data_8HU5 # _entry.id 8HU5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _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 8HU5 pdb_00008hu5 10.2210/pdb8hu5/pdb WWPDB D_1300033721 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.details '8HIS contains the same ligand and will be submitted to the same paper.' _pdbx_database_related.db_id 8HIS _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8HU5 _pdbx_database_status.recvd_initial_deposition_date 2022-12-22 _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 'Aoyama, H.' 1 0000-0001-7915-8975 'Obika, H.' 2 0000-0002-6842-6812 'Yamaguchi, T.' 3 0000-0003-3180-0257 # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 51 _citation.language ? _citation.page_first 7749 _citation.page_last 7761 _citation.title ;Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids. ; _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkad608 _citation.pdbx_database_id_PubMed 37462081 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Yamaguchi, T.' 1 ? primary 'Horie, N.' 2 ? primary 'Aoyama, H.' 3 ? primary 'Kumagai, S.' 4 ? primary 'Obika, S.' 5 ? # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 8HU5 _cell.details ? _cell.formula_units_Z ? _cell.length_a 42.494 _cell.length_a_esd ? _cell.length_b 42.494 _cell.length_b_esd ? _cell.length_c 24.315 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8HU5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? # 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 ;DNA (5'-D(*GP*(LR6)P*GP*(BRU)P*AP*CP*AP*C)-3') ; 2630.686 1 ? ? ? ? 2 water nat water 18.015 50 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(LR6)(DG)(BRU)(DA)(DC)(DA)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GXGUACAC _entity_poly.pdbx_strand_id A _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 DG n 1 2 LR6 n 1 3 DG n 1 4 BRU n 1 5 DA n 1 6 DC n 1 7 DA n 1 8 DC 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 8 _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 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 8HU5 _struct_ref.pdbx_db_accession 8HU5 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 8HU5 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 8HU5 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 8 # 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 BRU 'DNA linking' n "5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O8 P' 387.078 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 HOH non-polymer . WATER ? 'H2 O' 18.015 LR6 'DNA linking' . ;[(1R,3R,4R,7S)-5-(N'-tert-butyl-N-methyl-carbamimidoyl)-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-oxidanyl-2-oxa-5-azabicyclo[2.2.1]heptan-1-yl]methyl dihydrogen phosphate ; ? 'C17 H28 N5 O8 P' 461.407 # _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 8HU5 _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 2.11 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 41.69 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040M Sodium cacodylate trihydrate pH 6.0, 0.012M Spermine tetrahydrochloride, 0.012M Sodium chloride, 0.080M Potassium chloride ; _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293.15 # _diffrn.ambient_environment ? _diffrn.ambient_temp 90 _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 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2019-06-26 _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 0.9199 _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 'SPRING-8 BEAMLINE BL44XU' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9199 