data_7EDU # _entry.id 7EDU # _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 7EDU pdb_00007edu 10.2210/pdb7edu/pdb WWPDB D_1300021230 ? ? # 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 2022-03-23 2 'Structure model' 1 1 2024-04-03 # _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' 'Data collection' 2 2 'Structure model' 'Refinement description' # 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 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' pdbx_initial_refinement_model # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7EDU _pdbx_database_status.recvd_initial_deposition_date 2021-03-17 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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 Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kondo, J.' 1 0000-0002-5682-3685 'Iwase, E.' 2 ? # _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 primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'RNA duplex containing C-Au-C base pair' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 0000-0002-5682-3685 primary 'Iwase, E.' 2 ? # 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 (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3') ; 3787.312 4 ? ? ? ? 2 non-polymer syn 'GOLD ION' 196.967 4 ? ? ? ? 3 water nat water 18.015 15 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGACUCGACUCC _entity_poly.pdbx_seq_one_letter_code_can GGACUCGACUCC _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'GOLD ION' AU 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 A n 1 4 C n 1 5 U n 1 6 C n 1 7 G n 1 8 A n 1 9 C n 1 10 U n 1 11 C n 1 12 C 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 12 _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 AU non-polymer . 'GOLD ION' ? 'Au 1' 196.967 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 HOH non-polymer . WATER ? 'H2 O' 18.015 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 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 C 4 4 4 C C A . n A 1 5 U 5 5 5 U U A . n A 1 6 C 6 6 6 C C A . n A 1 7 G 7 7 7 G G A . n A 1 8 A 8 8 8 A A A . n A 1 9 C 9 9 9 C C A . n A 1 10 U 10 10 10 U U A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n B 1 1 G 1 1 1 G G B . n B 1 2 G 2 2 2 G G B . n B 1 3 A 3 3 3 A A B . n B 1 4 C 4 4 4 C C B . n B 1 5 U 5 5 5 U U B . n B 1 6 C 6 6 6 C C B . n B 1 7 G 7 7 7 G G B . n B 1 8 A 8 8 8 A A B . n B 1 9 C 9 9 9 C C B . n B 1 10 U 10 10 10 U U B . n B 1 11 C 11 11 11 C C B . n B 1 12 C 12 12 12 C C B . n C 1 1 G 1 1 1 G G C . n C 1 2 G 2 2 2 G G C . n C 1 3 A 3 3 3 A A C . n C 1 4 C 4 4 4 C C C . n C 1 5 U 5 5 5 U U C . n C 1 6 C 6 6 6 C C C . n C 1 7 G 7 7 7 G G C . n C 1 8 A 8 8 8 A A C . n C 1 9 C 9 9 9 C C C . n C 1 10 U 10 10 10 U U C . n C 1 11 C 11 11 11 C C C . n C 1 12 C 12 12 12 C C C . n D 1 1 G 1 1 1 G G D . n D 1 2 G 2 2 2 G G D . n D 1 3 A 3 3 3 A A D . n D 1 4 C 4 4 4 C C D . n D 1 5 U 5 5 5 U U D . n D 1 6 C 6 6 6 C C D . n D 1 7 G 7 7 7 G G D . n D 1 8 A 8 8 8 A A D . n D 1 9 C 9 9 9 C C D . n D 1 10 U 10 10 10 U U D . n D 1 11 C 11 11 11 C C D . n D 1 12 C 12 12 12 C C D . 