data_7ECJ # _entry.id 7ECJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 7ECJ pdb_00007ecj 10.2210/pdb7ecj/pdb WWPDB D_1300021140 ? ? # 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 2022-03-16 2 'Structure model' 1 1 2024-05-29 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Data collection' # 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 # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7ECJ _pdbx_database_status.recvd_initial_deposition_date 2021-03-12 _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 'Uchida, Y.' 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-A base pairs' _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 'Uchida, Y.' 2 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3') ; _entity.formula_weight 3874.232 _entity.pdbx_number_of_molecules 3 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _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 'GGACU(CBR)GAAUCC' _entity_poly.pdbx_seq_one_letter_code_can GGACUCGAAUCC _entity_poly.pdbx_strand_id A,B,C _entity_poly.pdbx_target_identifier ? # 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 CBR n 1 7 G n 1 8 A n 1 9 A 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 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 CBR 'DNA linking' n "5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 Br N3 O7 P' 386.093 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 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 CBR 6 6 6 CBR C32 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 A 9 9 9 A A 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 CBR 6 6 6 CBR C32 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 A 9 9 9 A A 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 CBR 6 6 6 CBR C32 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 A 9 9 9 A A 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 # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.17.1 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 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 7ECJ _cell.details ? _cell.formula_units_Z ? _cell.length_a 47.780 _cell.length_a_esd ? _cell.length_b 47.780 _cell.length_b_esd ? _cell.length_c 186.215 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 36 _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 7ECJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' _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 7ECJ _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 2.64 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 53.40 _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 'MPD, sodium cacodylate, spermine tetrahydrochloride, lithium nitrate' _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 EIGER X 4M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-05-25 _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 1.1 _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-1A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-1A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate 66.095 _reflns.entry_id 7ECJ _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 3.100 _reflns.d_resolution_low 46.550 _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 2674 _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 99.700 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 8.588 _reflns.pdbx_Rmerge_I_obs 0.070 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 21.510 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 0.897 _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 0.075 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 22964 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _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 3.100 3.180 ? 