOH HOH A . C 3 HOH 48 2721 48 HOH HOH A . C 3 HOH 49 2722 49 HOH HOH A . C 3 HOH 50 2723 50 HOH HOH A . C 3 HOH 51 2724 51 HOH HOH A . C 3 HOH 52 2725 52 HOH HOH A . C 3 HOH 53 2726 53 HOH HOH A . C 3 HOH 54 2727 54 HOH HOH A . C 3 HOH 55 2728 55 HOH HOH A . C 3 HOH 56 2729 56 HOH HOH A . C 3 HOH 57 2730 57 HOH HOH A . C 3 HOH 58 2731 58 HOH HOH A . C 3 HOH 59 2732 59 HOH HOH A . C 3 HOH 60 2733 60 HOH HOH A . C 3 HOH 61 2734 61 HOH HOH A . C 3 HOH 62 2735 62 HOH HOH A . C 3 HOH 63 2736 63 HOH HOH A . C 3 HOH 64 2737 64 HOH HOH A . C 3 HOH 65 2738 65 HOH HOH A . C 3 HOH 66 2739 66 HOH HOH A . C 3 HOH 67 2740 67 HOH HOH A . C 3 HOH 68 2741 68 HOH HOH A . C 3 HOH 69 2742 69 HOH HOH A . C 3 HOH 70 2743 70 HOH HOH A . C 3 HOH 71 2744 71 HOH HOH A . C 3 HOH 72 2745 72 HOH HOH A . C 3 HOH 73 2746 73 HOH HOH A . C 3 HOH 74 2747 74 HOH HOH A . C 3 HOH 75 2748 75 HOH HOH A . C 3 HOH 76 2749 76 HOH HOH A . C 3 HOH 77 2750 77 HOH HOH A . C 3 HOH 78 2751 78 HOH HOH A . C 3 HOH 79 2752 79 HOH HOH A . C 3 HOH 80 2753 80 HOH HOH A . C 3 HOH 81 2754 81 HOH HOH A . C 3 HOH 82 2755 82 HOH HOH A . C 3 HOH 83 2756 83 HOH HOH A . C 3 HOH 84 2757 84 HOH HOH A . C 3 HOH 85 2758 85 HOH HOH A . C 3 HOH 86 2759 86 HOH HOH A . C 3 HOH 87 2760 87 HOH HOH A . C 3 HOH 88 2761 88 HOH HOH A . C 3 HOH 89 2762 89 HOH HOH A . C 3 HOH 90 2763 90 HOH HOH A . C 3 HOH 91 2764 91 HOH HOH A . C 3 HOH 92 2765 92 HOH HOH A . C 3 HOH 93 2766 93 HOH HOH A . C 3 HOH 94 2767 94 HOH HOH A . C 3 HOH 95 2768 95 HOH HOH A . C 3 HOH 96 2769 96 HOH HOH A . C 3 HOH 97 2770 97 HOH HOH A . C 3 HOH 98 2771 98 HOH HOH A . C 3 HOH 99 2772 99 HOH HOH A . C 3 HOH 100 2773 100 HOH HOH A . C 3 HOH 101 2774 101 HOH HOH A . C 3 HOH 102 2775 102 HOH HOH A . C 3 HOH 103 2776 103 HOH HOH A . C 3 HOH 104 2777 104 HOH HOH A . C 3 HOH 105 2778 105 HOH HOH A . C 3 HOH 106 2779 106 HOH HOH A . C 3 HOH 107 2780 107 HOH HOH A . C 3 HOH 108 2781 108 HOH HOH A . C 3 HOH 109 2782 109 HOH HOH A . C 3 HOH 110 2783 110 HOH HOH A . C 3 HOH 111 2784 111 HOH HOH A . C 3 HOH 112 2785 112 HOH HOH A . C 3 HOH 113 2786 113 HOH HOH A . C 3 HOH 114 2787 114 HOH HOH A . C 3 HOH 115 2788 115 HOH HOH A . C 3 HOH 116 2789 116 HOH HOH A . C 3 HOH 117 2790 117 HOH HOH A . C 3 HOH 118 2791 118 HOH HOH A . C 3 HOH 119 2792 119 HOH HOH A . C 3 HOH 120 2793 120 HOH HOH A . C 3 HOH 121 2794 121 HOH HOH A . C 3 HOH 122 2795 122 HOH HOH A . C 3 HOH 123 2796 123 HOH HOH A . C 3 HOH 124 2797 124 HOH HOH A . C 3 HOH 125 2798 125 HOH HOH A . C 3 HOH 126 2799 126 HOH HOH A . C 3 HOH 127 2800 127 HOH HOH A . C 3 HOH 128 2801 128 HOH HOH A . C 3 HOH 129 2802 129 HOH HOH A . C 3 HOH 130 2803 130 HOH HOH A . C 3 HOH 131 2804 131 HOH HOH A . C 3 HOH 132 2805 132 HOH HOH A . C 3 HOH 133 2806 133 HOH