data_7URK # _entry.id 7URK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 7URK pdb_00007urk 10.2210/pdb7urk/pdb WWPDB D_1000262971 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7URK _pdbx_database_status.recvd_initial_deposition_date 2022-04-22 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 'Sha, R.' 1 0000-0002-0807-734X 'Vecchioni, S.' 2 0000-0001-8243-650X # _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 'Self-assembling DNA tensegrity triangle motif with intercalating internal Cy3 modification' _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 'Sha, R.' 1 0000-0002-0807-734X primary 'Vecchioni, S.' 2 0000-0001-8243-650X # _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 7URK _cell.details ? _cell.formula_units_Z ? _cell.length_a 113.785 _cell.length_a_esd ? _cell.length_b 113.785 _cell.length_b_esd ? _cell.length_c 95.709 _cell.length_c_esd ? _cell.volume 1073132.723 _cell.volume_esd ? _cell.Z_PDB 9 _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 7URK _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall 'H 3' _symmetry.space_group_name_H-M 'H 3' _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*AP*GP*CP*A*(96T)P*GP*CP*CP*TP*GP*TP*A)-3') ; 4115.018 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3') ; 2082.400 1 ? ? ? ? 3 polymer syn ;DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3') ; 4302.788 1 ? ? ? ? 4 polymer syn ;DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3') ; 2724.813 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no yes '(DG)(DA)(DG)(DC)(DA)(96T)(DG)(DC)(DC)(DT)(DG)(DT)(DA)' GAGCAXGCCTGTA A ? 2 polydeoxyribonucleotide no no '(DA)(DC)(DA)(DC)(DC)(DG)(DT)' ACACCGT B ? 3 polydeoxyribonucleotide no no '(DT)(DC)(DT)(DG)(DA)(DT)(DG)(DT)(DG)(DG)(DC)(DT)(DG)(DC)' TCTGATGTGGCTGC C ? 4 polydeoxyribonucleotide no no '(DC)(DG)(DG)(DA)(DC)(DA)(DT)(DC)(DA)' CGGACATCA D ? # 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 DA n 1 3 DG n 1 4 DC n 1 5 DA n 1 6 96T n 1 7 DG n 1 8 DC n 1 9 DC n 1 10 DT n 1 11 DG n 1 12 DT n 1 13 DA n 2 1 DA n 2 2 DC n 2 3 DA n 2 4 DC n 2 5 DC n 2 6 DG n 2 7 DT n 3 1 DT n 3 2 DC n 3 3 DT n 3 4 DG n 3 5 DA n 3 6 DT n 3 7 DG n 3 8 DT n 3 9 DG n 3 10 DG n 3 11 DC n 3 12 DT n 3 13 DG n 3 14 DC n 4 1 DC n 4 2 DG n 4 3 DG n 4 4 DA n 4 5 DC n 4 6 DA n 4 7 DT n 4 8 DC n 4 9 DA n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 13 'synthetic construct' ? 32630 ? 2 1 sample 1 7 'synthetic construct' ? 32630 ? 3 1 sample 1 14 'synthetic construct' ? 32630 ? 4 1 sample 1 9 'synthetic construct' ? 32630 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 7URK 7URK ? 1 ? 1 2 PDB 7URK 7URK ? 2 ? 1 3 PDB 7URK 7URK ? 3 ? 1 4 PDB 7URK 7URK ? 4 ? 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 7URK A 1 ? 13 ? 7URK 101 ? 113 ? 101 113 2 2 7URK B 1 ? 7 ? 7URK 105 ? 111 ? 105 111 3 3 7URK C 1 ? 14 ? 7URK 101 ? 114 ? 101 114 4 4 7URK D 1 ? 9 ? 7URK 113 ? 121 ? 113 121 # 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 96T non-polymer . '3-[(2~{Z})-2-[(~{E})-3-[3,3-dimethyl-1-(3-oxidanylpropyl)indol-1-ium-2-yl]prop-2-enylidene]-3,3-dimethyl-indol-1-yl]propan-1-ol' ? 'C29 H37 N2 O2 1' 445.616 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # _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 7URK _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 8.41 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 86.36 _exptl_crystal.description rhombohedral _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 8.0 _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 '338-293 at 0.4/hr' _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '120 mM Tris, 583 mM ammonium sulfate, 37.5 mM magnesium acetate, 60 mM acetic acid, 6 mM EDTA' _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 2016-05-22 _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 1.18076 _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 'APS BEAMLINE 19-ID' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.18076 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 19-ID _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate 113.93 _reflns.entry_id 7URK _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 3.119 _reflns.d_resolution_low 34.33 _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 4656 _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 75.0 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 9.9 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 12.5 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 1.000 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _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_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 _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 3.119 3.439 ? 2.9 ? ? ? ? 233 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 1 0.857 ? ? ? ? ? ? ? ? ? ? 10.101 34.328 ? 46.4 ? ? ? ? 230 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 1.000 ? ? ? ? ? ? ? ? ? ? # _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 169.80 _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 7URK _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 3.12 _refine.ls_d_res_low 34.33 _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 4656 _refine.ls_number_reflns_R_free 458 _refine.ls_number_reflns_R_work 8849 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 56.44 _refine.ls_percent_reflns_R_free 4.92 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1551 _refine.ls_R_factor_R_free 0.1566 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1550 _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 1.92 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'PDB entry 3GBI' _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 26.1539 _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 0.1160 _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 3.12 _refine_hist.d_res_low 34.33 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 870 _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 870 _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' ? 0.0153 ? 970 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.5902 ? 1483 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0717 ? 162 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0644 ? 45 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 37.4132 ? 427 ? f_dihedral_angle_d ? ? # 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' 3.12 3.57 . . 56 666 13.18 . . . 0.3859 . 0.2750 . . . . . . . . . . . 'X-RAY DIFFRACTION' 3.57 4.50 . . 142 2978 56.89 . . . 0.3304 . 0.2959 . . . . . . . . . . . 'X-RAY DIFFRACTION' 4.50 34.33 . . 260 5205 99.22 . . . 0.1166 . 0.1275 . . . . . . . . . . . # _struct.entry_id 7URK _struct.title 'Self-assembling DNA tensegrity triangle motif with intercalating internal Cy3 modification' _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 7URK _struct_keywords.text 'Tensegrity triangle, Cy3, dye, self-assembly, DNA' _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 ? C N N 3 ? D N N 4 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale one ? A DA 5 P ? ? ? 1_555 A 96T 6 OBD ? ? A DA 105 A 96T 106 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale2 covale one ? A 96T 6 OBG ? ? ? 1_555 A DG 7 P ? ? A 96T 106 A DG 107 1_555 ? ? ? ? ? ? ? 1.623 ? ? hydrog1 hydrog ? ? A DG 3 N1 ? ? ? 1_555 C DC 14 N3 ? ? A DG 103 C DC 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 3 N2 ? ? ? 1_555 C DC 14 O2 ? ? A DG 103 C DC 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 3 O6 ? ? ? 1_555 C DC 14 N4 ? ? A DG 103 C DC 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 4 N3 ? ? ? 1_555 C DG 13 N1 ? ? A DC 104 C DG 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 4 N4 ? ? ? 1_555 C DG 13 O6 ? ? A DC 104 C DG 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 4 O2 ? ? ? 1_555 C DG 13 N2 ? ? A DC 104 C DG 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 7 N1 ? ? ? 1_555 C DC 11 N3 ? ? A DG 107 C DC 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 7 N2 ? ? ? 1_555 C DC 11 O2 ? ? A DG 107 C DC 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 7 O6 ? ? ? 1_555 C DC 11 N4 ? ? A DG 107 C DC 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 8 N3 ? ? ? 