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 E 2 AU 1 101 1 AU AU B . F 2 AU 1 102 2 AU AU B . G 2 AU 1 101 3 AU AU C . H 2 AU 1 102 4 AU AU C . I 3 HOH 1 101 16 HOH HOH A . I 3 HOH 2 102 14 HOH HOH A . I 3 HOH 3 103 7 HOH HOH A . I 3 HOH 4 104 8 HOH HOH A . I 3 HOH 5 105 18 HOH HOH A . J 3 HOH 1 201 9 HOH HOH B . J 3 HOH 2 202 3 HOH HOH B . J 3 HOH 3 203 4 HOH HOH B . K 3 HOH 1 201 6 HOH HOH C . K 3 HOH 2 202 5 HOH HOH C . K 3 HOH 3 203 2 HOH HOH C . K 3 HOH 4 204 1 HOH HOH C . K 3 HOH 5 205 13 HOH HOH C . K 3 HOH 6 206 17 HOH HOH C . L 3 HOH 1 101 10 HOH HOH D . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.17.1 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 120.000 _cell.angle_gamma_esd ? _cell.entry_id 7EDU _cell.details ? _cell.formula_units_Z ? _cell.length_a 29.216 _cell.length_a_esd ? _cell.length_b 29.216 _cell.length_b_esd ? _cell.length_c 257.794 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 24 _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 ? # _symmetry.entry_id 7EDU _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' _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 7EDU _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 2.10 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 41.33 _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_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING 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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'sodium cacodylate, MPD, spermine tetrahydrochloride, ammonium chloride, gold chloride' _exptl_crystal_grow.pdbx_pH_range ? # _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 PILATUS3 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2016-11-09 _diffrn_detector.pdbx_frequency ? # _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 1.03906 _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 'PHOTON FACTORY BEAMLINE BL-17A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.03906 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-17A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate 48.631 _reflns.entry_id 7EDU _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.300 _reflns.d_resolution_low 25.180 _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 10301 _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 94.100 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 2.580 _reflns.pdbx_Rmerge_I_obs 0.057 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 11.100 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 3.113 _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 0.073 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 26576 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.997 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _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 _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_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_Rsym_value _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 _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split 2.300 2.360 ? 2.730 ? 1947 789 ? 738 93.500 ? ? ? ? 0.316 ? ? ? ? ? ? ? ? 2.638 ? ? ? ? 0.394 ? ? 1 1 0.885 ? ? 2.360 2.420 ? 2.910 ? 2209 858 ? 840 97.900 ? ? ? ? 0.270 ? ? ? ? ? ? ? ? 