HOH A . C 3 HOH 134 2807 134 HOH HOH A . C 3 HOH 135 2808 135 HOH HOH A . C 3 HOH 136 2809 136 HOH HOH A . C 3 HOH 137 2810 137 HOH HOH A . C 3 HOH 138 2811 138 HOH HOH A . C 3 HOH 139 2812 139 HOH HOH A . C 3 HOH 140 2813 140 HOH HOH A . C 3 HOH 141 2814 141 HOH HOH A . C 3 HOH 142 2815 142 HOH HOH A . C 3 HOH 143 2816 143 HOH HOH A . C 3 HOH 144 2817 144 HOH HOH A . C 3 HOH 145 2818 145 HOH HOH A . C 3 HOH 146 2819 146 HOH HOH A . C 3 HOH 147 2820 147 HOH HOH A . C 3 HOH 148 2821 148 HOH HOH A . C 3 HOH 149 2822 149 HOH HOH A . C 3 HOH 150 2823 150 HOH HOH A . C 3 HOH 151 2824 151 HOH HOH A . C 3 HOH 152 2825 152 HOH HOH A . C 3 HOH 153 2826 153 HOH HOH A . C 3 HOH 154 2827 154 HOH HOH A . C 3 HOH 155 2828 155 HOH HOH A . C 3 HOH 156 2829 156 HOH HOH A . C 3 HOH 157 2830 157 HOH HOH A . C 3 HOH 158 2831 158 HOH HOH A . C 3 HOH 159 2832 159 HOH HOH A . C 3 HOH 160 2833 160 HOH HOH A . C 3 HOH 161 2834 161 HOH HOH A . C 3 HOH 162 2835 162 HOH HOH A . C 3 HOH 163 2836 163 HOH HOH A . C 3 HOH 164 2837 164 HOH HOH A . C 3 HOH 165 2838 165 HOH HOH A . C 3 HOH 166 2839 166 HOH HOH A . C 3 HOH 167 2840 167 HOH HOH A . C 3 HOH 168 2841 168 HOH HOH A . C 3 HOH 169 2842 169 HOH HOH A . C 3 HOH 170 2843 170 HOH HOH A . C 3 HOH 171 2844 171 HOH HOH A . C 3 HOH 172 2845 172 HOH HOH A . C 3 HOH 173 2846 173 HOH HOH A . C 3 HOH 174 2847 174 HOH HOH A . C 3 HOH 175 2848 175 HOH HOH A . C 3 HOH 176 2849 176 HOH HOH A . C 3 HOH 177 2850 177 HOH HOH A . C 3 HOH 178 2851 178 HOH HOH A . C 3 HOH 179 2852 179 HOH HOH A . C 3 HOH 180 2853 180 HOH HOH A . C 3 HOH 181 2854 181 HOH HOH A . C 3 HOH 182 2855 182 HOH HOH A . C 3 HOH 183 2856 183 HOH HOH A . C 3 HOH 184 2857 184 HOH HOH A . # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal XSCALE . ? package 'Wolfgang Kabsch' ? 'data processing' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 1 PHENIX . ? package 'Paul D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 PDB_EXTRACT 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 XDS . ? ? ? ? 'data reduction' ? ? ? 4 XSCALE . ? ? ? ? 'data scaling' ? ? ? 5 SHELX . ? ? ? ? phasing ? ? ? 6 # _cell.length_a 29.600 _cell.length_b 29.600 _cell.length_c 76.530 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 3DW6 _cell.pdbx_unique_axis ? _cell.Z_PDB 4 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.space_group_name_H-M 'P 43' _symmetry.entry_id 3DW6 _symmetry.Int_Tables_number 78 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 3DW6 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.90 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 35.27 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.pdbx_details '3.2 M (NH4)2SO4, 50 mM K-MOPS pH 7.0, 10 mM MgCl2, 10 mM MnCl2, vapor diffusion, hanging drop, temperature 293K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 '(NH4)2SO4' ? ? ? 