1_555 C DG 10 N1 ? ? A DC 108 C DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 8 N4 ? ? ? 1_555 C DG 10 O6 ? ? A DC 108 C DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 8 O2 ? ? ? 1_555 C DG 10 N2 ? ? A DC 108 C DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 9 N3 ? ? ? 1_555 C DG 9 N1 ? ? A DC 109 C DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 9 N4 ? ? ? 1_555 C DG 9 O6 ? ? A DC 109 C DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 9 O2 ? ? ? 1_555 C DG 9 N2 ? ? A DC 109 C DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 110 B DA 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 110 B DA 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 111 B DC 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 111 B DC 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 111 B DC 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 12 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 112 B DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DT 12 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 112 B DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? B DC 4 N3 ? ? ? 1_555 D DG 3 N1 ? ? B DC 108 D DG 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? B DC 4 N4 ? ? ? 1_555 D DG 3 O6 ? ? B DC 108 D DG 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B DC 4 O2 ? ? ? 1_555 D DG 3 N2 ? ? B DC 108 D DG 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B DC 5 N3 ? ? ? 1_555 D DG 2 N1 ? ? B DC 109 D DG 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B DC 5 N4 ? ? ? 1_555 D DG 2 O6 ? ? B DC 109 D DG 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B DC 5 O2 ? ? ? 1_555 D DG 2 N2 ? ? B DC 109 D DG 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B DG 6 N1 ? ? ? 1_555 D DC 1 N3 ? ? B DG 110 D DC 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B DG 6 N2 ? ? ? 1_555 D DC 1 O2 ? ? B DG 110 D DC 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B DG 6 O6 ? ? ? 1_555 D DC 1 N4 ? ? B DG 110 D DC 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C DT 3 N3 ? ? ? 1_555 D DA 9 N1 ? ? C DT 103 D DA 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C DT 3 O4 ? ? ? 1_555 D DA 9 N6 ? ? C DT 103 D DA 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C DG 4 N1 ? ? ? 1_555 D DC 8 N3 ? ? C DG 104 D DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C DG 4 N2 ? ? ? 1_555 D DC 8 O2 ? ? C DG 104 D DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C DG 4 O6 ? ? ? 1_555 D DC 8 N4 ? ? C DG 104 D DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C DA 5 N1 ? ? ? 1_555 D DT 7 N3 ? ? C DA 105 D DT 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C DA 5 N6 ? ? ? 1_555 D DT 7 O4 ? ? C DA 105 D DT 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C DT 6 N3 ? ? ? 1_555 D DA 6 N1 ? ? C DT 106 D DA 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C DT 6 O4 ? ? ? 1_555 D DA 6 N6 ? ? C DT 106 D DA 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C DG 7 N1 ? ? ? 1_555 D DC 5 N3 ? ? C DG 107 D DC 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C DG 7 N2 ? ? ? 1_555 D DC 5 O2 ? ? C DG 107 D DC 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C DG 7 O6 ? ? ? 1_555 D DC 5 N4 ? ? C DG 107 D DC 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C DT 8 N3 ? ? ? 1_555 D DA 4 N1 ? ? C DT 108 D DA 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C DT 8 O4 ? ? ? 1_555 D DA 4 N6 ? ? C DT 108 D DA 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 7URK _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] 0.008789 _atom_sites.fract_transf_matrix[1][2] 0.005074 _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] 0.010148 _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] 0.010448 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 6.96715 ? ? ? 11.43723 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 7.96527 ? ? ? 