data_8D93 # _entry.id 8D93 # _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 8D93 pdb_00008d93 10.2210/pdb8d93/pdb WWPDB D_1000266242 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.details 'Original Solution at 4.0 A, with a duplex ASU' _pdbx_database_related.db_id 3GBI _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 8D93 _pdbx_database_status.recvd_initial_deposition_date 2022-06-09 _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 'Vecchioni, S.' 1 0000-0001-8243-650X 'Woloszyn, K.' 2 0000-0003-1200-583X 'Lu, B.' 3 0000-0001-6424-2197 'Sha, R.' 4 0000-0002-0807-734X 'Ohayon, Y.P.' 5 0000-0001-7500-4282 'Seeman, N.C.' 6 0000-0002-9680-4649 # loop_ _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 _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_full _citation.journal_issue _citation.journal_volume _citation.language _citation.page_first _citation.page_last _citation.title _citation.year _citation.database_id_CSD _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_patent _citation.unpublished_flag ? ? ? ? ? ? ? DE ? ? primary Small ? ? 1613-6829 ? ? 19 ? e2206511 e2206511 'The Rule of Thirds: Controlling Junction Chirality and Polarity in 3D DNA Tiles.' 2023 ? 10.1002/smll.202206511 36585389 ? ? ? ? ? ? ? ? ? ? ? ? 1 'To Be Published' ? 0353 ? ? ? ? ? ? ? 'Mirror Nanomaterials: Self-Assembly of Left-Handed, Anti-Tensegrity DNA Triangles' ? ? ? ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Vecchioni, S.' 1 ? primary 'Lu, B.' 2 ? primary 'Janowski, J.' 3 ? primary 'Woloszyn, K.' 4 ? primary 'Jonoska, N.' 5 ? primary 'Seeman, N.C.' 6 ? primary 'Mao, C.' 7 ? primary 'Ohayon, Y.P.' 8 ? primary 'Sha, R.' 9 0000-0002-0807-734X 1 'Vecchioni, S.' 10 0000-0001-8243-650X 1 'Janowski, J.' 11 0000-0002-6990-5719 1 'Lu, B.' 12 0000-0001-6424-2197 1 'Ohayon, Y.P.' 13 0000-0002-0807-734X 1 'Sha, R.' 14 0000-0002-0807-734X 1 'Woloszyn, K.' 15 0000-0003-1200-583X 1 'Mao, C.' 16 0000-0001-7516-8666 1 'Seeman, N.C.' 17 0000-0002-9680-4649 # _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 8D93 _cell.details ? _cell.formula_units_Z ? _cell.length_a 105.547 _cell.length_a_esd ? _cell.length_b 105.547 _cell.length_b_esd ? _cell.length_c 96.268 _cell.length_c_esd ? _cell.volume 928761.851 _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 ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8D93 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall 'R 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*AP*GP*CP*CP*TP*GP*TP*A)-3') ; 3687.417 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 no '(DG)(DA)(DG)(DC)(DA)(DG)(DC)(DC)(DT)(DG)(DT)(DA)' GAGCAGCCTGTA 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 DG n 1 7 DC n 1 8 DC n 1 9 DT n 1 10 DG n 1 11 DT n 1 12 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 12 '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 8D93 8D93 ? 1 ? 1 2 PDB 8D93 8D93 ? 2 ? 1 3 PDB 8D93 8D93 ? 3 ? 1 4 PDB 8D93 8D93 ? 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 8D93 A 1 ? 12 ? 8D93 101 ? 112 ? 101 112 2 2 8D93 B 1 ? 7 ? 8D93 105 ? 114 ? 105 114 3 3 8D93 C 1 ? 14 ? 8D93 101 ? 114 ? 101 114 4 4 8D93 D 1 ? 9 ? 8D93 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 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 8D93 _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 7.53 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 83.66 _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 7.8 _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 degrees C at 0.4 degrees C / hr' _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '40 mM Tris, 2 mM EDTA, 20 mM acetic acid, 125 mM magnesium acetate, 583 mM ammonium sulfate' _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 EIGER2 X 9M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2021-07-18 _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 1.007 _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 17-ID' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.007 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 17-ID _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate 44.76 _reflns.entry_id 8D93 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.96 _reflns.d_resolution_low 66.29 _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 3342 _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 57 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 10.4 _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 9.8 _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 ? _reflns.pdbx_CC_split_method ? # 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 2.96 3.41 ? 