5.140 ? 1914 204 ? 202 99.000 ? ? ? ? 0.415 ? ? ? ? ? ? ? ? 9.475 ? ? ? ? 0.439 ? ? 1 1 0.993 ? ? 3.180 3.270 ? 7.700 ? 1557 166 ? 166 100.000 ? ? ? ? 0.229 ? ? ? ? ? ? ? ? 9.380 ? ? ? ? 0.242 ? ? 2 1 0.996 ? ? 3.270 3.370 ? 7.620 ? 1650 177 ? 177 100.000 ? ? ? ? 0.264 ? ? ? ? ? ? ? ? 9.322 ? ? ? ? 0.279 ? ? 3 1 0.995 ? ? 3.370 3.470 ? 7.390 ? 1608 181 ? 181 100.000 ? ? ? ? 0.274 ? ? ? ? ? ? ? ? 8.884 ? ? ? ? 0.291 ? ? 4 1 0.995 ? ? 3.470 3.580 ? 10.160 ? 1480 163 ? 163 100.000 ? ? ? ? 0.196 ? ? ? ? ? ? ? ? 9.080 ? ? ? ? 0.208 ? ? 5 1 0.998 ? ? 3.580 3.710 ? 11.070 ? 1497 164 ? 164 100.000 ? ? ? ? 0.185 ? ? ? ? ? ? ? ? 9.128 ? ? ? ? 0.196 ? ? 6 1 0.998 ? ? 3.710 3.850 ? 12.620 ? 1282 157 ? 157 100.000 ? ? ? ? 0.123 ? ? ? ? ? ? ? ? 8.166 ? ? ? ? 0.131 ? ? 7 1 0.998 ? ? 3.850 4.010 ? 15.640 ? 1306 163 ? 163 100.000 ? ? ? ? 0.102 ? ? ? ? ? ? ? ? 8.012 ? ? ? ? 0.109 ? ? 8 1 0.998 ? ? 4.010 4.180 ? 20.240 ? 1291 143 ? 143 100.000 ? ? ? ? 0.098 ? ? ? ? ? ? ? ? 9.028 ? ? ? ? 0.104 ? ? 9 1 0.998 ? ? 4.180 4.390 ? 23.420 ? 1330 143 ? 142 99.300 ? ? ? ? 0.091 ? ? ? ? ? ? ? ? 9.366 ? ? ? ? 0.096 ? ? 10 1 0.995 ? ? 4.390 4.630 ? 29.970 ? 1146 135 ? 134 99.300 ? ? ? ? 0.057 ? ? ? ? ? ? ? ? 8.552 ? ? ? ? 0.061 ? ? 11 1 0.999 ? ? 4.630 4.910 ? 29.270 ? 1136 135 ? 134 99.300 ? ? ? ? 0.058 ? ? ? ? ? ? ? ? 8.478 ? ? ? ? 0.062 ? ? 12 1 0.998 ? ? 4.910 5.250 ? 32.410 ? 997 127 ? 126 99.200 ? ? ? ? 0.053 ? ? ? ? ? ? ? ? 7.913 ? ? ? ? 0.056 ? ? 13 1 0.998 ? ? 5.250 5.670 ? 39.580 ? 916 109 ? 109 100.000 ? ? ? ? 0.042 ? ? ? ? ? ? ? ? 8.404 ? ? ? ? 0.045 ? ? 14 1 0.999 ? ? 5.670 6.210 ? 36.910 ? 986 115 ? 115 100.000 ? ? ? ? 0.045 ? ? ? ? ? ? ? ? 8.574 ? ? ? ? 0.048 ? ? 15 1 0.999 ? ? 6.210 6.940 ? 37.630 ? 886 105 ? 105 100.000 ? ? ? ? 0.044 ? ? ? ? ? ? ? ? 8.438 ? ? ? ? 0.046 ? ? 16 1 0.999 ? ? 6.940 8.010 ? 44.640 ? 751 97 ? 97 100.000 ? ? ? ? 0.036 ? ? ? ? ? ? ? ? 7.742 ? ? ? ? 0.038 ? ? 17 1 0.999 ? ? 8.010 9.810 ? 48.240 ? 586 78 ? 78 100.000 ? ? ? ? 0.034 ? ? ? ? ? ? ? ? 7.513 ? ? ? ? 0.036 ? ? 18 1 1.000 ? ? 9.810 13.880 ? 50.430 ? 438 72 ? 72 100.000 ? ? ? ? 0.026 ? ? ? ? ? ? ? ? 6.083 ? ? ? ? 0.029 ? ? 19 1 0.999 ? ? 13.880 46.550 ? 44.630 ? 207 47 ? 46 97.900 ? ? ? ? 0.030 ? ? ? ? ? ? ? ? 4.500 ? ? ? ? 0.034 ? ? 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 153.070 _refine.B_iso_mean 73.9224 _refine.B_iso_min 32.020 _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 7ECJ _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 3.1000 _refine.ls_d_res_low 46.5500 _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 2642 _refine.ls_number_reflns_R_free 263 _refine.ls_number_reflns_R_work 2379 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.5100 _refine.ls_percent_reflns_R_free 9.9500 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2364 _refine.ls_R_factor_R_free 0.2829 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2311 _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 1.390 _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 ? _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 22.0700 _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 0.2100 _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 3.1000 _refine_hist.d_res_low 46.5500 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 756 _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 36 _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 756 _refine_hist.pdbx_number_atoms_ligand 0 _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' 3.1000 3.9100 1242 . 