9.05267 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_ _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 1 101 101 DG DG A . n A 1 2 DA 2 102 102 DA DA A . n A 1 3 DG 3 103 103 DG DG A . n A 1 4 DC 4 104 104 DC DC A . n A 1 5 DA 5 105 105 DA DA A . n A 1 6 96T 6 106 106 96T 96T A . n A 1 7 DG 7 107 107 DG DG A . n A 1 8 DC 8 108 108 DC DC A . n A 1 9 DC 9 109 109 DC DC A . n A 1 10 DT 10 110 110 DT DT A . n A 1 11 DG 11 111 111 DG DG A . n A 1 12 DT 12 112 112 DT DT A . n A 1 13 DA 13 113 113 DA DA A . n B 2 1 DA 1 105 105 DA DA B . n B 2 2 DC 2 106 106 DC DC B . n B 2 3 DA 3 107 107 DA DA B . n B 2 4 DC 4 108 108 DC DC B . n B 2 5 DC 5 109 109 DC DC B . n B 2 6 DG 6 110 110 DG DG B . n B 2 7 DT 7 111 111 DT DT B . n C 3 1 DT 1 101 101 DT DT C . n C 3 2 DC 2 102 102 DC DC C . n C 3 3 DT 3 103 103 DT DT C . n C 3 4 DG 4 104 104 DG DG C . n C 3 5 DA 5 105 105 DA DA C . n C 3 6 DT 6 106 106 DT DT C . n C 3 7 DG 7 107 107 DG DG C . n C 3 8 DT 8 108 108 DT DT C . n C 3 9 DG 9 109 109 DG DG C . n C 3 10 DG 10 110 110 DG DG C . n C 3 11 DC 11 111 111 DC DC C . n C 3 12 DT 12 112 112 DT DT C . n C 3 13 DG 13 113 113 DG DG C . n C 3 14 DC 14 114 114 DC DC C . n D 4 1 DC 1 113 113 DC DC D . n D 4 2 DG 2 114 114 DG DG D . n D 4 3 DG 3 115 115 DG DG D . n D 4 4 DA 4 116 116 DA DA D . n D 4 5 DC 5 117 117 DC DC D . n D 4 6 DA 6 118 118 DA DA D . n D 4 7 DT 7 119 119 DT DT D . n D 4 8 DC 8 120 120 DC DC D . n D 4 9 DA 9 121 121 DA DA D . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email rs17@nyu.edu _pdbx_contact_author.name_first Ruojie _pdbx_contact_author.name_last Sha _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-0807-734X # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D 1 2 A,B,C,D 1 3 A,B,C,D # 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' 2_555 -y,x-y,z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # 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 2023-04-26 2 'Structure model' 1 1 2023-10-25 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' pdbx_initial_refinement_model # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y,x-y,z 3 -x+y,-x,z 4 x+1/3,y+2/3,z+2/3 5 -y+1/3,x-y+2/3,z+2/3 6 -x+y+1/3,-x+2/3,z+2/3 7 x+2/3,y+1/3,z+1/3 8 -y+2/3,x-y+1/3,z+1/3 9 -x+y+2/3,-x+1/3,z+1/3 # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined 32.300 3.977 0.140 2.02165501383 2.41149290224 1.28454696894 -0.536794489834 -0.627219475547 -0.13651585438 5.59133169302 5.29686713856 7.99591602622 5.29557362659 5.95746281683 4.9653859462 -1.14394663771 0.771240418841 -0.45719184413 1.99123483145 -0.0507854777552 -2.18037915394 -0.875059250829 -2.2791118482 0.607776657116 'X-RAY DIFFRACTION' 2 ? refined 13.038 1.613 -10.944 1.33714172772 1.96926972944 0.96948321712 -0.0277972793812 0.137637759484 -0.36080726342 8.33470324481 8.20155113507 5.33417951055 0.585955072741 0.640470288324 -6.44271308208 0.560849009458 -0.511268315093 0.0983843853805 -0.119722792806 0.548137952043 0.590221034266 -1.06189864134 0.962545549017 -0.741824895468 'X-RAY DIFFRACTION' 3 ? refined 25.008 -2.622 -12.748 1.10925229831 1.44051451386 1.68693160599 0.208542249829 -0.150643490971 -0.37851512269 8.95225271134 9.61554051703 8.47706703779 2.18264222963 1.62140543155 5.6571770328 1.5486573926 -0.479695920642 -1.07284284341 0.23424197636 -0.297506510515 -1.50235153228 -0.296632896331 0.474324583169 -0.227632031315 'X-RAY DIFFRACTION' 4 ? refined 19.393 2.764 -18.749 1.61087839607 1.81532130841 0.852318582732 0.135107943172 0.382321326728 -0.103709714206 5.50899342327 5.04342688339 2.63704312518 0.656089298894 2.1218665047 0.797360543919 0.570680365471 0.364695140637 -1.02775757151 -0.249796996757 1.05624689115 -0.73547379414 -0.565576906424 -0.402604680466 -0.277573464467 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 101 A 113 '( CHAIN A AND RESID 101:113 )' ? ? ? ? ? 'X-RAY DIFFRACTION' 2 2 B 105 B 111 '( CHAIN B AND RESID 105:111 )' ? ? ? ? ? 'X-RAY DIFFRACTION' 3 3 C 101 C 114 '( CHAIN C AND RESID 101:114 )' ? ? ? ? ? 'X-RAY DIFFRACTION' 4 4 D 113 D 121 '( CHAIN D AND RESID 113:121 )' ? ? ? ? ? # 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 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? 1.18.2_3874 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.18.2_3874 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? STARANISO ? ? ? . 