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL44XU _diffrn_source.pdbx_synchrotron_site SPring-8 # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 8HU5 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 0.93 _reflns.d_resolution_low 21.1 _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 27813 _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 97.7 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.56 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 15.97 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.09 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.99 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.083 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # 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_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_redundancy_anomalous _reflns_shell.pdbx_CC_half_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_percent_possible_anomalous 0.93 0.99 ? ? ? ? ? ? 3969 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.281 ? ? 1 1 0.9259999999999999 ? ? ? ? 0.237 ? ? ? ? ? ? ? ? ? 0.99 1.06 ? ? ? ? ? ? 4352 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.159 ? ? 2 1 0.988 ? ? ? ? 0.147 ? ? ? ? ? ? ? ? ? 1.06 1.14 ? ? ? ? ? ? 4016 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.106 ? ? 3 1 0.9940000000000001 ? ? ? ? 0.099 ? ? ? ? ? ? ? ? ? 1.14 1.25 ? ? ? ? ? ? 3685 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.08800000000000001 ? ? 4 1 0.996 ? ? ? ? 0.081 ? ? ? ? ? ? ? ? ? 1.25 1.4 ? ? ? ? ? ? 3349 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.086 ? ? 5 1 0.996 ? ? ? ? 0.08 ? ? ? ? ? ? ? ? ? 1.40 1.61 ? ? ? ? ? ? 2961 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.081 ? ? 6 1 0.997 ? ? ? ? 0.075 ? ? ? ? ? ? ? ? ? 1.61 1.97 ? ? ? ? ? ? 2493 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.07200000000000001 ? ? 7 1 0.997 ? ? ? ? 0.067 ? ? ? ? ? ? ? ? ? 1.97 2.77 ? ? ? ? ? ? 1931 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.079 ? ? 8 1 0.992 ? ? ? ? 0.073 ? ? ? ? ? ? ? ? ? 2.77 10 ? ? ? ? ? ? 1057 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.115 ? ? 9 1 0.977 ? ? ? ? 0.10300000000000001 ? ? ? ? ? ? ? ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8HU5 _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 0.93 _refine.ls_d_res_low 21.10 _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 27813 _refine.ls_number_reflns_R_free 2778 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 97.73 _refine.ls_percent_reflns_R_free 9.99 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1944 _refine.ls_R_factor_R_free 0.2134 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1923 _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 1.41 _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 SAD _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 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 22.27 _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 0.11 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 0.93 _refine_hist.d_res_low 21.10 _refine_hist.number_atoms_solvent 51 _refine_hist.number_atoms_total 222 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 171 _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_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.008 ? 191 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 2.399 ? 296 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 23.321 ? 85 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.088 ? 