123 1119 97.0000 . . . 0.3412 0.0000 0.2745 . . . . . . . 2 . . . 'X-RAY DIFFRACTION' 3.9100 46.5500 1400 . 140 1260 100.0000 . . . 0.2649 0.0000 0.2165 . . . . . . . 2 . . . # _struct.entry_id 7ECJ _struct.title 'RNA duplex containing C-A base pairs' _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 7ECJ _struct_keywords.text 'mismatch, 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 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7ECJ _struct_ref.pdbx_db_accession 7ECJ _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 7ECJ A 1 ? 12 ? 7ECJ 1 ? 12 ? 1 12 2 1 7ECJ B 1 ? 12 ? 7ECJ 1 ? 12 ? 1 12 3 1 7ECJ C 1 ? 12 ? 7ECJ 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 author_and_software_defined_assembly PISA dimeric 2 2 author_and_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)' 2240 ? 1 MORE 3 ? 1 'SSA (A^2)' 4220 ? 2 'ABSA (A^2)' 2150 ? 2 MORE 2 ? 2 'SSA (A^2)' 4370 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B 2 1,2 C # _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 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 11_555 -x+y,y,-z+1/2 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 93.1075000000 # 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 U 5 "O3'" ? ? ? 1_555 A CBR 6 P ? ? A U 5 A CBR 6 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale2 covale both ? A CBR 6 "O3'" ? ? ? 1_555 A G 7 P ? ? A CBR 6 A G 7 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale3 covale both ? B U 5 "O3'" ? ? ? 1_555 B CBR 6 P ? ? B U 5 B CBR 6 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale4 covale both ? B CBR 6 "O3'" ? ? ? 1_555 B G 7 P ? ? B CBR 6 B G 7 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale5 covale both ? C U 5 "O3'" ? ? ? 1_555 C CBR 6 P ? ? C U 5 C CBR 6 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale6 covale both ? C CBR 6 "O3'" ? ? ? 1_555 C G 7 P ? ? C CBR 6 C G 7 1_555 ? ? ? ? ? ? ? 1.615 ? ? 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 C 4 N3 ? ? ? 1_555 B A 9 N6 ? ? A C 4 B A 9 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog10 hydrog ? ? A U 5 N3 ? ? ? 1_555 B A 8 N1 ? ? A U 5 B A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U 5 O4 ? ? ? 1_555 B A 8 N6 ? ? A U 5 B A 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A CBR 6 N3 ? ? ? 1_555 B G 7 N1 ? ? A CBR 6 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A CBR 6 N4 ? ? ? 1_555 B G 7 O6 ? ? A CBR 6 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A CBR 6 O2 ? ? ? 1_555 B G 7 N2 ? ? A CBR 6 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 N1 ? ? ? 1_555 B CBR 6 N3 ? ? A G 7 B CBR 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 N2 ? ? ? 1_555 B CBR 6 O2 ? ? A G 7 B CBR 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 O6 ? ? ? 1_555 B CBR 6 N4 ? ? A G 7 B CBR 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N1 ? ? ? 1_555 B U 5 N3 ? ? A A 8 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 8 N6 ? ? ? 1_555 B U 5 O4 ? ? A A 8 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 9 N6 ? ? ? 1_555 B C 4 N3 ? ? A A 9 B C 4 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog21 hydrog ? ? A U 10 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 10 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 10 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 10 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 11 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 12 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O3'" A U 5 ? ? P A CBR 6 ? ? OP2 A CBR 6 ? ? 