4 # _pdbx_entry_details.entry_id 7URK _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_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" B DA 107 ? ? "C3'" B DA 107 ? ? 1.362 1.419 -0.057 0.006 N 2 1 "O3'" C DC 102 ? ? "C3'" C DC 102 ? ? 1.383 1.419 -0.036 0.006 N 3 1 "O3'" C DG 110 ? ? "C3'" C DG 110 ? ? 1.377 1.419 -0.042 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DA 102 ? ? "C1'" A DA 102 ? ? N9 A DA 102 ? ? 111.87 108.30 3.57 0.30 N 2 1 "O4'" A DG 107 ? ? "C1'" A DG 107 ? ? N9 A DG 107 ? ? 111.86 108.30 3.56 0.30 N 3 1 "O4'" A DT 112 ? ? "C1'" A DT 112 ? ? N1 A DT 112 ? ? 111.07 108.30 2.77 0.30 N 4 1 "O4'" B DC 106 ? ? "C1'" B DC 106 ? ? N1 B DC 106 ? ? 110.40 108.30 2.10 0.30 N 5 1 "O4'" B DC 109 ? ? "C1'" B DC 109 ? ? N1 B DC 109 ? ? 110.41 108.30 2.11 0.30 N 6 1 "C3'" C DT 101 ? ? "C2'" C DT 101 ? ? "C1'" C DT 101 ? ? 95.98 102.40 -6.42 0.80 N 7 1 "O4'" C DT 101 ? ? "C1'" C DT 101 ? ? N1 C DT 101 ? ? 111.29 108.30 2.99 0.30 N 8 1 "O4'" C DG 104 ? ? "C1'" C DG 104 ? ? N9 C DG 104 ? ? 110.29 108.30 1.99 0.30 N 9 1 "C3'" C DT 106 ? ? "C2'" C DT 106 ? ? "C1'" C DT 106 ? ? 96.47 102.40 -5.93 0.80 N 10 1 "O4'" C DT 106 ? ? "C1'" C DT 106 ? ? N1 C DT 106 ? ? 110.94 108.30 2.64 0.30 N 11 1 "O4'" C DT 112 ? ? "C1'" C DT 112 ? ? N1 C DT 112 ? ? 110.58 108.30 2.28 0.30 N 12 1 "C3'" D DC 117 ? ? "C2'" D DC 117 ? ? "C1'" D DC 117 ? ? 95.85 102.40 -6.55 0.80 N 13 1 "O4'" D DC 117 ? ? "C1'" D DC 117 ? ? N1 D DC 117 ? ? 111.03 108.30 2.73 0.30 N # 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 96T OBD O N N 1 96T CBC C N N 2 96T CBB C N N 3 96T CAZ C N N 4 96T NAU N N N 5 96T CAT C Y N 6 96T CAS C Y N 7 96T CAR C Y N 8 96T CAC C Y N 9 96T CAD C Y N 10 96T CAE C Y N 11 96T CAF C N N 12 96T CAP C N N 13 96T CAA C N N 14 96T CAG C N N 15 96T CAH C N N 16 96T CAI C N N 17 96T CAJ C N N 18 96T CAK C N N 19 96T CAL C N N 20 96T CAQ C N N 21 96T CAB C N N 22 96T CAM C Y N 23 96T CAN C Y N 24 96T CAO C Y N 25 96T CAY C Y N 26 96T CAX C Y N 27 96T CAW C Y N 28 96T NAV N N N 29 96T CBA C N N 30 96T CBE C N N 31 96T CBF C N N 32 96T OBG O N N 33 96T H1 H N N 34 96T H2 H N N 35 96T H3 H N N 36 96T H4 H N N 37 96T H5 H N N 38 96T H6 H N N 39 96T H7 H N N 40 96T H8 H N N 41 96T H9 H N N 42 96T H10 H N N 43 96T H11 H N N 44 96T H12 H N N 45 96T H13 H N N 46 96T H14 H N N 47 96T H15 H N N 48 96T H16 H N N 49 96T H17 H N N 50 96T H18 H N N 51 96T H19 H N N 52 96T H21 H N N 53 96T H22 H N N 54 96T H23 H N N 55 96T H24 H N N 56 96T H25 H N N 57 96T H26 H N N 58 96T H27 H N N 59 96T H28 H N N 60 96T H29 H N N 61 96T H30 H N N 62 96T H31 H N N 63 96T H32 H N N 64 96T H33 H N N 65 96T H34 H N N 66 96T H35 H N N 67 96T H36 H N N 68 96T H20 H N N 69 96T H37 H N N 70 DA OP3 O N N 71 DA P P N N 72 DA OP1 O N N 73 DA OP2 O N N 74 DA "O5'" O N N 75 DA "C5'" C N N 76 DA "C4'" C N R 77 DA "O4'" O N N 78 DA "C3'" C N S 79 DA "O3'" O N N 80 DA "C2'" C N N 81 DA "C1'" C N R 82 DA N9 N Y N 83 DA C8 C Y N 84 DA N7 N Y N 85 DA C5 C Y N 86 DA C6 C Y N 87 DA N6 N N N 88 DA N1 N Y N 89 DA C2 C Y N 90 DA N3 N Y N 91 DA C4 C Y N 92 DA HOP3 H N N 93 DA HOP2 H N N 94 DA "H5'" H N N 95 DA "H5''" H N N 96 DA "H4'" H N N 97 DA "H3'" H N N 98 DA "HO3'" H N N 99 DA "H2'" H N N 100 DA "H2''" H N N 101 DA "H1'" H N N 102 DA H8 H N N 103 DA H61 H N N 104 DA H62 H N N 105 DA H2 H N N 106 DC OP3 O N N 107 DC P P N N 108 DC OP1 O N N 109 DC OP2 O N N 110 DC "O5'" O N N 111 DC "C5'" C N N 112 DC "C4'" C N R 113 DC "O4'" O N N 114 DC "C3'" C N S 115 DC "O3'" O N N 116 DC "C2'" C N N 117 DC "C1'" C N R 118 DC N1 N N N 119 DC C2 C N N 120 DC O2 O N N 121 DC N3 N N N 122 DC C4 C N N 123 DC N4 N N N 124 DC C5 C N N 125 DC C6 C N N 126 DC HOP3 H N N 127 DC HOP2 H N N 128 DC "H5'" H N N 129 DC "H5''" H N N 130 DC "H4'" H N N 131 DC "H3'" H N N 132 DC "HO3'" H N N 133 DC "H2'" H N N 134 DC "H2''" H N N 135 DC "H1'" H N N 136 DC H41 H N N 137 DC H42 H N N 138 DC H5 H N N 139 DC H6 H N N 140 DG OP3 O N N 141 DG P P N N 142 DG OP1 O N N 143 DG OP2 O N N 144 DG "O5'" O N N 145 DG "C5'" C N N 146 DG "C4'" C N R 147 DG "O4'" O N N 148 DG "C3'" C N S 149 DG "O3'" O N N 150 DG "C2'" C N N 151 DG "C1'" C N R 152 DG N9 N Y N 153 DG C8 C Y N 154 DG N7 N Y N 155 DG C5 C Y N 156 DG C6 C N N 157 DG O6 O N N 158 DG N1 N N N 159 DG C2 C N N 160 DG N2 N N N 161 DG N3 N N N 162 DG C4 C Y N 163 DG HOP3 H N N 164 DG HOP2 H N N 165 DG "H5'" H N N 166 DG "H5''" H N N 167 DG "H4'" H N N 168 DG "H3'" H N N 169 DG "HO3'" H N N 170 DG "H2'" H N N 171 DG "H2''" H N N 172 DG "H1'" H N N 173 DG H8 H N N 174 DG H1 H N N 175 DG H21 H N N 176 DG H22 H N N 177 DT OP3 O N N 178 DT P P N N 179 DT OP1 O N N 180 DT OP2 O N N 181 DT "O5'" O N N 182 DT "C5'" C N N 183 DT "C4'" C N R 184 DT "O4'" O N N 185 DT "C3'" C N S 186 DT "O3'" O N N 187 DT "C2'" C N N 188 DT "C1'" C N R 189 DT N1 N N N 190 DT C2 C N N 191 DT O2 O N N 192 DT N3 N N N 193 DT C4 C N N 194 DT O4 O N N 195 DT C5 C N N 196 DT C7 C N N 197 DT C6 C N N 198 DT HOP3 H N N 199 DT HOP2 H N N 200 DT "H5'" H N N 201 DT "H5''" H N N 202 DT "H4'" H N N 203 DT "H3'" H N N 204 DT "HO3'" H N N 205 DT "H2'" H N N 206 DT "H2''" H N N 207 DT "H1'" H N N 208 DT H3 H N N 209 DT H71 H N N 210 DT H72 H N N 211 DT H73 H N N 212 DT H6 H N N 213 # 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 96T CBC OBD sing N N 1 96T CBC CBB sing N N 2 96T CAR CAS doub Y N 3 96T CAR CAC sing Y N 4 96T CBB CAZ sing N N 5 96T CAS CAT sing Y N 6 96T CAC CAD doub Y N 7 96T CAT CAE doub Y N 8 96T CAT NAU sing N N 9 96T CAZ NAU sing N N 10 96T CAD CAE sing Y N 11 96T CAE CAF sing N N 12 96T NAU CAG doub N N 13 96T CAP CAF sing N N 14 96T CAG CAF sing N N 15 96T CAG CAH sing N N 16 96T CAF CAA sing N N 17 96T CAH CAI doub N E 18 96T CAI CAJ sing N N 19 96T CBA CBE sing N N 20 96T CBA NAV sing N N 21 96T CBE CBF sing N N 22 96T CAJ CAK doub N Z 23 96T NAV CAK sing N N 24 96T NAV CAW sing N N 25 96T CAK CAL sing N N 26 96T CBF OBG sing N N 27 96T CAW CAX doub Y N 28 96T CAW CAM sing Y N 29 96T CAX CAY sing Y N 30 96T CAQ CAL sing N N 31 96T CAL CAM sing N N 32 96T CAL CAB sing N N 33 96T CAM CAN doub Y N 34 96T CAY CAO doub Y N 35 96T CAN CAO sing Y N 36 96T OBD H1 sing N N 37 96T CBC H2 sing N N 38 96T CBC H3 sing N N 39 96T CBB H4 sing N N 40 96T CBB H5 sing N N 41 96T CAZ H6 sing N N 42 96T CAZ H7 sing N N 43 96T CAS H8 sing N N 44 96T CAR H9 sing N N 45 96T CAC H10 sing N N 46 96T CAD H11 sing N N 47 96T CAP H12 sing N N 48 96T CAP H13 sing N N 49 96T CAP H14 sing N N 50 96T CAA H15 sing N N 51 96T CAA H16 sing N N 52 96T CAA H17 sing N N 53 96T CAH H18 sing N N 54 96T CAI H19 sing N N 55 96T CAJ H21 sing N N 56 96T CAQ H22 sing N N 57 96T CAQ H23 sing N N 58 96T CAQ H24 sing N N 59 96T CAB H25 sing N N 60 96T CAB H26 sing N N 61 96T CAB H27 sing N N 62 96T CAN H28 sing N N 63 96T CAO H29 sing N N 64 96T CAY H30 sing N N 65 96T CAX H31 sing N N 66 96T CBA H32 sing N N 67 96T CBA H33 sing N N 68 96T CBE H34 sing N N 69 96T CBE H35 sing N N 70 96T CBF H36 sing N N 71 96T CBF H20 sing N N 72 96T OBG H37 sing N N 73 DA OP3 P sing N N 74 DA OP3 HOP3 sing N N 75 DA P OP1 doub N N 76 DA P OP2 sing N N 77 DA P "O5'" sing N N 78 DA OP2 HOP2 sing N N 79 DA "O5'" "C5'" sing N N 80 DA "C5'" "C4'" sing N N 81 DA "C5'" "H5'" sing N N 82 DA "C5'" "H5''" sing N N 83 DA "C4'" "O4'" sing N N 84 DA "C4'" "C3'" sing N N 85 DA "C4'" "H4'" sing N N 86 DA "O4'" "C1'" sing N N 87 DA "C3'" "O3'" sing N N 88 DA "C3'" "C2'" sing N N 89 DA "C3'" "H3'" sing N N 90 DA "O3'" "HO3'" sing N N 91 DA "C2'" "C1'" sing N N 92 DA "C2'" "H2'" sing N N 93 DA "C2'" "H2''" sing N N 94 DA "C1'" N9 sing N N 95 DA "C1'" "H1'" sing N N 96 DA N9 C8 sing Y N 97 DA N9 C4 sing Y N 98 DA C8 N7 doub Y N 99 DA C8 H8 sing N N 100 DA N7 C5 sing Y N 101 DA C5 C6 sing Y N 102 DA C5 C4 doub Y N 103 DA C6 N6 sing N N 104 DA C6 N1 doub Y N 105 DA N6 H61 sing N N 106 DA N6 H62 sing N N 107 DA N1 C2 sing Y N 108 DA C2 N3 doub Y N 109 DA C2 H2 sing N N 110 DA N3 C4 sing Y N 111 DC OP3 P sing N N 112 DC OP3 HOP3 sing N N 113 DC P OP1 doub N N 114 DC P OP2 sing N N 115 DC P "O5'" sing N N 116 DC OP2 HOP2 sing N N 117 DC "O5'" "C5'" sing N N 118 DC "C5'" "C4'" sing N N 119 DC "C5'" "H5'" sing N N 120 DC "C5'" "H5''" sing N N 121 