1 2 1 K-MOPS ? ? ? 1 3 1 MgCl2 ? ? ? 1 4 1 MnCl2 ? ? ? 1 5 1 H2O ? ? ? 1 6 2 '(NH4)2SO4' ? ? ? 1 7 2 K-MOPS ? ? ? 1 8 2 MgCl2 ? ? ? 1 9 2 MnCl2 ? ? ? 1 10 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 90 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date 2008-05-26 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97916 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X10SA' _diffrn_source.pdbx_wavelength_list 0.97916 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X10SA # _reflns.entry_id 3DW6 _reflns.d_resolution_high 1.000 _reflns.number_obs 64959 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_netI_over_sigmaI 16.990 _reflns.percent_possible_obs 92.500 _reflns.B_iso_Wilson_estimate 11.318 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.number_all ? _reflns.pdbx_Rsym_value 0.054 _reflns.pdbx_redundancy 6.3 _reflns.R_free_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.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.00 _reflns_shell.d_res_low 1.10 _reflns_shell.number_measured_obs 45575 _reflns_shell.number_measured_all ? _reflns_shell.number_unique_obs 12469 _reflns_shell.Rmerge_I_obs ? _reflns_shell.meanI_over_sigI_obs 2.8 _reflns_shell.pdbx_Rsym_value 0.417 _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.percent_possible_all 71.20 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3DW6 _refine.ls_d_res_high 1.000 _refine.ls_d_res_low 20.189 _refine.pdbx_ls_sigma_F 1.38 _refine.ls_percent_reflns_obs 92.550 _refine.ls_number_reflns_obs 64959 _refine.ls_R_factor_obs 0.132 _refine.ls_R_factor_R_work 0.131 _refine.ls_R_factor_R_free 0.149 _refine.ls_percent_reflns_R_free 5.010 _refine.ls_number_reflns_R_free 3256 _refine.B_iso_mean 13.601 _refine.solvent_model_param_bsol 60.316 _refine.solvent_model_param_ksol 0.460 _refine.aniso_B[1][1] -2.191 _refine.aniso_B[2][2] -2.191 _refine.aniso_B[3][3] 0.957 _refine.aniso_B[1][2] -0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] -0.000 _refine.overall_SU_ML 0.070 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.110 _refine.pdbx_solvent_shrinkage_radii 0.900 _refine.pdbx_method_to_determine_struct ? _refine.pdbx_stereochemistry_target_values ML _refine.B_iso_max 41.07 _refine.B_iso_min 7.45 _refine.occupancy_max 1.00 _refine.occupancy_min 0.00 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_isotropic_thermal_model ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_ion_probe_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 184 _refine_hist.number_atoms_total 770 _refine_hist.d_res_high 1.000 _refine_hist.d_res_low 20.189 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 666 0.005 ? ? 