2.630 ? ? ? ? 0.337 ? ? 2 1 0.931 ? ? 2.420 2.490 ? 3.820 ? 1932 733 ? 714 97.400 ? ? ? ? 0.235 ? ? ? ? ? ? ? ? 2.706 ? ? ? ? 0.291 ? ? 3 1 0.927 ? ? 2.490 2.570 ? 4.500 ? 1863 739 ? 721 97.600 ? ? ? ? 0.198 ? ? ? ? ? ? ? ? 2.584 ? ? ? ? 0.245 ? ? 4 1 0.950 ? ? 2.570 2.650 ? 5.440 ? 1889 790 ? 760 96.200 ? ? ? ? 0.159 ? ? ? ? ? ? ? ? 2.486 ? ? ? ? 0.201 ? ? 5 1 0.957 ? ? 2.650 2.750 ? 7.580 ? 1546 612 ? 595 97.200 ? ? ? ? 0.122 ? ? ? ? ? ? ? ? 2.598 ? ? ? ? 0.153 ? ? 6 1 0.972 ? ? 2.750 2.850 ? 8.020 ? 1800 705 ? 688 97.600 ? ? ? ? 0.132 ? ? ? ? ? ? ? ? 2.616 ? ? ? ? 0.167 ? ? 7 1 0.955 ? ? 2.850 2.970 ? 11.200 ? 1741 663 ? 643 97.000 ? ? ? ? 0.097 ? ? ? ? ? ? ? ? 2.708 ? ? ? ? 0.121 ? ? 8 1 0.973 ? ? 2.970 3.100 ? 13.600 ? 1496 592 ? 568 95.900 ? ? ? ? 0.075 ? ? ? ? ? ? ? ? 2.634 ? ? ? ? 0.094 ? ? 9 1 0.984 ? ? 3.100 3.250 ? 15.310 ? 1451 619 ? 562 90.800 ? ? ? ? 0.065 ? ? ? ? ? ? ? ? 2.582 ? ? ? ? 0.083 ? ? 10 1 0.986 ? ? 3.250 3.430 ? 17.040 ? 1248 524 ? 484 92.400 ? ? ? ? 0.061 ? ? ? ? ? ? ? ? 2.579 ? ? ? ? 0.078 ? ? 11 1 0.985 ? ? 3.430 3.630 ? 17.310 ? 1270 589 ? 512 86.900 ? ? ? ? 0.056 ? ? ? ? ? ? ? ? 2.480 ? ? ? ? 0.071 ? ? 12 1 0.990 ? ? 3.630 3.890 ? 17.720 ? 959 467 ? 406 86.900 ? ? ? ? 0.051 ? ? ? ? ? ? ? ? 2.362 ? ? ? ? 0.066 ? ? 13 1 0.992 ? ? 3.890 4.200 ? 18.740 ? 1034 494 ? 444 89.900 ? ? ? ? 0.047 ? ? ? ? ? ? ? ? 2.329 ? ? ? ? 0.061 ? ? 14 1 0.990 ? ? 4.200 4.600 ? 19.980 ? 926 397 ? 359 90.400 ? ? ? ? 0.047 ? ? ? ? ? ? ? ? 2.579 ? ? ? ? 0.060 ? ? 15 1 0.990 ? ? 4.600 5.140 ? 20.180 ? 924 394 ? 360 91.400 ? ? ? ? 0.045 ? ? ? ? ? ? ? ? 2.567 ? ? ? ? 0.057 ? ? 16 1 0.993 ? ? 5.140 5.940 ? 20.030 ? 818 354 ? 325 91.800 ? ? ? ? 0.044 ? ? ? ? ? ? ? ? 2.517 ? ? ? ? 0.055 ? ? 17 1 0.995 ? ? 5.940 7.270 ? 20.650 ? 649 297 ? 263 88.600 ? ? ? ? 0.037 ? ? ? ? ? ? ? ? 2.468 ? ? ? ? 0.047 ? ? 18 1 0.995 ? ? 7.270 10.280 ? 21.950 ? 559 216 ? 209 96.800 ? ? ? ? 0.030 ? ? ? ? ? ? ? ? 2.675 ? ? ? ? 0.038 ? ? 19 1 0.997 ? ? 10.280 25.180 ? 24.030 ? 315 117 ? 110 94.000 ? ? ? ? 0.020 ? ? ? ? ? ? ? ? 2.864 ? ? ? ? 0.024 ? ? 20 1 0.999 ? ? # _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 59.120 _refine.B_iso_mean 35.8100 _refine.B_iso_min 22.450 _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 7EDU _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 2.3000 _refine.ls_d_res_low 25.1800 _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 10292 _refine.ls_number_reflns_R_free 1037 _refine.ls_number_reflns_R_work 9255 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 93.7500 _refine.ls_percent_reflns_R_free 10.0800 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1819 _refine.ls_R_factor_R_free 0.2292 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1766 _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.