3.0 ? ? ? ? 199 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 10.3 ? ? ? ? ? ? ? 1 1 0.920 ? ? ? ? ? ? ? ? ? ? 10.42 66.29 ? 36.8 ? ? ? ? 196 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 10.8 ? ? ? ? ? ? ? 2 1 0.999 ? ? ? ? ? ? ? ? ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 119.01 _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 8D93 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.96 _refine.ls_d_res_low 41.29 _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 3333 _refine.ls_number_reflns_R_free 176 _refine.ls_number_reflns_R_work 3157 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 39.96 _refine.ls_percent_reflns_R_free 5.28 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1869 _refine.ls_R_factor_R_free 0.2258 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1847 _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 1.96 _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 32.3960 _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 0.0410 _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 2.96 _refine_hist.d_res_low 41.29 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 855 _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 794 _refine_hist.pdbx_number_atoms_ligand 61 _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' ? 0.0115 ? 955 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.4102 ? 1463 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0715 ? 166 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0103 ? 42 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 42.7284 ? 403 ? f_dihedral_angle_d ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 2.96 _refine_ls_shell.d_res_low 41.29 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 176 _refine_ls_shell.number_reflns_R_work 3157 _refine_ls_shell.percent_reflns_obs 39.96 _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 0.2258 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.1847 _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 ? # _struct.entry_id 8D93 _struct.title '[2T7] Self-assembling tensegrity triangle with R3 symmetry at 2.96 A resolution, update and junction cut for entry 3GBI' _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 8D93 _struct_keywords.text 'Tensegrity triangle, DNA nanotechnology, nanomaterials, linking number, 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 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 DA 5 N1 ? ? ? 1_555 C DT 12 N3 ? ? A DA 105 C DT 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 5 N6 ? ? ? 1_555 C DT 12 O4 ? ? A DA 105 C DT 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 6 N1 ? ? ? 1_555 C DC 11 N3 ? ? A DG 106 C DC 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 6 N2 ? ? ? 1_555 C DC 11 O2 ? ? A DG 106 C DC 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 6 O6 ? ? ? 1_555 C DC 11 N4 ? ? A DG 106 C DC 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 7 N3 ? ? ? 1_555 C DG 10 N1 ? ? A DC 107 C DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 7 N4 ? ? ? 1_555 C DG 10 O6 ? ? A DC 107 C DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 7 O2 ? ? ? 1_555 C DG 10 N2 ? ? A DC 107 C DG 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 N3 ? ? ? 1_555 C DG 9 N1 ? ? A DC 108 C DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 N4 ? ? ? 1_555 C DG 9 O6 ? ? A DC 108 C DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 8 O2 ? ? ? 