'X-RAY DIFFRACTION' ? f_angle_d 1044 1.268 ? ? 'X-RAY DIFFRACTION' ? f_chiral_restr 131 0.055 ? ? 'X-RAY DIFFRACTION' ? f_plane_restr 27 0.012 ? ? 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 293 26.164 ? ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id 1.000 1.015 23 51.000 1493 . 0.299 0.319 . 69 . 1562 . . 'X-RAY DIFFRACTION' 1.015 1.031 23 60.000 1703 . 0.250 0.279 . 93 . 1796 . . 'X-RAY DIFFRACTION' 1.031 1.048 23 66.000 1961 . 0.220 0.204 . 78 . 2039 . . 'X-RAY DIFFRACTION' 1.048 1.066 23 77.000 2288 . 0.198 0.196 . 84 . 2372 . . 'X-RAY DIFFRACTION' 1.066 1.085 23 85.000 2471 . 0.179 0.197 . 122 . 2593 . . 'X-RAY DIFFRACTION' 1.085 1.106 23 95.000 2775 . 0.158 0.177 . 118 . 2893 . . 'X-RAY DIFFRACTION' 1.106 1.129 23 99.000 2857 . 0.147 0.182 . 178 . 3035 . . 'X-RAY DIFFRACTION' 1.129 1.153 23 100.000 2821 . 0.138 0.151 . 156 . 2977 . . 'X-RAY DIFFRACTION' 1.153 1.180 23 100.000 2939 . 0.123 0.152 . 182 . 3121 . . 'X-RAY DIFFRACTION' 1.180 1.209 23 100.000 2872 . 0.123 0.138 . 161 . 3033 . . 'X-RAY DIFFRACTION' 1.209 1.242 23 100.000 2918 . 0.115 0.128 . 137 . 3055 . . 'X-RAY DIFFRACTION' 1.242 1.279 23 100.000 2923 . 0.114 0.123 . 145 . 3068 . . 'X-RAY DIFFRACTION' 1.279 1.320 23 100.000 2864 . 0.123 0.153 . 168 . 3032 . . 'X-RAY DIFFRACTION' 1.320 1.367 23 100.000 2896 . 0.118 0.170 . 172 . 3068 . . 'X-RAY DIFFRACTION' 1.367 1.422 23 100.000 2903 . 0.121 0.127 . 141 . 3044 . . 'X-RAY DIFFRACTION' 1.422 1.487 23 100.000 2901 . 0.118 0.125 . 178 . 3079 . . 'X-RAY DIFFRACTION' 1.487 1.565 23 100.000 2897 . 0.126 0.133 . 150 . 3047 . . 'X-RAY DIFFRACTION' 1.565 1.663 23 100.000 2900 . 0.111 0.142 . 135 . 3035 . . 'X-RAY DIFFRACTION' 1.663 1.791 23 100.000 2854 . 0.111 0.124 . 171 . 3025 . . 'X-RAY DIFFRACTION' 1.791 1.971 23 100.000 2891 . 0.122 0.150 . 172 . 3063 . . 'X-RAY DIFFRACTION' 1.971 2.256 23 100.000 2889 . 0.137 0.153 . 149 . 3038 . . 'X-RAY DIFFRACTION' 2.256 2.842 23 99.000 2858 . 0.150 0.190 . 165 . 3023 . . 'X-RAY DIFFRACTION' 2.842 20.193 23 97.000 2829 . 0.119 0.117 . 132 . 2961 . . 'X-RAY DIFFRACTION' # _struct.entry_id 3DW6 _struct.title 'Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-SECH3 modified' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3DW6 _struct_keywords.text 'RNA, Sarcin Ricin Loop' _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.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3DW6 _struct_ref.pdbx_db_accession 3DW6 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 2647 _struct_ref.pdbx_seq_one_letter_code UGCUCCUAGUACGAGAGGACCGGAGUG _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3DW6 _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 3DW6 _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 # _struct_biol.id 1 _struct_biol.details ? # 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 UMS 4 P ? ? A C 2649 A UMS 2650 1_555 ? ? ? ? ? ? ? 