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 1.470 _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 THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'RNA duplex constructed using Coot' _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 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _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 26.8500 _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 0.3800 _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 final _refine_hist.details ? _refine_hist.d_res_high 2.3000 _refine_hist.d_res_low 25.1800 _refine_hist.number_atoms_solvent 15 _refine_hist.number_atoms_total 1019 _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 48 _refine_hist.pdbx_B_iso_mean_ligand 45.39 _refine_hist.pdbx_B_iso_mean_solvent 32.96 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1000 _refine_hist.pdbx_number_atoms_ligand 4 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # 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 _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.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.3000 2.4200 1515 . 158 1357 94.0000 . . . 0.3886 0.0000 0.2862 . . . . . . . 7 . . . 'X-RAY DIFFRACTION' 2.4200 2.5700 1494 . 151 1343 97.0000 . . . 0.3152 0.0000 0.2445 . . . . . . . 7 . . . 'X-RAY DIFFRACTION' 2.5700 2.7700 1509 . 154 1355 97.0000 . . . 0.2956 0.0000 0.2499 . . . . . . . 7 . . . 'X-RAY DIFFRACTION' 2.7700 3.0500 1495 . 153 1342 97.0000 . . . 0.2983 0.0000 0.2321 . . . . . . . 7 . . . 'X-RAY DIFFRACTION' 3.0500 3.4900 1439 . 155 1284 92.0000 . . . 0.2454 0.0000 0.2010 . . . . . . . 7 . . . 'X-RAY DIFFRACTION' 3.4900 4.3900 1393 . 122 1271 89.0000 . . . 0.2235 0.0000 0.1526 . . . . . . . 7 . . . 'X-RAY DIFFRACTION' 4.3900 25.1800 1447 . 144 1303 91.0000 . . . 0.1270 0.0000 0.1047 . . . . . . . 7 . . . # _struct.entry_id 7EDU _struct.title 'RNA duplex containing C-Au-C 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 7EDU _struct_keywords.text 'Metal-mediated base pair, Gold, RNA' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 3 ? J N N 3 ? K N N 3 ? L N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7EDU _struct_ref.pdbx_db_accession 7EDU _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 7EDU A 1 ? 12 ? 7EDU 1 ? 12 ? 1 12 2 1 7EDU B 1 ? 12 ? 7EDU 1 ? 12 ? 1 12 3 1 7EDU C 1 ? 12 ? 7EDU 1 ? 12 ? 1 12 4 1 7EDU D 1 ? 12 ? 7EDU 1 ? 12 ? 1 12 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 software_defined_assembly PISA dimeric 2 2 software_defined_assembly PISA dimeric 2 # 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)' 1440 ? 1 MORE -19 ? 1 'SSA (A^2)' 4320 ? 2 'ABSA (A^2)' 1440 ? 2 MORE -19 ? 2 'SSA (A^2)' 4350 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E,F,I,J 2 1 C,D,G,H,K,L # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _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 metalc1 metalc ? ? A C 4 N3 ? ? ? 1_555 E AU . AU ? ? A C 4 B AU 101 1_555 ? ? ? ? ? ? ? 2.246 ? ? metalc2 metalc ? ? A C 9 N3 ? ? ? 1_555 F AU . AU ? ? A C 9 B AU 102 1_555 ? ? ? ? ? ? ? 2.204 ? ? metalc3 metalc ? ? B C 4 N3 ? ? ? 1_555 F AU . AU ? ? B C 4 B AU 102 1_555 ? ? ? ? ? ? ? 2.163 ? ? metalc4 metalc ? ? B C 9 N3 ? ? ? 1_555 E AU . AU ? ? B C 9 B AU 101 1_555 ? ? ? ? ? ? ? 2.149 ? ? metalc5 metalc ? ? C C 4 N3 ? ? ? 1_555 G AU . AU ? ? C C 4 C AU 101 1_555 ? ? ? ? ? ? ? 2.103 ? ? metalc6 metalc ? ? C C 9 N3 ? ? ? 1_555 H AU . AU ? ? C C 9 C AU 102 1_555 ? ? ? ? ? ? ? 2.017 ? ? metalc7 metalc ? ? G AU . AU ? ? ? 1_555 D C 9 N3 ? ? C AU 101 D C 9 1_555 ? ? ? ? ? ? ? 