31 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.017 ? 10 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 0.93 0.95 . . 87 794 62.00 . . . . 0.3031 . . . . . . . . . . . 0.2761 'X-RAY DIFFRACTION' 0.95 0.96 . . 138 1241 95.00 . . . . 0.2928 . . . . . . . . . . . 0.3228 'X-RAY DIFFRACTION' 0.96 0.98 . . 135 1272 99.00 . . . . 0.2793 . . . . . . . . . . . 0.2963 'X-RAY DIFFRACTION' 0.98 1.00 . . 144 1263 100.00 . . . . 0.2508 . . . . . . . . . . . 0.2956 'X-RAY DIFFRACTION' 1.00 1.03 . . 144 1272 100.00 . . . . 0.2422 . . . . . . . . . . . 0.2460 'X-RAY DIFFRACTION' 1.03 1.05 . . 138 1293 100.00 . . . . 0.2468 . . . . . . . . . . . 0.3015 'X-RAY DIFFRACTION' 1.05 1.08 . . 142 1278 100.00 . . . . 0.2342 . . . . . . . . . . . 0.2676 'X-RAY DIFFRACTION' 1.08 1.10 . . 143 1275 100.00 . . . . 0.2303 . . . . . . . . . . . 0.2418 'X-RAY DIFFRACTION' 1.10 1.14 . . 141 1299 100.00 . . . . 0.2141 . . . . . . . . . . . 0.2669 'X-RAY DIFFRACTION' 1.14 1.17 . . 145 1265 100.00 . . . . 0.2084 . . . . . . . . . . . 0.2211 'X-RAY DIFFRACTION' 1.17 1.22 . . 140 1290 100.00 . . . . 0.2044 . . . . . . . . . . . 0.2337 'X-RAY DIFFRACTION' 1.22 1.26 . . 137 1274 100.00 . . . . 0.1945 . . . . . . . . . . . 0.1970 'X-RAY DIFFRACTION' 1.26 1.32 . . 148 1287 100.00 . . . . 0.1988 . . . . . . . . . . . 0.1972 'X-RAY DIFFRACTION' 1.32 1.39 . . 142 1262 100.00 . . . . 0.2036 . . . . . . . . . . . 0.2211 'X-RAY DIFFRACTION' 1.39 1.48 . . 143 1285 100.00 . . . . 0.1981 . . . . . . . . . . . 0.2298 'X-RAY DIFFRACTION' 1.48 1.59 . . 140 1283 100.00 . . . . 0.1851 . . . . . . . . . . . 0.2032 'X-RAY DIFFRACTION' 1.59 1.75 . . 146 1291 100.00 . . . . 0.1556 . . . . . . . . . . . 0.1800 'X-RAY DIFFRACTION' 1.75 2.01 . . 144 1275 100.00 . . . . 0.1712 . . . . . . . . . . . 0.1896 'X-RAY DIFFRACTION' 2.01 2.53 . . 136 1276 100.00 . . . . 0.1814 . . . . . . . . . . . 0.2162 'X-RAY DIFFRACTION' 2.53 10 . . 145 1260 98.00 . . . . 0.1846 . . . . . . . . . . . 0.1995 # _struct.entry_id 8HU5 _struct.title 'Crystal structure of DNA octamer containing GuNA[Me,tBu]' _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 8HU5 _struct_keywords.text 'DNA, OLIGONUCLEOTIDE, MODIFIED BASE, Artificial nucleic acid' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # 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 DG 1 "O3'" ? ? ? 1_555 A LR6 2 P ? ? A DG 1 A LR6 2 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale both ? A LR6 2 "O3'" ? ? ? 1_555 A DG 3 P ? ? A LR6 2 A DG 3 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale3 covale both ? A DG 3 "O3'" ? ? ? 1_555 A BRU 4 P ? ? A DG 3 A BRU 4 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale4 covale both ? A BRU 4 "O3'" ? ? ? 1_555 A DA 5 P ? ? A BRU 4 A DA 5 1_555 ? ? ? ? ? ? ? 1.598 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 1 A DC 8 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 1 A DC 8 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 1 A DC 8 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 6 N3 ? ? A DG 3 A DC 6 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 6 O2 ? ? A DG 3 A DC 6 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 6 N4 ? ? A DG 3 A DC 6 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A BRU 4 N3 ? ? ? 1_555 A DA 5 N1 ? ? A BRU 4 A DA 5 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A BRU 4 O4 ? ? ? 1_555 A DA 5 N6 ? ? A BRU 4 A DA 5 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 5 N1 ? ? ? 