1.593 ? ? covale2 covale both ? A UMS 4 "O3'" ? ? ? 1_555 A C 5 P ? ? A UMS 2650 A C 2651 1_555 ? ? ? ? ? ? ? 1.602 ? ? 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 C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A UMS 4 N3 ? ? ? 1_555 A A 24 N1 ? ? A UMS 2650 A A 2670 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A UMS 4 O4 ? ? ? 1_555 A A 24 N6 ? ? A UMS 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 G 9 N2 ? ? ? 1_555 A U 10 O4 ? ? A G 2655 A U 2656 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog16 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 19 N7 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog17 hydrog ? ? A U 10 O2 ? ? ? 1_555 A A 19 N6 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog18 hydrog ? ? A A 11 N6 ? ? ? 1_555 A G 18 N3 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog19 hydrog ? ? A A 11 N7 ? ? ? 1_555 A G 18 N2 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog20 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 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 1 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 10 _struct_site.details 'BINDING SITE FOR RESIDUE GOL A 1' # 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 10 U A 1 ? U A 2647 . ? 1_655 ? 2 AC1 10 U A 7 ? U A 2653 . ? 1_555 ? 3 AC1 10 A A 8 ? A A 2654 . ? 1_555 ? 4 AC1 10 U A 10 ? U A 2656 . ? 1_555 ? 5 AC1 10 A A 14 ? A A 2660 . ? 1_565 ? 6 AC1 10 C A 20 ? C A 2666 . ? 1_555 ? 7 AC1 10 HOH C . ? HOH A 2719 . ? 1_555 ? 8 AC1 10 HOH C . ? HOH A 2757 . ? 1_655 ? 9 AC1 10 HOH C . ? HOH A 2802 . ? 1_555 ? 10 AC1 10 HOH C . ? HOH A 2841 . ? 1_555 ? # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id UMS _pdbx_struct_mod_residue.label_seq_id 4 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id UMS _pdbx_struct_mod_residue.auth_seq_id 2650 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DU _pdbx_struct_mod_residue.details ? # 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 U OP3 O N N 128 U P P N N 129 U OP1 O N N 130 U OP2 O N N 131 U "O5'" O N N 132 U "C5'" C N N 133 U "C4'" C N R 134 U "O4'" O N N 135 U "C3'" C N S 136 U "O3'" O N N 137 U "C2'" C N R 138 U "O2'" O N N 139 U "C1'" C N R 140 U N1 N N N 141 U C2 C N N 142 U O2 O N N 143 U N3 N N N 144 U C4 C N N 145 U O4 O N N 146 U C5 C N N 147 U C6 C N N 148 U HOP3 H N N 149 U HOP2 H N N 150 U "H5'" H N N 151 U "H5''" H N N 152 U "H4'" H N N 153 U "H3'" H N N 154 U "HO3'" H N N 155 U "H2'" H N N 156 U "HO2'" H N N 157 U "H1'" H N N 158 U H3 H N N 159 U H5 H N N 160 U H6 H N N 161 UMS OP3 