2.121 ? ? metalc8 metalc ? ? H AU . AU ? ? ? 1_555 D C 4 N3 ? ? C AU 102 D C 4 1_555 ? ? ? ? ? ? ? 2.220 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 1 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 1 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 1 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 2 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 2 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 2 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 10 N3 ? ? A A 3 B U 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 10 O4 ? ? A A 3 B U 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 5 N3 ? ? ? 1_555 B A 8 N1 ? ? A U 5 B A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 5 O4 ? ? ? 1_555 B A 8 N6 ? ? A U 5 B A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 6 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 6 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 6 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 7 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 7 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 7 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 8 N1 ? ? ? 1_555 B U 5 N3 ? ? A A 8 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N6 ? ? ? 1_555 B U 5 O4 ? ? A A 8 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 10 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 10 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 10 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 10 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C G 1 N1 ? ? ? 1_555 D C 12 N3 ? ? C G 1 D C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C G 1 N2 ? ? ? 1_555 D C 12 O2 ? ? C G 1 D C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C G 1 O6 ? ? ? 1_555 D C 12 N4 ? ? C G 1 D C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C G 2 N1 ? ? ? 1_555 D C 11 N3 ? ? C G 2 D C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C G 2 N2 ? ? ? 1_555 D C 11 O2 ? ? C G 2 D C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C G 2 O6 ? ? ? 1_555 D C 11 N4 ? ? C G 2 D C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C A 3 N1 ? ? ? 1_555 D U 10 N3 ? ? C A 3 D U 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C A 3 N6 ? ? ? 1_555 D U 10 O4 ? ? C A 3 D U 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C U 5 N3 ? ? ? 1_555 D A 8 N1 ? ? C U 5 D A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C U 5 O4 ? ? ? 1_555 D A 8 N6 ? ? C U 5 D A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C C 6 N3 ? ? ? 1_555 D G 7 N1 ? ? C C 6 D G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C C 6 N4 ? ? ? 1_555 D G 7 O6 ? ? C C 6 D G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C C 6 O2 ? ? ? 1_555 D G 7 N2 ? ? C C 6 D G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C G 7 N1 ? ? ? 1_555 D C 6 N3 ? ? C G 7 D C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C G 7 N2 ? ? ? 1_555 D C 6 O2 ? ? C G 7 D C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C G 7 O6 ? ? ? 1_555 D C 6 N4 ? ? C G 7 D C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C A 8 N1 ? ? ? 