DC "C4'" "O4'" sing N N 122 DC "C4'" "C3'" sing N N 123 DC "C4'" "H4'" sing N N 124 DC "O4'" "C1'" sing N N 125 DC "C3'" "O3'" sing N N 126 DC "C3'" "C2'" sing N N 127 DC "C3'" "H3'" sing N N 128 DC "O3'" "HO3'" sing N N 129 DC "C2'" "C1'" sing N N 130 DC "C2'" "H2'" sing N N 131 DC "C2'" "H2''" sing N N 132 DC "C1'" N1 sing N N 133 DC "C1'" "H1'" sing N N 134 DC N1 C2 sing N N 135 DC N1 C6 sing N N 136 DC C2 O2 doub N N 137 DC C2 N3 sing N N 138 DC N3 C4 doub N N 139 DC C4 N4 sing N N 140 DC C4 C5 sing N N 141 DC N4 H41 sing N N 142 DC N4 H42 sing N N 143 DC C5 C6 doub N N 144 DC C5 H5 sing N N 145 DC C6 H6 sing N N 146 DG OP3 P sing N N 147 DG OP3 HOP3 sing N N 148 DG P OP1 doub N N 149 DG P OP2 sing N N 150 DG P "O5'" sing N N 151 DG OP2 HOP2 sing N N 152 DG "O5'" "C5'" sing N N 153 DG "C5'" "C4'" sing N N 154 DG "C5'" "H5'" sing N N 155 DG "C5'" "H5''" sing N N 156 DG "C4'" "O4'" sing N N 157 DG "C4'" "C3'" sing N N 158 DG "C4'" "H4'" sing N N 159 DG "O4'" "C1'" sing N N 160 DG "C3'" "O3'" sing N N 161 DG "C3'" "C2'" sing N N 162 DG "C3'" "H3'" sing N N 163 DG "O3'" "HO3'" sing N N 164 DG "C2'" "C1'" sing N N 165 DG "C2'" "H2'" sing N N 166 DG "C2'" "H2''" sing N N 167 DG "C1'" N9 sing N N 168 DG "C1'" "H1'" sing N N 169 DG N9 C8 sing Y N 170 DG N9 C4 sing Y N 171 DG C8 N7 doub Y N 172 DG C8 H8 sing N N 173 DG N7 C5 sing Y N 174 DG C5 C6 sing N N 175 DG C5 C4 doub Y N 176 DG C6 O6 doub N N 177 DG C6 N1 sing N N 178 DG N1 C2 sing N N 179 DG N1 H1 sing N N 180 DG C2 N2 sing N N 181 DG C2 N3 doub N N 182 DG N2 H21 sing N N 183 DG N2 H22 sing N N 184 DG N3 C4 sing N N 185 DT OP3 P sing N N 186 DT OP3 HOP3 sing N N 187 DT P OP1 doub N N 188 DT P OP2 sing N N 189 DT P "O5'" sing N N 190 DT OP2 HOP2 sing N N 191 DT "O5'" "C5'" sing N N 192 DT "C5'" "C4'" sing N N 193 DT "C5'" "H5'" sing N N 194 DT "C5'" "H5''" sing N N 195 DT "C4'" "O4'" sing N N 196 DT "C4'" "C3'" sing N N 197 DT "C4'" "H4'" sing N N 198 DT "O4'" "C1'" sing N N 199 DT "C3'" "O3'" sing N N 200 DT "C3'" "C2'" sing N N 201 DT "C3'" "H3'" sing N N 202 DT "O3'" "HO3'" sing N N 203 DT "C2'" "C1'" sing N N 204 DT "C2'" "H2'" sing N N 205 DT "C2'" "H2''" sing N N 206 DT "C1'" N1 sing N N 207 DT "C1'" "H1'" sing N N 208 DT N1 C2 sing N N 209 DT N1 C6 sing N N 210 DT C2 O2 doub N N 211 DT C2 N3 sing N N 212 DT N3 C4 sing N N 213 DT N3 H3 sing N N 214 DT C4 O4 doub N N 215 DT C4 C5 sing N N 216 DT C5 C7 sing N N 217 DT C5 C6 doub N N 218 DT C7 H71 sing N N 219 DT C7 H72 sing N N 220 DT C7 H73 sing N N 221 DT C6 H6 sing N N 222 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7URK 'double helix' 7URK 'a-form double helix' 7URK 'b-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 DG 3 1_555 C DC 14 1_555 -0.178 -0.159 -0.451 -14.856 -0.385 1.045 1 A_DG103:DC114_C A 103 ? C 114 ? 19 1 1 A DC 4 1_555 C DG 13 1_555 0.150 -0.185 0.269 -6.203 3.157 0.146 2 A_DC104:DG113_C A 104 ? C 113 ? 19 1 1 A DG 7 1_555 C DC 11 1_555 -0.186 -0.201 -0.096 3.884 5.966 2.315 3 A_DG107:DC111_C A 107 ? C 111 ? 19 1 1 A DC 8 1_555 C DG 10 1_555 0.266 -0.200 0.079 7.048 -5.315 -0.212 4 A_DC108:DG110_C A 108 ? C 110 ? 19 1 1 A DC 9 1_555 C DG 9 1_555 0.213 -0.144 0.316 -2.454 -5.828 0.349 5 A_DC109:DG109_C A 109 ? C 109 ? 19 1 1 A DT 10 1_555 B DA 3 1_555 -0.120 -0.262 0.525 1.219 -2.106 4.867 6 A_DT110:DA107_B A 110 ? B 107 ? 20 1 1 A DG 11 1_555 B DC 2 1_555 -0.131 -0.112 0.299 3.215 0.351 1.692 7 A_DG111:DC106_B A 111 ? B 106 ? 19 1 1 A DT 12 1_555 B DA 1 1_555 0.117 -0.394 -0.069 1.949 2.318 7.989 8 A_DT112:DA105_B A 112 ? B 105 ? 20 1 1 C DT 3 1_555 D DA 9 1_555 -0.508 -0.366 0.796 -12.465 -16.149 -7.981 9 C_DT103:DA121_D C 103 ? D 121 ? 20 1 1 C DG 4 1_555 D DC 8 1_555 -0.024 -0.265 0.864 11.631 -7.170 -1.943 10 C_DG104:DC120_D C 104 ? D 120 ? 19 1 1 C DA 5 1_555 D DT 7 1_555 0.121 -0.136 0.427 1.283 -5.674 3.387 11 C_DA105:DT119_D C 105 ? D 119 ? 20 1 1 C DT 6 1_555 D DA 6 1_555 -0.029 -0.128 0.293 -2.543 -4.406 0.372 12 C_DT106:DA118_D C 106 ? D 118 ? 20 1 1 C DG 7 1_555 D DC 5 1_555 -0.178 -0.222 -0.223 -7.669 -4.376 2.205 13 C_DG107:DC117_D C 107 ? D 117 ? 