1_555 A BRU 4 N3 ? ? A DA 5 A BRU 4 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A BRU 4 O4 ? ? A DA 5 A BRU 4 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 6 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 6 A DG 3 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 6 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 6 A DG 3 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 6 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 6 A DG 3 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 1 N1 ? ? A DC 8 A DG 1 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 8 A DG 1 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 1 N2 ? ? A DC 8 A DG 1 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 8HU5 _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] 0.023533 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.023533 _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] 0.041127 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol BR C N O P # 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 DG 1 1 1 DG DG A . n A 1 2 LR6 2 2 2 LR6 LR6 A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 BRU 4 4 4 BRU BRU A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DC 6 6 6 DC DC A . n A 1 7 DA 7 7 7 DA DA A . n A 1 8 DC 8 8 8 DC DC A . n # loop_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 2 obika@phs.osaka-u.ac.jp Satoshi Obika ? 'principal investigator/group leader' 0000-0002-6842-6812 3 yamaguchi-ta@phs.osaka-u.ac.jp Takao Yamaguchi ? 'principal investigator/group leader' 0000-0003-3180-0257 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HOH 1 101 40 HOH HOH A . B 2 HOH 2 102 47 HOH HOH A . B 2 HOH 3 103 42 HOH HOH A . B 2 HOH 4 104 11 HOH HOH A . B 2 HOH 5 105 31 HOH HOH A . B 2 HOH 6 106 26 HOH HOH A . B 2 HOH 7 107 18 HOH HOH A . B 2 HOH 8 108 17 HOH HOH A . B 2 HOH 9 109 24 HOH HOH A . B 2 HOH 10 110 29 HOH HOH A . B 2 HOH 11 111 37 HOH HOH A . B 2 HOH 12 112 19 HOH HOH A . B 2 HOH 13 113 32 HOH HOH A . B 2 HOH 14 114 39 HOH HOH A . B 2 HOH 15 115 23 HOH HOH A . B 2 HOH 16 116 14 HOH HOH A . B 2 HOH 17 117 4 HOH HOH A . B 2 HOH 18 118 6 HOH HOH A . B 2 HOH 19 119 43 HOH HOH A . B 2 HOH 20 120 12 HOH HOH A . B 2 HOH 21 121 25 HOH HOH A . B 2 HOH 22 122 8 HOH HOH A . B 2 HOH 23 123 5 HOH HOH A . B 2 HOH 24 124 22 HOH HOH A . B 2 HOH 25 125 3 HOH HOH A . B 2 HOH 26 126 21 HOH HOH A . B 2 HOH 27 127 1 HOH HOH A . B 2 HOH 28 128 30 HOH HOH A . B 2 HOH 29 129 7 HOH HOH A . B 2 HOH 30 130 15 HOH HOH A . B 2 HOH 31 131 28 HOH HOH A . B 2 HOH 32 132 10 HOH HOH A . B 2 HOH 33 133 35 HOH HOH A . B 2 HOH 34 134 27 HOH HOH A . B 2 HOH 35 135 20 HOH HOH A . B 2 HOH 36 136 16 HOH HOH A . B 2 HOH 37 137 9 HOH HOH A . B 2 HOH 38 138 13 HOH HOH A . B 2 HOH 39 139 44 HOH HOH A . B 2 HOH 40 140 46 HOH HOH A . B 2 HOH 41 141 33 HOH HOH A . B 2 HOH 42 142 36 HOH HOH A . B 2 HOH 43 143 2 HOH HOH A . B 2 HOH 44 144 51 HOH HOH A . B 2 HOH 45 145 49 HOH HOH A . B 2 HOH 46 146 48 HOH HOH A . B 2 HOH 47 147 38 HOH HOH A . B 2 HOH 48 148 34 HOH HOH A . B 2 HOH 49 149 50 HOH HOH A . B 2 HOH 50 150 45 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B # 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)' 2030 ? 1 MORE 10 ? 