1_555 D U 5 N3 ? ? C A 8 D U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C A 8 N6 ? ? ? 1_555 D U 5 O4 ? ? C A 8 D U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C U 10 N3 ? ? ? 1_555 D A 3 N1 ? ? C U 10 D A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C U 10 O4 ? ? ? 1_555 D A 3 N6 ? ? C U 10 D A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C C 11 N3 ? ? ? 1_555 D G 2 N1 ? ? C C 11 D G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C C 11 N4 ? ? ? 1_555 D G 2 O6 ? ? C C 11 D G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C C 11 O2 ? ? ? 1_555 D G 2 N2 ? ? C C 11 D G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? C C 12 N3 ? ? ? 1_555 D G 1 N1 ? ? C C 12 D G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? C C 12 N4 ? ? ? 1_555 D G 1 O6 ? ? C C 12 D G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C C 12 O2 ? ? ? 1_555 D G 1 N2 ? ? C C 12 D G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N3 ? A C 4 ? A C 4 ? 1_555 AU ? E AU . ? B AU 101 ? 1_555 N3 ? B C 9 ? B C 9 ? 1_555 174.2 ? 2 N3 ? A C 9 ? A C 9 ? 1_555 AU ? F AU . ? B AU 102 ? 1_555 N3 ? B C 4 ? B C 4 ? 1_555 175.5 ? 3 N3 ? C C 4 ? C C 4 ? 1_555 AU ? G AU . ? C AU 101 ? 1_555 N3 ? D C 9 ? D C 9 ? 1_555 172.5 ? 4 N3 ? C C 9 ? C C 9 ? 1_555 AU ? H AU . ? C AU 102 ? 1_555 N3 ? D C 4 ? D C 4 ? 1_555 173.1 ? # _pdbx_entry_details.entry_id 7EDU _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_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 AU AU AU N N 38 C OP3 O N N 39 C P P N N 40 C OP1 O N N 41 C OP2 O N N 42 C "O5'" O N N 43 C "C5'" C N N 44 C "C4'" C N R 45 C "O4'" O N N 46 C "C3'" C N S 47 C "O3'" O N N 48 C "C2'" C N R 49 C "O2'" O N N 50 C "C1'" C N R 51 C N1 N N N 52 C C2 C N N 53 C O2 O N N 54 C N3 N N N 55 C C4 C N N 56 C N4 N N N 57 C C5 C N N 58 C C6 C N N 59 C HOP3 H N N 60 C HOP2 H N N 61 C "H5'" H N N 62 C "H5''" H N N 63 C "H4'" H N N 64 C "H3'" H N N 65 C "HO3'" H N N 66 C "H2'" H N N 67 C "HO2'" H N N 68 C "H1'" H N N 69 C H41 H N N 70 C H42 H N N 71 C H5 H N N 72 C H6 H N N 73 G OP3 O N N 74 G P P N N 75 G OP1 O N N 76 G OP2 O N N 77 G "O5'" O N N 78 G "C5'" C N N 79 G "C4'" C N R 80 G "O4'" O N N 81 G "C3'" C N S 82 G "O3'" O N N 83 G "C2'" C N R 84 G "O2'" O N N 85 G "C1'" C N R 86 G N9 N Y N 87 G C8 C Y N 88 G N7 N Y N 89 G C5 C Y N 90 G C6 C N N 91 G O6 O N N 92 G N1 N N N 93 G C2 C N N 94 G N2 N N N 95 G N3 N N N 96 G C4 C Y N 97 G HOP3 H N N 98 G HOP2 H N N 99 G "H5'" H N N 100 G "H5''" H N N 101 G "H4'" H N N 102 G "H3'" H N N 103 G "HO3'" H N N 104 G "H2'" H N N 105 G "HO2'" H N N 106 G "H1'" H N N 107 G H8 H N N 108 G H1 H N N 109 G H21 H N N 110 G H22 H N N 111 HOH O O N N 112 HOH H1 H N N 113 HOH H2 H N N 114 U OP3 O N N 115 U P P N N 116 U OP1 O N N 117 U OP2 O N N 118 U "O5'" O N N 119 U "C5'" C N N 120 U "C4'" C N R 121 U "O4'" O N N 122 U "C3'" C N S 123 U "O3'" O N N 124 U "C2'" C N R 125 U "O2'" O N N 126 U "C1'" C N R 127 U N1 N N N 128 U C2 C N N 129 U O2 O N N 130 U N3 N N N 131 U C4 C N N 132 U O4 O N N 133 U C5 C N N 134 U C6 C N N 135 U HOP3 H N N 136 U HOP2 H N N 137 U "H5'" H N N 138 U "H5''" H N N 139 U "H4'" H N N 140 U "H3'" H N N 141 U "HO3'" H N N 142 U "H2'" H N N 143 U "HO2'" H N N 144 U "H1'" H N N 145 U H3 H N N 146 U H5 H N N 147 U H6 H N N 148 # 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 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7EDU 'double helix' 7EDU 'a-form double 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 1 1_555 B C 12 1_555 -0.166 -0.434 0.178 -11.004 -1.177 -4.029 1 A_G1:C12_B A 1 ? B 12 ? 