O N N 162 UMS P P N N 163 UMS OP1 O N N 164 UMS OP2 O N N 165 UMS "O5'" O N N 166 UMS "C5'" C N N 167 UMS "C4'" C N R 168 UMS "O4'" O N N 169 UMS "C3'" C N R 170 UMS "O3'" O N N 171 UMS "C2'" C N R 172 UMS "SE2'" SE N N 173 UMS "C1'" C N R 174 UMS "CA'" C N N 175 UMS N1 N N N 176 UMS C2 C N N 177 UMS O2 O N N 178 UMS N3 N N N 179 UMS C4 C N N 180 UMS O4 O N N 181 UMS C5 C N N 182 UMS C6 C N N 183 UMS HOP3 H N N 184 UMS HOP2 H N N 185 UMS "H5'" H N N 186 UMS "H5'2" H N N 187 UMS "H4'" H N N 188 UMS "H3'" H N N 189 UMS "HO3'" H N N 190 UMS "H2'" H N N 191 UMS "H1'" H N N 192 UMS "HA'" H N N 193 UMS "HA'2" H N N 194 UMS "HA'3" H N N 195 UMS H3 H N N 196 UMS H5 H N N 197 UMS 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 U OP3 P sing N N 131 U OP3 HOP3 sing N N 132 U P OP1 doub N N 133 U P OP2 sing N N 134 U P "O5'" sing N N 135 U OP2 HOP2 sing N N 136 U "O5'" "C5'" sing N N 137 U "C5'" "C4'" sing N N 138 U "C5'" "H5'" sing N N 139 U "C5'" "H5''" sing N N 140 U "C4'" "O4'" sing N N 141 U "C4'" "C3'" sing N N 142 U "C4'" "H4'" sing N N 143 U "O4'" "C1'" sing N N 144 U "C3'" "O3'" sing N N 145 U "C3'" "C2'" sing N N 146 U "C3'" "H3'" sing N N 147 U "O3'" "HO3'" sing N N 148 U "C2'" "O2'" sing N N 149 U "C2'" "C1'" sing N N 150 U "C2'" "H2'" sing N N 151 U "O2'" "HO2'" sing N N 152 U "C1'" N1 sing N N 153 U "C1'" "H1'" sing N N 154 U N1 C2 sing N N 155 U N1 C6 sing N N 156 U C2 O2 doub N N 157 U C2 N3 sing N N 158 U N3 C4 sing N N 159 U N3 H3 sing N N 160 U C4 O4 doub N N 161 U C4 C5 sing N N 162 U C5 C6 doub N N 163 U C5 H5 sing N N 164 U C6 H6 sing N N 165 UMS OP3 P sing N N 166 UMS OP3 HOP3 sing N N 167 UMS P OP1 doub N N 168 UMS P OP2 sing N N 169 UMS P "O5'" sing N N 170 UMS OP2 HOP2 sing N N 171 UMS "O5'" "C5'" sing N N 172 UMS "C5'" "C4'" sing N N 173 UMS "C5'" "H5'" sing N N 174 UMS "C5'" "H5'2" sing N N 175 UMS "C4'" "O4'" sing N N 176 UMS "C4'" "C3'" sing N N 177 UMS "C4'" "H4'" sing N N 178 UMS "O4'" "C1'" sing N N 179 UMS "C3'" "O3'" sing N N 180 UMS "C3'" "C2'" sing N N 181 UMS "C3'" "H3'" sing N N 182 UMS "O3'" "HO3'" sing N N 183 UMS "C2'" "SE2'" sing N N 184 UMS "C2'" "C1'" sing N N 185 UMS "C2'" "H2'" sing N N 186 UMS "SE2'" "CA'" sing N N 187 UMS "C1'" N1 sing N N 188 UMS "C1'" "H1'" sing N N 189 UMS "CA'" "HA'" sing N N 190 UMS "CA'" "HA'2" sing N N 191 UMS "CA'" "HA'3" sing N N 192 UMS N1 C2 sing N N 193 UMS N1 C6 sing N N 194 UMS C2 O2 doub N N 195 UMS C2 N3 sing N N 196 UMS N3 C4 sing N N 197 UMS N3 H3 sing N N 198 UMS C4 O4 doub N N 199 UMS C4 C5 sing N N 200 UMS C5 C6 doub N N 201 UMS C5 H5 sing N N 202 UMS C6 H6 sing N N 203 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3DW6 'double helix' 3DW6 'a-form double helix' 3DW6 'mismatched base pair' 3DW6 'triple helix' # 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 -2.370 -0.533 0.247 4.600 -13.450 1.752 1 A_G2648:U2672_A A 2648 ? A 2672 ? 