117.38 110.50 6.88 1.10 Y 2 1 C6 B C 4 ? ? N1 B C 4 ? ? C2 B C 4 ? ? 117.63 120.30 -2.67 0.40 N 3 1 N1 B C 4 ? ? C2 B C 4 ? ? N3 B C 4 ? ? 123.57 119.20 4.37 0.70 N 4 1 C5 B G 7 ? ? C6 B G 7 ? ? N1 B G 7 ? ? 114.54 111.50 3.04 0.50 N 5 1 N1 B G 7 ? ? C6 B G 7 ? ? O6 B G 7 ? ? 114.67 119.90 -5.23 0.60 N 6 1 "O5'" B C 11 ? ? P B C 11 ? ? OP2 B C 11 ? ? 100.01 105.70 -5.69 0.90 N # _pdbx_entry_details.entry_id 7ECJ _pdbx_entry_details.has_ligand_of_interest N _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 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 CBR BR BR N N 73 CBR P P N N 74 CBR OP1 O N N 75 CBR OP2 O N N 76 CBR "O5'" O N N 77 CBR N1 N N N 78 CBR C6 C N N 79 CBR C2 C N N 80 CBR O2 O N N 81 CBR N3 N N N 82 CBR C4 C N N 83 CBR N4 N N N 84 CBR C5 C N N 85 CBR "C2'" C N N 86 CBR "C5'" C N N 87 CBR "C4'" C N R 88 CBR "O4'" O N N 89 CBR "C1'" C N R 90 CBR "C3'" C N S 91 CBR "O3'" O N N 92 CBR OP3 O N N 93 CBR HOP2 H N N 94 CBR H6 H N N 95 CBR H41 H N N 96 CBR H42 H N N 97 CBR "H2'" H N N 98 CBR "H2''" H N N 99 CBR "H5'" H N N 100 CBR "H5''" H N N 101 CBR "H4'" H N N 102 CBR "H1'" H N N 103 CBR "H3'" H N N 104 CBR "HO3'" H N N 105 CBR HOP3 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 U OP3 O N N 145 U P P N N 146 U OP1 O N N 147 U OP2 O N N 148 U "O5'" O N N 149 U "C5'" C N N 150 U "C4'" C N R 151 U "O4'" O N N 152 U "C3'" C N S 153 U "O3'" O N N 154 U "C2'" C N R 155 U "O2'" O N N 156 U "C1'" C N R 157 U N1 N N N 158 U C2 C N N 159 U O2 O N N 160 U N3 N N N 161 U C4 C N N 162 U O4 O N N 163 U C5 C N N 164 U C6 C N N 165 U HOP3 H N N 166 U HOP2 H N N 167 U "H5'" H N N 168 U "H5''" H N N 169 U "H4'" H N N 170 U "H3'" H N N 171 U "HO3'" H N N 172 U "H2'" H N N 173 U "HO2'" H N N 174 U "H1'" H N N 175 U H3 H N N 176 U H5 H N N 177 U H6 H N N 178 # 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 CBR BR C5 sing N N 76 CBR P OP1 doub N N 77 CBR P OP2 sing N N 78 CBR P "O5'" sing N N 79 CBR P OP3 sing N N 80 CBR OP2 HOP2 sing N N 81 CBR "O5'" "C5'" sing N N 82 CBR N1 C6 sing N N 83 CBR N1 C2 sing N N 84 CBR N1 "C1'" sing N N 85 CBR C6 C5 doub N N 86 CBR C6 H6 sing N N 87 CBR C2 O2 doub N N 88 CBR C2 N3 sing N N 89 CBR N3 C4 doub N N 90 CBR C4 N4 sing N N 91 CBR C4 C5 sing N N 92 CBR N4 H41 sing N N 93 CBR N4 H42 sing N N 94 CBR "C2'" "C1'" sing N N 95 CBR "C2'" "C3'" sing N N 96 CBR "C2'" "H2'" sing N N 97 CBR "C2'" "H2''" sing N N 98 CBR "C5'" "C4'" sing N N 99 CBR "C5'" "H5'" sing N N 100 CBR "C5'" "H5''" sing N N 101 CBR "C4'" "O4'" sing N N 102 CBR "C4'" "C3'" sing N N 103 CBR "C4'" "H4'" sing N N 104 CBR "O4'" "C1'" sing N N 105 CBR "C1'" "H1'" sing N N 106 CBR "C3'" "O3'" sing N N 107 CBR "C3'" "H3'" sing N N 108 CBR "O3'" "HO3'" sing N N 109 CBR OP3 HOP3 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 U OP3 P sing N N 151 U OP3 HOP3 sing N N 152 U P OP1 doub N N 153 U P OP2 sing N N 154 U P "O5'" sing N N 155 U OP2 HOP2 sing N N 156 U "O5'" "C5'" sing N N 157 U "C5'" "C4'" sing N N 158 U "C5'" "H5'" sing N N 159 U "C5'" "H5''" sing N N 160 U "C4'" "O4'" sing N N 161 U "C4'" "C3'" sing N N 162 U "C4'" "H4'" sing N N 163 U "O4'" "C1'" sing N N 164 U "C3'" "O3'" sing N N 165 U "C3'" "C2'" sing N N 166 U "C3'" "H3'" sing N N 167 U "O3'" "HO3'" sing N N 168 U "C2'" "O2'" sing N N 169 U "C2'" "C1'" sing N N 170 U "C2'" "H2'" sing N N 171 U "O2'" "HO2'" sing N N 172 U "C1'" N1 sing N N 173 U "C1'" "H1'" sing N N 174 U N1 C2 sing N N 175 U N1 C6 sing N N 176 U C2 O2 doub N N 177 U C2 N3 sing N N 178 U N3 C4 sing N N 179 U N3 H3 sing N N 180 U C4 O4 doub N N 181 U C4 C5 sing N N 182 U C5 C6 doub N N 183 U C5 H5 sing N N 184 U C6 H6 sing N N 185 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7ECJ 'double helix' 7ECJ '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 -0.133 -0.211 -0.026 -9.591 -1.430 -0.290 1 A_G1:C12_B A 1 ? B 12 ? 