19 1 1 A G 2 1_555 B C 11 1_555 -0.230 -0.082 0.209 4.584 -6.144 0.430 2 A_G2:C11_B A 2 ? B 11 ? 19 1 1 A A 3 1_555 B U 10 1_555 -0.076 -0.233 0.460 16.453 -10.292 8.107 3 A_A3:U10_B A 3 ? B 10 ? 20 1 1 A U 5 1_555 B A 8 1_555 -0.216 -0.266 0.290 -6.739 -19.028 4.276 4 A_U5:A8_B A 5 ? B 8 ? 20 1 1 A C 6 1_555 B G 7 1_555 0.119 -0.001 0.315 0.364 -14.514 1.367 5 A_C6:G7_B A 6 ? B 7 ? 19 1 1 A G 7 1_555 B C 6 1_555 -0.032 -0.117 0.315 -2.381 -10.455 3.916 6 A_G7:C6_B A 7 ? B 6 ? 19 1 1 A A 8 1_555 B U 5 1_555 0.238 -0.199 -0.190 -0.947 -18.731 4.419 7 A_A8:U5_B A 8 ? B 5 ? 20 1 1 A U 10 1_555 B A 3 1_555 0.274 -0.178 0.548 -12.760 -16.808 6.812 8 A_U10:A3_B A 10 ? B 3 ? 20 1 1 A C 11 1_555 B G 2 1_555 0.005 -0.128 0.077 2.714 -7.773 -0.677 9 A_C11:G2_B A 11 ? B 2 ? 19 1 1 A C 12 1_555 B G 1 1_555 0.151 -0.193 0.348 -0.868 -15.921 0.258 10 A_C12:G1_B A 12 ? B 1 ? 19 1 1 C G 1 1_555 D C 12 1_555 -0.376 -0.295 -0.346 -5.782 -13.861 -2.769 11 C_G1:C12_D C 1 ? D 12 ? 19 1 1 C G 2 1_555 D C 11 1_555 -0.112 -0.107 0.227 -1.848 -12.103 2.937 12 C_G2:C11_D C 2 ? D 11 ? 19 1 1 C A 3 1_555 D U 10 1_555 -0.011 -0.310 -0.091 -6.814 -13.464 2.527 13 C_A3:U10_D C 3 ? D 10 ? 20 1 1 C U 5 1_555 D A 8 1_555 -0.247 -0.129 -0.055 -4.177 -11.359 1.979 14 C_U5:A8_D C 5 ? D 8 ? 20 1 1 C C 6 1_555 D G 7 1_555 0.240 -0.357 -0.198 -2.437 -4.802 -2.294 15 C_C6:G7_D C 6 ? D 7 ? 19 1 1 C G 7 1_555 D C 6 1_555 -0.057 -0.060 -0.258 -0.307 -9.664 2.136 16 C_G7:C6_D C 7 ? D 6 ? 19 1 1 C A 8 1_555 D U 5 1_555 0.030 -0.288 0.142 3.910 -18.046 5.765 17 C_A8:U5_D C 8 ? D 5 ? 20 1 1 C U 10 1_555 D A 3 1_555 -0.218 -0.049 0.585 -7.841 -10.107 -2.169 18 C_U10:A3_D C 10 ? D 3 ? 20 1 1 C C 11 1_555 D G 2 1_555 0.097 -0.062 0.013 10.612 -19.248 -0.015 19 C_C11:G2_D C 11 ? D 2 ? 19 1 1 C C 12 1_555 D G 1 1_555 0.097 -0.191 0.113 5.192 -10.490 -0.986 20 C_C12:G1_D C 12 ? D 1 ? 19 1 # 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 1 1_555 B C 12 1_555 A G 2 1_555 B C 11 1_555 -0.071 -1.595 2.917 -1.318 4.415 32.170 -3.515 -0.072 2.681 7.916 2.364 32.489 1 AA_G1G2:C11C12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A G 2 1_555 B C 11 1_555 A A 3 1_555 B U 10 1_555 0.463 -1.491 2.903 -1.264 3.244 28.977 -3.566 -1.156 2.701 6.454 2.514 29.181 2 AA_G2A3:U10C11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A A 3 1_555 B U 10 1_555 A U 5 1_555 B A 8 1_555 -0.030 -3.564 6.376 3.809 27.051 69.232 -4.513 0.242 4.889 22.935 -3.229 73.797 3 AA_A3U5:A8U10_BB A 3 ? B 10 ? A 5 ? B 8 ? 1 A U 5 1_555 B A 8 1_555 A C 6 1_555 B G 7 1_555 -0.239 -1.996 2.860 0.842 10.230 27.777 -5.576 0.606 2.006 20.445 -1.684 29.577 4 AA_U5C6:G7A8_BB A 5 ? B 8 ? A 6 ? B 7 ? 1 A C 6 1_555 B G 7 1_555 A G 7 1_555 B C 6 1_555 -0.364 -1.654 3.119 -1.634 10.815 32.297 -4.338 0.393 2.468 18.783 2.838 34.052 5 AA_C6G7:C6G7_BB A 6 ? B 7 ? A 7 ? B 6 ? 