1 'SSA (A^2)' 2900 ? # 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' 8_665 -y+1,-x+1,-z+1/2 0.0000000000 -1.0000000000 0.0000000000 42.4940000000 -1.0000000000 0.0000000000 0.0000000000 42.4940000000 0.0000000000 0.0000000000 -1.0000000000 12.1575000000 # 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 2023-08-09 2 'Structure model' 1 1 2023-09-06 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' citation 4 2 'Structure model' citation_author # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation.title' 5 2 'Structure model' '_citation_author.identifier_ORCID' # _pdbx_refine_tls.id 1 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 32.3033 _pdbx_refine_tls.origin_y 8.7428 _pdbx_refine_tls.origin_z 3.6578 _pdbx_refine_tls.T[1][1] 0.0966 _pdbx_refine_tls.T[1][1]_esd ? _pdbx_refine_tls.T[1][2] 0.0064 _pdbx_refine_tls.T[1][2]_esd ? _pdbx_refine_tls.T[1][3] 0.0010 _pdbx_refine_tls.T[1][3]_esd ? _pdbx_refine_tls.T[2][2] 0.0867 _pdbx_refine_tls.T[2][2]_esd ? _pdbx_refine_tls.T[2][3] -0.0018 _pdbx_refine_tls.T[2][3]_esd ? _pdbx_refine_tls.T[3][3] 0.0760 _pdbx_refine_tls.T[3][3]_esd ? _pdbx_refine_tls.L[1][1] 1.3772 _pdbx_refine_tls.L[1][1]_esd ? _pdbx_refine_tls.L[1][2] 0.8143 _pdbx_refine_tls.L[1][2]_esd ? _pdbx_refine_tls.L[1][3] 0.2878 _pdbx_refine_tls.L[1][3]_esd ? _pdbx_refine_tls.L[2][2] 2.3202 _pdbx_refine_tls.L[2][2]_esd ? _pdbx_refine_tls.L[2][3] -0.0906 _pdbx_refine_tls.L[2][3]_esd ? _pdbx_refine_tls.L[3][3] 0.6077 _pdbx_refine_tls.L[3][3]_esd ? _pdbx_refine_tls.S[1][1] -0.0083 _pdbx_refine_tls.S[1][1]_esd ? _pdbx_refine_tls.S[1][2] 0.1349 _pdbx_refine_tls.S[1][2]_esd ? _pdbx_refine_tls.S[1][3] 0.0310 _pdbx_refine_tls.S[1][3]_esd ? _pdbx_refine_tls.S[2][1] -0.1852 _pdbx_refine_tls.S[2][1]_esd ? _pdbx_refine_tls.S[2][2] 0.0768 _pdbx_refine_tls.S[2][2]_esd ? _pdbx_refine_tls.S[2][3] 0.0455 _pdbx_refine_tls.S[2][3]_esd ? _pdbx_refine_tls.S[3][1] 0.0354 _pdbx_refine_tls.S[3][1]_esd ? _pdbx_refine_tls.S[3][2] 0.0713 _pdbx_refine_tls.S[3][2]_esd ? _pdbx_refine_tls.S[3][3] -0.0560 _pdbx_refine_tls.S[3][3]_esd ? # _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_label_asym_id ? _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.beg_auth_asym_id ? _pdbx_refine_tls_group.beg_auth_seq_id ? _pdbx_refine_tls_group.beg_PDB_ins_code ? _pdbx_refine_tls_group.end_label_asym_id ? _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id ? _pdbx_refine_tls_group.end_auth_seq_id ? _pdbx_refine_tls_group.end_PDB_ins_code ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details ;chain 'A' and (resid 1 through 8 ) ; # 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 ? ? ? 1.20-1-4487 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 3 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.25 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELXDE ? ? ? . 5 # _pdbx_entry_details.entry_id 8HU5 _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 BRU N1 N N N 1 BRU C2 C N N 2 BRU N3 N N N 3 BRU C4 C N N 4 BRU C5 C N N 5 BRU C6 C N N 6 BRU O2 O N N 7 BRU O4 O N N 8 BRU BR BR N N 9 BRU "C1'" C N R 10 BRU "C2'" C N N 11 BRU "C3'" C N S 12 BRU "C4'" C N R 13 BRU "O3'" O N N 14 BRU "O4'" O N N 15 BRU "C5'" C N N 16 BRU "O5'" O N N 17 BRU P P N N 18 BRU OP1 O N N 19 BRU OP2 O N N 20 BRU OP3 O N N 21 BRU HN3 H N N 22 BRU H6 H N N 23 BRU "H1'" H N N 24 BRU "H2'" H N N 25 BRU "H2''" H N N 26 BRU "H3'" H N N 27 BRU "H4'" H N N 28 BRU "HO3'" H N N 29 BRU "H5'" H N N 30 BRU "H5''" H N N 31 BRU HOP2 H N N 32 BRU HOP3 H N N 33 DA OP3 O N N 34 DA P P N N 35 DA OP1 O N N 36 DA OP2 O N N 37 DA "O5'" O N N 38 DA "C5'" C N N 39 DA "C4'" C N R 40 DA "O4'" O N N 41 DA "C3'" C N S 42 DA "O3'" O N N 43 DA "C2'" C N N 44 DA "C1'" C N R 45 DA N9 N Y N 46 DA C8 C Y N 47 DA N7 N Y N 48 DA C5 C Y N 49 DA C6 C Y N 50 DA N6 N N N 51 DA N1 N Y N 52 DA C2 C Y N 53 DA N3 N Y N 54 DA C4 C Y N 55 DA HOP3 H N N 56 DA HOP2 H N N 57 DA "H5'" H N N 58 