19 1 1 C DT 8 1_555 D DA 4 1_555 -0.414 -0.129 0.007 2.959 2.193 -4.751 14 C_DT108:DA116_D C 108 ? D 116 ? 20 1 1 B DC 4 1_555 D DG 3 1_555 -0.064 -0.351 -0.206 -0.710 -2.823 -4.217 15 B_DC108:DG115_D B 108 ? D 115 ? 19 1 1 B DC 5 1_555 D DG 2 1_555 0.158 -0.163 0.507 -4.790 -0.400 -2.504 16 B_DC109:DG114_D B 109 ? D 114 ? 19 1 1 B DG 6 1_555 D DC 1 1_555 -0.147 -0.253 0.031 0.684 -0.025 -4.751 17 B_DG110:DC113_D B 110 ? D 113 ? 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 3 1_555 C DC 14 1_555 A DC 4 1_555 C DG 13 1_555 0.180 -0.060 3.125 -2.361 8.373 23.540 -2.493 -1.078 2.900 19.682 5.550 25.075 1 AA_DG103DC104:DG113DC114_CC A 103 ? C 114 ? A 104 ? C 113 ? 1 A DG 7 1_555 C DC 11 1_555 A DC 8 1_555 C DG 10 1_555 -0.682 -0.826 3.171 -5.947 4.875 35.425 -1.993 0.286 3.104 7.897 9.634 36.224 2 AA_DG107DC108:DG110DC111_CC A 107 ? C 111 ? A 108 ? C 110 ? 1 A DC 8 1_555 C DG 10 1_555 A DC 9 1_555 C DG 9 1_555 0.035 -1.526 3.427 -4.123 1.802 39.782 -2.444 -0.541 3.337 2.637 6.036 40.025 3 AA_DC108DC109:DG109DG110_CC A 108 ? C 110 ? A 109 ? C 109 ? 1 A DC 9 1_555 C DG 9 1_555 A DT 10 1_555 B DA 3 1_555 -1.116 -1.174 3.228 -3.776 -1.817 20.644 -2.424 1.414 3.463 -5.004 10.398 21.061 4 AA_DC109DT110:DA107DG109_BC A 109 ? C 109 ? A 110 ? B 107 ? 1 A DT 10 1_555 B DA 3 1_555 A DG 11 1_555 B DC 2 1_555 -0.326 0.646 3.475 0.880 2.153 32.981 0.747 0.732 3.499 3.786 -1.547 33.061 5 AA_DT110DG111:DC106DA107_BB A 110 ? B 107 ? A 111 ? B 106 ? 1 A DG 11 1_555 B DC 2 1_555 A DT 12 1_555 B DA 1 1_555 0.552 -0.628 3.364 3.049 3.274 25.948 -2.281 -0.374 3.303 7.223 -6.727 26.325 6 AA_DG111DT112:DA105DC106_BB A 111 ? B 106 ? A 112 ? B 105 ? 1 C DT 3 1_555 D DA 9 1_555 C DG 4 1_555 D DC 8 1_555 0.228 -0.809 2.621 -3.163 4.213 35.104 -1.812 -0.737 2.481 6.936 5.207 35.485 7 CC_DT103DG104:DC120DA121_DD C 103 ? D 121 ? C 104 ? D 120 ? 1 C DG 4 1_555 D DC 8 1_555 C DA 5 1_555 D DT 7 1_555 0.051 -0.410 3.441 1.409 -5.283 40.455 0.028 0.091 3.465 -7.597 -2.026 40.807 8 CC_DG104DA105:DT119DC120_DD C 104 ? D 120 ? C 105 ? D 119 ? 1 C DA 5 1_555 D DT 7 1_555 C DT 6 1_555 D DA 6 1_555 -0.372 -0.834 3.405 -0.404 -3.392 31.598 -0.867 0.601 3.477 -6.206 0.739 31.777 9 CC_DA105DT106:DA118DT119_DD C 105 ? D 119 ? C 106 ? D 118 ? 1 C DT 6 1_555 D DA 6 1_555 C DG 7 1_555 D DC 5 1_555 0.045 0.656 3.456 1.472 -6.319 46.222 1.380 0.071 3.343 -8.002 -1.864 46.651 10 CC_DT106DG107:DC117DA118_DD C 106 ? D 118 ? C 107 ? D 117 ? 1 C DG 7 1_555 D DC 5 1_555 C DT 8 1_555 D DA 4 1_555 -0.130 -0.508 3.061 -1.952 2.218 25.498 -1.725 -0.220 3.008 5.004 4.404 25.665 11 CC_DG107DT108:DA116DC117_DD C 107 ? D 117 ? C 108 ? D 116 ? 1 C DT 8 1_555 D DA 4 1_555 B DC 4 1_555 D DG 3 1_555 0.536 -0.473 3.368 2.884 -0.638 27.812 -0.821 -0.398 3.414 -1.323 -5.978 27.965 12 CB_DT108DC108:DG115DA116_DD C 108 ? D 116 ? B 108 ? D 115 ? 1 B DC 4 1_555 D DG 3 1_555 B DC 5 1_555 D DG 2 1_555 0.417 1.905 3.856 0.554 2.238 46.651 2.180 -0.471 3.943 2.824 -0.699 46.705 13 BB_DC108DC109:DG114DG115_DD B 108 ? D 115 ? B 109 ? D 114 ? 1 B DC 5 1_555 D DG 2 1_555 B DG 6 1_555 D DC 1 1_555 -0.655 2.398 3.210 1.395 -4.662 40.757 3.897 1.077 2.907 -6.665 -1.994 41.035 14 BB_DC109DG110:DC113DG114_DD B 109 ? D 114 ? B 110 ? D 113 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Office of Naval Research (ONR)' 'United States' N000141912596 1 'Department of Energy (DOE, United States)' 'United States' DE-SC0007991 2 'National Science Foundation (NSF, United States)' 'United States' 2106790 3 'Human Frontier Science Program (HFSP)' France RPG0010/2017 4 'National Science Foundation (NSF, United States)' 'United States' DMR-1420073 5 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id 96T _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id 96T _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3GBI _pdbx_initial_refinement_model.details 'PDB entry 3GBI' # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'native gel electrophoresis' _pdbx_struct_assembly_auth_evidence.details ? # _space_group.name_H-M_alt 'H 3' _space_group.name_Hall 'H 3' _space_group.IT_number 146 _space_group.crystal_system trigonal _space_group.id 1 #