1_555 C DG 9 N2 ? ? A DC 108 C DG 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 109 B DA 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 109 B DA 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 110 B DC 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 110 B DC 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 110 B DC 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DT 11 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 111 B DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DT 11 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 111 B DA 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B DC 4 N3 ? ? ? 1_555 D DG 3 N1 ? ? B DC 111 D DG 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B DC 4 N4 ? ? ? 1_555 D DG 3 O6 ? ? B DC 111 D DG 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B DC 4 O2 ? ? ? 1_555 D DG 3 N2 ? ? B DC 111 D DG 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B DC 5 N3 ? ? ? 1_555 D DG 2 N1 ? ? B DC 112 D DG 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B DC 5 N4 ? ? ? 1_555 D DG 2 O6 ? ? B DC 112 D DG 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B DC 5 O2 ? ? ? 1_555 D DG 2 N2 ? ? B DC 112 D DG 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B DG 6 N1 ? ? ? 1_555 D DC 1 O2 ? ? B DG 113 D DC 113 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog32 hydrog ? ? B DG 6 N2 ? ? ? 1_555 D DC 1 N3 ? ? B DG 113 D DC 113 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog33 hydrog ? ? C DT 3 N3 ? ? ? 1_555 D DA 9 N1 ? ? C DT 103 D DA 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C DT 3 O4 ? ? ? 1_555 D DA 9 N6 ? ? C DT 103 D DA 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C DG 4 N1 ? ? ? 1_555 D DC 8 N3 ? ? C DG 104 D DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C DG 4 N2 ? ? ? 1_555 D DC 8 O2 ? ? C DG 104 D DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C DG 4 O6 ? ? ? 1_555 D DC 8 N4 ? ? C DG 104 D DC 120 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C DA 5 N1 ? ? ? 1_555 D DT 7 N3 ? ? C DA 105 D DT 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C DA 5 N6 ? ? ? 1_555 D DT 7 O4 ? ? C DA 105 D DT 119 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C DT 6 N3 ? ? ? 1_555 D DA 6 N1 ? ? C DT 106 D DA 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C DT 6 O4 ? ? ? 1_555 D DA 6 N6 ? ? C DT 106 D DA 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C DG 7 N1 ? ? ? 1_555 D DC 5 N3 ? ? C DG 107 D DC 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C DG 7 N2 ? ? ? 1_555 D DC 5 O2 ? ? C DG 107 D DC 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C DG 7 O6 ? ? ? 1_555 D DC 5 N4 ? ? C DG 107 D DC 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C DT 8 N3 ? ? ? 1_555 D DA 4 N1 ? ? C DT 108 D DA 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C DT 8 O4 ? ? ? 1_555 D DA 4 N6 ? ? C DT 108 D DA 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 8D93 _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] 0.009474 _atom_sites.fract_transf_matrix[1][2] 0.005470 _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] 0.010940 _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] 0.010388 _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 DG 6 106 106 DG DG A . n A 1 7 DC 7 107 107 DC DC A . n A 1 8 DC 8 108 108 DC DC A . n A 1 9 DT 9 109 109 DT DT A . n A 1 10 DG 10 110 110 DG DG A . n A 1 11 DT 11 111 111 DT DT A . n A 1 12 DA 12 112 112 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 4 111 108 DC DC B . n B 2 5 DC 5 112 109 DC DC B . n B 2 6 DG 6 113 110 DG DG B . n B 2 7 DT 7 114 111 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 ncs01@nyu.edu _pdbx_contact_author.name_first Nadrian _pdbx_contact_author.name_last Seeman _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-9680-4649 # _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 2023-01-25 2 'Structure model' 1 1 2023-04-05 3 'Structure model' 1 2 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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 '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' citation 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' pdbx_initial_refinement_model # 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.year' # 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 21.317 -5.367 -1.616 1.60555908015 1.9412819104 1.36407519852 -0.434482029023 -0.333443329271 -0.513876688561 4.44944026175 2.39879897991 0.454481989681 1.25370715621 1.23456080225 -0.153605950789 0.866044756489 -0.324284223267 -0.835206133929 -1.47203271808 -0.245295898276 -1.40974102069 0.769448342162 0.0756975671027 0.457485529782 'X-RAY DIFFRACTION' 2 ? refined 12.816 -6.587 -11.052 0.521984075396 1.80648016305 1.0922360525 -0.229752010745 0.606338663214 -0.598002096434 5.91444105936 5.37047535724 3.94898417929 -0.624287671583 3.19570881744 -3.76977688281 1.13092528772 0.572622486624 2.11558869695 1.88871667993 -0.497315147752 -0.497154614834 -0.932639418052 -0.00708975543066 -0.151562243482 'X-RAY DIFFRACTION' 3 ? refined 12.543 10.702 -9.944 0.923323464417 1.66940344268 1.40265055867 -0.246343751995 0.307118673721 -0.640150153328 1.43442708054 0.721820626096 7.02949651761 -0.175867769999 -1.81083057472 2.02380679531 0.109575367692 -0.320024604985 -0.233969473254 0.1404927323 0.962409237119 -0.0191112701454 -1.03692624756 -0.520823378542 -1.80085312187 'X-RAY DIFFRACTION' 4 ? refined 24.362 -0.909 -12.561 0.9061094907 1.20132164537 1.3720119062 0.233925804053 0.100957484464 -0.574244413816 7.29451799821 6.86526274584 7.1542610309 1.20538589681 2.43627255312 0.477619981824 1.77658050003 -0.768985904298 -1.64744279954 -0.311146189458 -0.0242015355578 -1.01741494654 -0.407029367899 0.519346598924 -0.21048181615 'X-RAY DIFFRACTION' 5 ? refined 18.690 5.349 -18.474 1.16961769249 1.27218755186 1.04940745335 0.232618214743 0.144315563316 -0.287201334979 6.43479108091 2.94519245759 0.695430845177 -1.26490930618 -1.26253136116 -0.85182498361 0.65656579051 0.172706891775 0.593358723349 0.408999640981 0.495934129442 0.00817806205081 -1.09574359887 -0.829553266584 -0.0192605075794 # 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 112 '( CHAIN A AND RESID 101:112 )' ? ? ? ? ? 'X-RAY DIFFRACTION' 2 2 B 105 B 107 '( CHAIN B AND RESID 105:107 )' ? ? ? ? ? 'X-RAY DIFFRACTION' 3 3 B 111 B 114 '( CHAIN B AND RESID 111:114 )' ? ? ? ? ? 'X-RAY DIFFRACTION' 4 4 C 101 C 114 '( CHAIN C AND RESID 101:114 )' ? ? ? ? ? 'X-RAY DIFFRACTION' 5 5 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 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.18.2_3874 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? STARANISO ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _pdbx_entry_details.entry_id 8D93 _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O6 _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 DG _pdbx_validate_close_contact.auth_seq_id_1 113 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 N4 _pdbx_validate_close_contact.auth_asym_id_2 D _pdbx_validate_close_contact.auth_comp_id_2 DC _pdbx_validate_close_contact.auth_seq_id_2 113 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.14 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O6 A DG 101 ? ? 1_555 N4 C DC 102 ? ? 6_555 2.11 2 1 "O5'" C DT 101 ? ? 1_555 "O3'" C DC 114 ? ? 8_544 2.16 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DC _pdbx_validate_rmsd_bond.auth_seq_id_1 106 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C3'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DC _pdbx_validate_rmsd_bond.auth_seq_id_2 106 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.369 _pdbx_validate_rmsd_bond.bond_target_value 1.419 _pdbx_validate_rmsd_bond.bond_deviation -0.050 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.006 _pdbx_validate_rmsd_bond.linker_flag 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 ? ? 112.89 108.30 4.59 0.30 N 2 1 "O4'" A DG 103 ? ? "C1'" A DG 103 ? ? N9 A DG 103 ? ? 112.23 108.30 3.93 0.30 N 3 1 "O4'" A DC 107 ? ? "C1'" A DC 107 ? ? N1 A DC 107 ? ? 111.57 108.30 3.27 0.30 N 4 1 "O4'" A DG 110 ? ? "C4'" A DG 110 ? ? "C3'" A DG 110 ? ? 102.03 104.50 -2.47 0.40 N 5 1 "O4'" A DT 111 ? ? "C1'" A DT 111 ? ? N1 A DT 111 ? ? 