DA "H5''" H N N 59 DA "H4'" H N N 60 DA "H3'" H N N 61 DA "HO3'" H N N 62 DA "H2'" H N N 63 DA "H2''" H N N 64 DA "H1'" H N N 65 DA H8 H N N 66 DA H61 H N N 67 DA H62 H N N 68 DA H2 H N N 69 DC OP3 O N N 70 DC P P N N 71 DC OP1 O N N 72 DC OP2 O N N 73 DC "O5'" O N N 74 DC "C5'" C N N 75 DC "C4'" C N R 76 DC "O4'" O N N 77 DC "C3'" C N S 78 DC "O3'" O N N 79 DC "C2'" C N N 80 DC "C1'" C N R 81 DC N1 N N N 82 DC C2 C N N 83 DC O2 O N N 84 DC N3 N N N 85 DC C4 C N N 86 DC N4 N N N 87 DC C5 C N N 88 DC C6 C N N 89 DC HOP3 H N N 90 DC HOP2 H N N 91 DC "H5'" H N N 92 DC "H5''" H N N 93 DC "H4'" H N N 94 DC "H3'" H N N 95 DC "HO3'" H N N 96 DC "H2'" H N N 97 DC "H2''" H N N 98 DC "H1'" H N N 99 DC H41 H N N 100 DC H42 H N N 101 DC H5 H N N 102 DC H6 H N N 103 DG OP3 O N N 104 DG P P N N 105 DG OP1 O N N 106 DG OP2 O N N 107 DG "O5'" O N N 108 DG "C5'" C N N 109 DG "C4'" C N R 110 DG "O4'" O N N 111 DG "C3'" C N S 112 DG "O3'" O N N 113 DG "C2'" C N N 114 DG "C1'" C N R 115 DG N9 N Y N 116 DG C8 C Y N 117 DG N7 N Y N 118 DG C5 C Y N 119 DG C6 C N N 120 DG O6 O N N 121 DG N1 N N N 122 DG C2 C N N 123 DG N2 N N N 124 DG N3 N N N 125 DG C4 C Y N 126 DG HOP3 H N N 127 DG HOP2 H N N 128 DG "H5'" H N N 129 DG "H5''" H N N 130 DG "H4'" H N N 131 DG "H3'" H N N 132 DG "HO3'" H N N 133 DG "H2'" H N N 134 DG "H2''" H N N 135 DG "H1'" H N N 136 DG H8 H N N 137 DG H1 H N N 138 DG H21 H N N 139 DG H22 H N N 140 HOH O O N N 141 HOH H1 H N N 142 HOH H2 H N N 143 LR6 C2 C N N 144 LR6 C4 C N N 145 LR6 C5 C N N 146 LR6 C6 C N N 147 LR6 N1 N N N 148 LR6 N3 N N N 149 LR6 CD C N N 150 LR6 "C1'" C N R 151 LR6 "C2'" C N R 152 LR6 "C3'" C N S 153 LR6 "C4'" C N R 154 LR6 "C5'" C N N 155 LR6 C5M C N N 156 LR6 "C6'" C N N 157 LR6 "C7'" C N N 158 LR6 "C8'" C N N 159 LR6 "C9'" C N N 160 LR6 "N2'" N N N 161 LR6 "N3'" N N N 162 LR6 "N4'" N N N 163 LR6 O2 O N N 164 LR6 "O3'" O N N 165 LR6 O4 O N N 166 LR6 "O4'" O N N 167 LR6 "O5'" O N N 168 LR6 OP1 O N N 169 LR6 OP2 O N N 170 LR6 P P N N 171 LR6 "C10'" C N N 172 LR6 "C11'" C N N 173 LR6 H1 H N N 174 LR6 H2 H N N 175 LR6 H3 H N N 176 LR6 H4 H N N 177 LR6 H5 H N N 178 LR6 H6 H N N 179 LR6 H7 H N N 180 LR6 H8 H N N 181 LR6 H9 H N N 182 LR6 H10 H N N 183 LR6 H11 H N N 184 LR6 H12 H N N 185 LR6 H13 H N N 186 LR6 H14 H N N 187 LR6 H15 H N N 188 LR6 H16 H N N 189 LR6 H17 H N N 190 LR6 H18 H N N 191 LR6 H19 H N N 192 LR6 "HO3'" H N N 193 LR6 HOP2 H N N 194 LR6 H23 H N N 195 LR6 H24 H N N 196 LR6 H25 H N N 197 LR6 H26 H N N 198 LR6 H27 H N N 199 LR6 H28 H N N 200 LR6 OP3 O N N 201 LR6 HOP3 H N N 202 # 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 BRU N1 C2 sing N N 1 BRU N1 C6 sing N N 2 BRU N1 "C1'" sing N N 3 BRU C2 N3 sing N N 4 BRU C2 O2 doub N N 5 BRU N3 C4 sing N N 6 BRU N3 HN3 sing N N 7 BRU C4 C5 sing N N 8 BRU C4 O4 doub N N 9 BRU C5 C6 doub N N 10 BRU C5 BR sing N N 11 BRU C6 H6 sing N N 12 BRU "C1'" "C2'" sing N N 13 BRU "C1'" "O4'" sing N N 14 BRU "C1'" "H1'" sing N N 15 BRU "C2'" "C3'" sing N N 16 BRU "C2'" "H2'" sing N N 17 BRU "C2'" "H2''" sing N N 18 BRU "C3'" "C4'" sing N N 19 BRU "C3'" "O3'" sing N N 20 BRU "C3'" "H3'" sing N N 21 BRU "C4'" "O4'" sing N N 22 BRU "C4'" "C5'" sing N N 23 BRU "C4'" "H4'" sing N N 24 BRU "O3'" "HO3'" sing N N 25 BRU "C5'" "O5'" sing N N 26 BRU "C5'" "H5'" sing N N 27 BRU "C5'" "H5''" sing N N 28 BRU "O5'" P sing N N 29 BRU P OP1 doub N N 30 BRU P OP2 sing N N 31 BRU P OP3 sing N N 32 BRU OP2 HOP2 sing N N 33 BRU OP3 HOP3 sing N N 34 DA OP3 P sing N N 35 DA OP3 HOP3 sing N N 36 DA P OP1 doub N N 37 DA P OP2 sing N