28 ? 1 A C 3 1_555 A G 25 1_555 0.264 -0.229 0.142 6.294 -20.248 -0.905 2 A_C2649:G2671_A A 2649 ? A 2671 ? 19 1 1 A UMS 4 1_555 A A 24 1_555 -0.188 -0.024 0.155 3.622 -13.873 1.303 3 A_UMS2650:A2670_A A 2650 ? A 2670 ? 20 1 1 A C 5 1_555 A G 23 1_555 0.274 -0.160 -0.004 7.948 -18.137 1.777 4 A_C2651:G2669_A A 2651 ? A 2669 ? 19 1 1 A C 6 1_555 A G 22 1_555 0.296 -0.161 0.072 -2.681 -12.977 -2.013 5 A_C2652:G2668_A A 2652 ? A 2668 ? 19 1 1 A U 7 1_555 A C 21 1_555 5.645 -2.132 -0.139 -3.189 -11.690 -11.832 6 A_U2653:C2667_A A 2653 ? A 2667 ? ? ? 1 A U 10 1_555 A A 19 1_555 4.073 -1.759 -0.681 6.349 -16.938 -103.312 7 A_U2656:A2665_A A 2656 ? A 2665 ? 24 4 1 A A 11 1_555 A G 18 1_555 -6.855 -4.340 -0.058 -1.830 2.172 -3.832 8 A_A2657:G2664_A A 2657 ? A 2664 ? 11 10 1 A C 12 1_555 A G 17 1_555 0.149 -0.090 -0.191 6.778 -1.751 0.758 9 A_C2658:G2663_A A 2658 ? A 2663 ? 19 1 1 A G 13 1_555 A A 16 1_555 7.194 -5.281 0.789 18.823 -4.579 -19.157 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 -0.009 -1.160 3.135 -0.649 3.685 44.166 -1.862 -0.044 3.034 4.890 0.861 44.316 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 UMS 4 1_555 A A 24 1_555 -0.689 -1.768 3.183 -4.127 9.661 28.058 -5.226 0.565 2.522 19.100 8.158 29.923 2 AA_C2649UMS2650:A2670G2671_AA A 2649 ? A 2671 ? A 2650 ? A 2670 ? 1 A UMS 4 1_555 A A 24 1_555 A C 5 1_555 A G 23 1_555 0.282 -1.016 3.058 0.057 4.299 34.861 -2.273 -0.460 2.916 7.141 -0.094 35.117 3 AA_UMS2650C2651: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 -0.606 -1.910 3.429 -0.947 8.383 32.365 -4.681 0.899 2.874 14.729 1.665 33.418 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 -0.402 -0.931 3.463 7.156 8.644 54.275 -1.527 0.866 3.219 9.363 -7.751 55.337 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 0.440 -0.785 6.294 5.091 -4.650 32.472 0.149 0.898 6.337 -8.200 -8.978 33.176 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 5.182 -1.251 3.548 -2.290 -1.613 -11.891 8.327 20.880 4.257 7.650 -10.859 -12.215 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 0.261 -1.201 3.189 -1.586 4.198 60.127 -1.394 -0.335 3.100 4.184 1.581 60.278 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 -2.832 -1.379 2.912 -7.544 6.488 49.540 -2.045 2.825 3.093 7.653 8.899 50.468 9 AA_C2658G2659:A2662G2663_AA A 2658 ? A 2663 ? A 2659 ? A 2662 ? # _atom_sites.entry_id 3DW6 _atom_sites.fract_transf_matrix[1][1] 0.033784 _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] 0.033784 _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] 0.013067 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C H N O P SE # loop_