19 1 1 A G 2 1_555 B C 11 1_555 0.168 -0.294 0.019 0.496 -4.652 4.555 2 A_G2:C11_B A 2 ? B 11 ? 19 1 1 A A 3 1_555 B U 10 1_555 1.016 -0.229 0.092 8.657 -7.258 -3.393 3 A_A3:U10_B A 3 ? B 10 ? 20 1 1 A C 4 1_555 B A 9 1_555 1.866 -0.598 0.174 -8.216 -10.225 -3.780 4 A_C4:A9_B A 4 ? B 9 ? ? 1 1 A U 5 1_555 B A 8 1_555 -0.068 -0.225 0.277 -6.663 -7.994 1.714 5 A_U5:A8_B A 5 ? B 8 ? 20 1 1 A CBR 6 1_555 B G 7 1_555 -0.292 -0.158 -0.015 3.427 -13.998 1.111 6 A_CBR6:G7_B A 6 ? B 7 ? 19 1 1 A G 7 1_555 B CBR 6 1_555 0.305 -0.089 -0.218 -5.709 -9.557 -0.851 7 A_G7:CBR6_B A 7 ? B 6 ? 19 1 1 A A 8 1_555 B U 5 1_555 0.242 -0.043 -0.463 -9.722 -9.619 -0.822 8 A_A8:U5_B A 8 ? B 5 ? 20 1 1 A A 9 1_555 B C 4 1_555 -1.611 -0.354 -0.725 -2.503 -23.134 19.161 9 A_A9:C4_B A 9 ? B 4 ? ? 1 1 A U 10 1_555 B A 3 1_555 0.123 0.011 -0.222 10.317 -7.756 -1.352 10 A_U10:A3_B A 10 ? B 3 ? 20 1 1 A C 11 1_555 B G 2 1_555 0.401 -0.044 -0.266 2.435 -12.484 -8.270 11 A_C11:G2_B A 11 ? B 2 ? 19 1 1 A C 12 1_555 B G 1 1_555 0.467 -0.109 0.150 8.014 -3.466 1.455 12 A_C12:G1_B A 12 ? B 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 0.287 -1.443 2.988 1.701 0.337 37.143 -2.305 -0.243 2.985 0.529 -2.669 37.182 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 -0.125 -1.846 3.021 1.981 3.011 32.603 -3.734 0.527 2.832 5.343 -3.515 32.796 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 C 4 1_555 B A 9 1_555 0.619 -1.711 3.559 5.093 12.816 34.422 -4.444 -0.281 2.826 20.659 -8.209 37.004 3 AA_A3C4:A9U10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A C 4 1_555 B A 9 1_555 A U 5 1_555 B A 8 1_555 -0.655 -2.157 2.800 0.940 17.355 24.008 -6.608 1.412 1.014 36.259 -1.963 29.564 4 AA_C4U5:A8A9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A U 5 1_555 B A 8 1_555 A CBR 6 1_555 B G 7 1_555 -0.313 -1.667 2.990 1.996 8.737 26.166 -5.254 1.058 2.294 18.617 -4.253 27.633 5 AA_U5CBR6:G7A8_BB A 5 ? B 8 ? A 6 ? B 7 ? 1 A CBR 6 1_555 B G 7 1_555 A G 7 1_555 B CBR 6 1_555 0.624 -1.417 3.456 0.644 15.947 36.361 -3.915 -0.847 2.642 24.175 -0.977 39.601 6 AA_CBR6G7:CBR6G7_BB A 6 ? B 7 ? A 7 ? B 6 ? 1 A G 7 1_555 B CBR 6 1_555 A A 8 1_555 B U 5 1_555 -0.198 -1.888 3.423 0.587 5.759 28.310 -5.051 0.526 2.984 11.621 -1.184 28.884 7 AA_G7A8:U5CBR6_BB A 7 ? B 6 ? A 8 ? B 5 ? 1 A A 8 1_555 B U 5 1_555 A A 9 1_555 B C 4 1_555 1.198 -1.174 3.140 2.605 10.560 21.278 -5.945 -2.129 2.419 26.484 -6.534 23.868 8 AA_A8A9:C4U5_BB A 8 ? B 5 ? A 9 ? B 4 ? 1 A A 9 1_555 B C 4 1_555 A U 10 1_555 B A 3 1_555 -1.497 -0.799 3.056 -7.535 5.784 38.085 -1.855 1.365 3.135 8.699 11.333 39.209 9 AA_A9U10:A3C4_BB A 9 ? B 4 ? 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 -0.583 -1.576 3.462 2.113 9.449 29.202 -4.790 1.506 2.781 18.124 -4.052 30.732 10 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 0.483 -1.901 2.964 0.195 10.476 34.957 -4.240 -0.750 2.320 16.974 -0.315 36.447 11 AA_C11C12:G1G2_BB A 11 ? B 2 ? A 12 ? B 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 # _atom_sites.entry_id 7ECJ _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] 0.020929 _atom_sites.fract_transf_matrix[1][2] 0.012084 _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] 0.024167 _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] 0.005370 _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 BR C N O P # loop_ #