N 38 DA P "O5'" sing N N 39 DA OP2 HOP2 sing N N 40 DA "O5'" "C5'" sing N N 41 DA "C5'" "C4'" sing N N 42 DA "C5'" "H5'" sing N N 43 DA "C5'" "H5''" sing N N 44 DA "C4'" "O4'" sing N N 45 DA "C4'" "C3'" sing N N 46 DA "C4'" "H4'" sing N N 47 DA "O4'" "C1'" sing N N 48 DA "C3'" "O3'" sing N N 49 DA "C3'" "C2'" sing N N 50 DA "C3'" "H3'" sing N N 51 DA "O3'" "HO3'" sing N N 52 DA "C2'" "C1'" sing N N 53 DA "C2'" "H2'" sing N N 54 DA "C2'" "H2''" sing N N 55 DA "C1'" N9 sing N N 56 DA "C1'" "H1'" sing N N 57 DA N9 C8 sing Y N 58 DA N9 C4 sing Y N 59 DA C8 N7 doub Y N 60 DA C8 H8 sing N N 61 DA N7 C5 sing Y N 62 DA C5 C6 sing Y N 63 DA C5 C4 doub Y N 64 DA C6 N6 sing N N 65 DA C6 N1 doub Y N 66 DA N6 H61 sing N N 67 DA N6 H62 sing N N 68 DA N1 C2 sing Y N 69 DA C2 N3 doub Y N 70 DA C2 H2 sing N N 71 DA N3 C4 sing Y N 72 DC OP3 P sing N N 73 DC OP3 HOP3 sing N N 74 DC P OP1 doub N N 75 DC P OP2 sing N N 76 DC P "O5'" sing N N 77 DC OP2 HOP2 sing N N 78 DC "O5'" "C5'" sing N N 79 DC "C5'" "C4'" sing N N 80 DC "C5'" "H5'" sing N N 81 DC "C5'" "H5''" sing N N 82 DC "C4'" "O4'" sing N N 83 DC "C4'" "C3'" sing N N 84 DC "C4'" "H4'" sing N N 85 DC "O4'" "C1'" sing N N 86 DC "C3'" "O3'" sing N N 87 DC "C3'" "C2'" sing N N 88 DC "C3'" "H3'" sing N N 89 DC "O3'" "HO3'" sing N N 90 DC "C2'" "C1'" sing N N 91 DC "C2'" "H2'" sing N N 92 DC "C2'" "H2''" sing N N 93 DC "C1'" N1 sing N N 94 DC "C1'" "H1'" sing N N 95 DC N1 C2 sing N N 96 DC N1 C6 sing N N 97 DC C2 O2 doub N N 98 DC C2 N3 sing N N 99 DC N3 C4 doub N N 100 DC C4 N4 sing N N 101 DC C4 C5 sing N N 102 DC N4 H41 sing N N 103 DC N4 H42 sing N N 104 DC C5 C6 doub N N 105 DC C5 H5 sing N N 106 DC C6 H6 sing N N 107 DG OP3 P sing N N 108 DG OP3 HOP3 sing N N 109 DG P OP1 doub N N 110 DG P OP2 sing N N 111 DG P "O5'" sing N N 112 DG OP2 HOP2 sing N N 113 DG "O5'" "C5'" sing N N 114 DG "C5'" "C4'" sing N N 115 DG "C5'" "H5'" sing N N 116 DG "C5'" "H5''" sing N N 117 DG "C4'" "O4'" sing N N 118 DG "C4'" "C3'" sing N N 119 DG "C4'" "H4'" sing N N 120 DG "O4'" "C1'" sing N N 121 DG "C3'" "O3'" sing N N 122 DG "C3'" "C2'" sing N N 123 DG "C3'" "H3'" sing N N 124 DG "O3'" "HO3'" sing N N 125 DG "C2'" "C1'" sing N N 126 DG "C2'" "H2'" sing N N 127 DG "C2'" "H2''" sing N N 128 DG "C1'" N9 sing N N 129 DG "C1'" "H1'" sing N N 130 DG N9 C8 sing Y N 131 DG N9 C4 sing Y N 132 DG C8 N7 doub Y N 133 DG C8 H8 sing N N 134 DG N7 C5 sing Y N 135 DG C5 C6 sing N N 136 DG C5 C4 doub Y N 137 DG C6 O6 doub N N 138 DG C6 N1 sing N N 139 DG N1 C2 sing N N 140 DG N1 H1 sing N N 141 DG C2 N2 sing N N 142 DG C2 N3 doub N N 143 DG N2 H21 sing N N 144 DG N2 H22 sing N N 145 DG N3 C4 sing N N 146 HOH O H1 sing N N 147 HOH O H2 sing N N 148 LR6 "C9'" "C8'" sing N N 149 LR6 "C11'" "C8'" sing N N 150 LR6 "C8'" "C10'" sing N N 151 LR6 "C8'" "N4'" sing N N 152 LR6 "C7'" "N3'" sing N N 153 LR6 "N4'" CD doub N N 154 LR6 "N3'" CD sing N N 155 LR6 CD "N2'" sing N N 156 LR6 "N2'" "C6'" sing N N 157 LR6 "N2'" "C2'" sing N N 158 LR6 "O3'" "C3'" sing N N 159 LR6 "C6'" "C4'" sing N N 160 LR6 "C2'" "C3'" sing N N 161 LR6 "C2'" "C1'" sing N N 162 LR6 "C3'" "C4'" sing N N 163 LR6 O2 C2 doub N N 164 LR6 "C1'" "O4'" sing N N 165 LR6 "C1'" N1 sing N N 166 LR6 "C4'" "O4'" sing N N 167 LR6 "C4'" "C5'" sing N N 168 LR6 C2 N1 sing N N 169 LR6 C2 N3 sing N N 170 LR6 N1 C6 sing N N 171 LR6 "C5'" "O5'" sing N N 172 LR6 N3 C4 sing N N 173 LR6 "O5'" P sing N N 174 LR6 C6 C5 doub N N 175 LR6 C4 C5 sing N N 176 LR6 C4 O4 doub N N 177 LR6 C5 C5M sing N N 178 LR6 OP1 P doub N N 179 LR6 P OP2 