1 A G 7 1_555 B C 6 1_555 A A 8 1_555 B U 5 1_555 0.372 -1.739 3.185 3.654 10.741 29.068 -5.062 -0.072 2.432 20.444 -6.954 31.159 6 AA_G7A8:U5C6_BB A 7 ? B 6 ? A 8 ? B 5 ? 1 A A 8 1_555 B U 5 1_555 A U 10 1_555 B A 3 1_555 0.094 -2.634 6.507 -4.796 21.693 67.718 -3.700 -0.397 5.539 18.955 4.190 70.854 7 AA_A8U10:A3U5_BB A 8 ? B 5 ? A 10 ? B 3 ? 1 A U 10 1_555 B A 3 1_555 A C 11 1_555 B G 2 1_555 -0.049 -1.695 2.765 5.842 6.678 27.701 -4.529 1.105 2.246 13.515 -11.823 29.061 8 AA_U10C11:G2A3_BB A 10 ? B 3 ? A 11 ? B 2 ? 1 A C 11 1_555 B G 2 1_555 A C 12 1_555 B G 1 1_555 0.385 -1.339 3.353 2.034 7.214 34.588 -3.256 -0.337 3.038 11.960 -3.373 35.366 9 AA_C11C12:G1G2_BB A 11 ? B 2 ? A 12 ? B 1 ? 1 C G 1 1_555 D C 12 1_555 C G 2 1_555 D C 11 1_555 0.067 -1.440 2.936 -8.403 8.613 36.425 -3.111 -0.997 2.470 13.338 13.014 38.297 10 CC_G1G2:C11C12_DD C 1 ? D 12 ? C 2 ? D 11 ? 1 C G 2 1_555 D C 11 1_555 C A 3 1_555 D U 10 1_555 0.249 -1.652 3.270 3.091 6.018 29.648 -4.303 0.116 2.896 11.572 -5.943 30.393 11 CC_G2A3:U10C11_DD C 2 ? D 11 ? C 3 ? D 10 ? 1 C A 3 1_555 D U 10 1_555 C U 5 1_555 D A 8 1_555 -0.342 -2.896 6.075 -4.111 23.253 67.331 -3.907 0.046 4.987 20.345 3.597 70.889 12 CC_A3U5:A8U10_DD C 3 ? D 10 ? C 5 ? D 8 ? 1 C U 5 1_555 D A 8 1_555 C C 6 1_555 D G 7 1_555 0.137 -1.527 3.192 3.282 8.195 29.322 -4.382 0.336 2.677 15.745 -6.306 30.594 13 CC_U5C6:G7A8_DD C 5 ? D 8 ? C 6 ? D 7 ? 1 C C 6 1_555 D G 7 1_555 C G 7 1_555 D C 6 1_555 0.333 -1.363 3.160 2.733 13.923 30.070 -4.456 -0.178 2.339 25.150 -4.936 33.179 14 CC_C6G7:C6G7_DD C 6 ? D 7 ? C 7 ? D 6 ? 1 C G 7 1_555 D C 6 1_555 C A 8 1_555 D U 5 1_555 -0.033 -1.700 3.058 -3.432 10.489 29.340 -4.834 -0.490 2.317 19.845 6.494 31.304 15 CC_G7A8:U5C6_DD C 7 ? D 6 ? C 8 ? D 5 ? 1 C A 8 1_555 D U 5 1_555 C U 10 1_555 D A 3 1_555 -0.064 -2.970 6.349 -1.745 21.652 70.997 -3.737 -0.048 5.384 18.225 1.469 73.827 16 CC_A8U10:A3U5_DD C 8 ? D 5 ? C 10 ? D 3 ? 1 C U 10 1_555 D A 3 1_555 C C 11 1_555 D G 2 1_555 0.634 -2.301 2.548 6.973 7.475 22.604 -6.944 -0.001 1.818 17.939 -16.733 24.781 17 CC_U10C11:G2A3_DD C 10 ? D 3 ? C 11 ? D 2 ? 1 C C 11 1_555 D G 2 1_555 C C 12 1_555 D G 1 1_555 -0.144 -1.810 3.358 -1.379 7.430 33.177 -4.244 0.033 2.900 12.806 2.377 34.004 18 CC_C11C12:G1G2_DD C 11 ? D 2 ? C 12 ? D 1 ? # _pdbx_audit_support.funding_organization 'Ministry of Education, Culture, Sports, Science and Technology (Japan)' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number 24245037 _pdbx_audit_support.ordinal 1 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id AU _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id AU _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type other _pdbx_initial_refinement_model.source_name ? _pdbx_initial_refinement_model.details 'RNA duplex constructed using Coot' # _atom_sites.entry_id 7EDU _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.fract_transf_matrix[1][1] 0.034228 _atom_sites.fract_transf_matrix[1][2] 0.019761 _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] 0.039523 _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] 0.003879 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol AU C N O P # loop_