sing N N 180 LR6 C6 H1 sing N N 181 LR6 N3 H2 sing N N 182 LR6 "C1'" H3 sing N N 183 LR6 "C2'" H4 sing N N 184 LR6 "C3'" H5 sing N N 185 LR6 "C5'" H6 sing N N 186 LR6 "C5'" H7 sing N N 187 LR6 C5M H8 sing N N 188 LR6 C5M H9 sing N N 189 LR6 C5M H10 sing N N 190 LR6 "C6'" H11 sing N N 191 LR6 "C6'" H12 sing N N 192 LR6 "C7'" H13 sing N N 193 LR6 "C7'" H14 sing N N 194 LR6 "C7'" H15 sing N N 195 LR6 "C9'" H16 sing N N 196 LR6 "C9'" H17 sing N N 197 LR6 "C9'" H18 sing N N 198 LR6 "N3'" H19 sing N N 199 LR6 "O3'" "HO3'" sing N N 200 LR6 OP2 HOP2 sing N N 201 LR6 "C10'" H23 sing N N 202 LR6 "C10'" H24 sing N N 203 LR6 "C10'" H25 sing N N 204 LR6 "C11'" H26 sing N N 205 LR6 "C11'" H27 sing N N 206 LR6 "C11'" H28 sing N N 207 LR6 P OP3 sing N N 208 LR6 OP3 HOP3 sing N N 209 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8HU5 'double helix' 8HU5 'a-form double helix' 8HU5 'mismatched base pair' # 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 DG 1 1_555 A DC 8 8_665 -0.300 -0.207 0.029 -10.515 -11.727 -2.573 1 A_DG1:DC8_A A 1 ? A 8 ? 19 1 1 A DG 3 1_555 A DC 6 8_665 -0.261 -0.151 0.103 -8.415 -15.928 1.942 2 A_DG3:DC6_A A 3 ? A 6 ? 19 1 1 A BRU 4 1_555 A DA 5 8_665 -0.061 -0.166 0.395 -8.046 -10.166 -2.294 3 A_BRU4:DA5_A A 4 ? A 5 ? 20 1 1 A DA 5 1_555 A BRU 4 8_665 0.061 -0.166 0.395 8.046 -10.166 -2.294 4 A_DA5:BRU4_A A 5 ? A 4 ? 20 1 1 A DC 6 1_555 A DG 3 8_665 0.261 -0.151 0.103 8.415 -15.928 1.942 5 A_DC6:DG3_A A 6 ? A 3 ? 19 1 1 A DC 8 1_555 A DG 1 8_665 0.300 -0.207 0.029 10.515 -11.727 -2.573 6 A_DC8:DG1_A A 8 ? A 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 DG 1 1_555 A DC 8 8_665 A DG 3 1_555 A DC 6 8_665 1.139 -3.201 6.270 0.343 16.739 64.994 -4.099 -1.009 5.405 15.315 -0.314 66.886 1 AA_DG1DG3:DC6DC8_AA A 1 ? A 8 ? A 3 ? A 6 ? 1 A DG 3 1_555 A DC 6 8_665 A BRU 4 1_555 A DA 5 8_665 -0.567 -1.421 3.205 -2.104 0.640 37.818 -2.270 0.609 3.207 0.986 3.243 37.880 2 AA_DG3BRU4:DA5DC6_AA A 3 ? A 6 ? A 4 ? A 5 ? 1 A BRU 4 1_555 A DA 5 8_665 A DA 5 1_555 A BRU 4 8_665 0.000 -1.424 2.767 0.000 4.542 27.947 -3.766 0.000 2.509 9.327 0.000 28.306 3 AA_BRU4DA5:BRU4DA5_AA A 4 ? A 5 ? A 5 ? A 4 ? 1 A DA 5 1_555 A BRU 4 8_665 A DC 6 1_555 A DG 3 8_665 0.567 -1.421 3.205 2.104 0.640 37.818 -2.270 -0.609 3.207 0.986 -3.243 37.880 4 AA_DA5DC6:DG3BRU4_AA A 5 ? A 4 ? A 6 ? A 3 ? 1 A DC 6 1_555 A DG 3 8_665 A DC 8 1_555 A DG 1 8_665 -1.139 -3.201 6.270 -0.343 16.739 64.994 -4.099 1.009 5.405 15.315 0.314 66.886 5 AA_DC6DC8:DG1DG3_AA A 6 ? A 3 ? A 8 ? A 1 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Japan Society for the Promotion of Science (JSPS)' Japan 21K06511 1 'Japan Society for the Promotion of Science (JSPS)' Japan 20K05748 2 'Japan Agency for Medical Research and Development (AMED)' Japan JP19am0101084 3 'Japan Agency for Medical Research and Development (AMED)' Japan JP18am0301004, 4 'Japan Agency for Medical Research and Development (AMED)' Japan 19am0401003 5 'Japan Agency for Medical Research and Development (AMED)' Japan JP21ae0121022, 6 'Japan Agency for Medical Research and Development (AMED)' Japan JP21ae0121023 7 'Japan Agency for Medical Research and Development (AMED)' Japan JP21ae012102 8 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id LR6 _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id LR6 _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_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name ? _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.details ? # _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 ? #