111.90 108.30 3.60 0.30 N 6 1 "O4'" A DA 112 ? ? "C1'" A DA 112 ? ? N9 A DA 112 ? ? 111.31 108.30 3.01 0.30 N 7 1 "C3'" B DA 107 ? ? "O3'" B DA 107 ? ? P B DC 111 ? ? 143.97 119.70 24.27 1.20 Y 8 1 "O3'" B DA 107 ? ? P B DC 111 ? ? "O5'" B DC 111 ? ? 77.73 104.00 -26.27 1.90 Y 9 1 "O3'" B DA 107 ? ? P B DC 111 ? ? OP2 B DC 111 ? ? 154.61 110.50 44.11 1.10 Y 10 1 "O3'" B DA 107 ? ? P B DC 111 ? ? OP1 B DC 111 ? ? 79.68 105.20 -25.52 2.20 Y 11 1 "O4'" C DC 102 ? ? "C1'" C DC 102 ? ? N1 C DC 102 ? ? 110.64 108.30 2.34 0.30 N 12 1 "O5'" C DT 103 ? ? P C DT 103 ? ? OP2 C DT 103 ? ? 97.52 105.70 -8.18 0.90 N 13 1 "O4'" C DT 103 ? ? "C1'" C DT 103 ? ? N1 C DT 103 ? ? 115.83 108.30 7.53 0.30 N 14 1 N3 C DT 103 ? ? C4 C DT 103 ? ? O4 C DT 103 ? ? 123.51 119.90 3.61 0.60 N 15 1 "C3'" C DG 104 ? ? "C2'" C DG 104 ? ? "C1'" C DG 104 ? ? 97.11 102.40 -5.29 0.80 N 16 1 "O4'" C DG 104 ? ? "C1'" C DG 104 ? ? N9 C DG 104 ? ? 112.42 108.30 4.12 0.30 N 17 1 "C3'" C DT 106 ? ? "C2'" C DT 106 ? ? "C1'" C DT 106 ? ? 96.58 102.40 -5.82 0.80 N 18 1 "O4'" C DG 110 ? ? "C1'" C DG 110 ? ? N9 C DG 110 ? ? 111.20 108.30 2.90 0.30 N 19 1 "O4'" D DC 113 ? ? "C1'" D DC 113 ? ? N1 D DC 113 ? ? 110.81 108.30 2.51 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8D93 'double helix' 8D93 'a-form double helix' 8D93 '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 -0.101 -0.027 0.339 1.299 -5.362 -0.713 1 A_DG103:DC114_C A 103 ? C 114 ? 19 1 1 A DC 4 1_555 C DG 13 1_555 0.109 -0.144 0.882 -11.113 -10.732 -3.250 2 A_DC104:DG113_C A 104 ? C 113 ? 19 1 1 A DA 5 1_555 C DT 12 1_555 0.232 -0.149 1.010 1.394 -5.413 -4.981 3 A_DA105:DT112_C A 105 ? C 112 ? 20 1 1 A DG 6 1_555 C DC 11 1_555 -0.190 -0.168 0.519 11.064 -1.367 -0.029 4 A_DG106:DC111_C A 106 ? C 111 ? 19 1 1 A DC 7 1_555 C DG 10 1_555 0.225 -0.235 0.131 6.037 -2.430 1.394 5 A_DC107:DG110_C A 107 ? C 110 ? 19 1 1 A DC 8 1_555 C DG 9 1_555 0.153 -0.233 0.191 -1.394 -6.764 -3.967 6 A_DC108:DG109_C A 108 ? C 109 ? 19 1 1 A DT 9 1_555 B DA 3 1_555 -0.096 -0.266 0.131 -4.741 -3.518 7.263 7 A_DT109:DA107_B A 109 ? B 107 ? 20 1 1 A DG 10 1_555 B DC 2 1_555 -0.213 -0.339 0.033 -1.784 -2.497 -0.779 8 A_DG110:DC106_B A 110 ? B 106 ? 19 1 1 A DT 11 1_555 B DA 1 1_555 -0.317 -0.111 -0.137 3.864 -2.253 -6.468 9 A_DT111:DA105_B A 111 ? B 105 ? 20 1 1 C DT 3 1_555 D DA 9 1_555 -0.647 -0.257 -0.675 13.207 2.954 -8.530 10 C_DT103:DA121_D C 103 ? D 121 ? 20 1 1 C DG 4 1_555 D DC 8 1_555 -0.133 -0.218 -0.051 8.378 -2.293 1.665 11 C_DG104:DC120_D C 104 ? D 120 ? 19 1 1 C DA 5 1_555 D DT 7 1_555 0.046 -0.240 0.225 3.140 -4.101 1.021 12 C_DA105:DT119_D C 105 ? D 119 ? 20 1 1 C DT 6 1_555 D DA 6 1_555 -0.134 -0.342 0.303 -3.319 -5.302 1.213 13 C_DT106:DA118_D C 106 ? D 118 ? 20 1 1 C DG 7 1_555 D DC 5 1_555 -0.181 -0.184 0.292 -5.336 -6.242 2.503 14 C_DG107:DC117_D C 107 ? D 117 ? 19 1 1 C DT 8 1_555 D DA 4 1_555 -0.348 -0.009 0.104 -2.474 -5.597 -1.318 15 C_DT108:DA116_D C 108 ? D 116 ? 20 1 1 B DC 4 1_555 D DG 3 1_555 0.069 -0.233 0.090 -3.443 -4.210 -3.242 16 B_DC111:DG115_D B 111 ? D 115 ? 19 1 1 B DC 5 1_555 D DG 2 1_555 0.142 -0.005 -0.150 1.612 -2.870 -5.530 17 B_DC112:DG114_D B 112 ? D 114 ? 19 1 1 B DG 6 1_555 D DC 1 1_555 -0.072 -0.696 -0.184 -3.614 -5.779 -7.234 18 B_DG113:DC113_D B 113 ? D 113 ? 22 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 0.475 -0.821 3.413 -1.349 3.865 34.155 -2.009 -1.020 3.283 6.550 2.286 34.392 1 AA_DG103DC104:DG113DC114_CC A 103 ? C 114 ? A 104 ? C 113 ? 1 A DC 4 1_555 C DG 13 1_555 A DA 5 1_555 C DT 12 1_555 -0.447 -0.407 2.700 -2.307 8.198 36.922 -1.488 0.446 2.576 12.737 3.585 37.858 2 AA_DC104DA105:DT112DG113_CC A 104 ? C 113 ? A 105 ? C 112 ? 1 A DA 5 1_555 C DT 12 1_555 A DG 6 1_555 C DC 11 1_555 0.240 -1.039 3.000 1.049 3.100 29.616 -2.604 -0.269 2.885 6.042 -2.044 29.792 3 AA_DA105DG106:DC111DT112_CC A 105 ? C 112 ? A 106 ? C 111 ? 1 A DG 6 1_555 C DC 11 1_555 A DC 7 1_555 C DG 10 1_555 0.589 -1.133 3.457 0.297 -1.082 34.977 -1.711 -0.932 3.494 -1.800 -0.493 34.995 4 AA_DG106DC107:DG110DC111_CC A 106 ? C 111 ? A 107 ? C 110 ? 1 A DC 7 1_555 C DG 10 1_555 A DC 8 1_555 C DG 9 1_555 -0.020 -1.019 3.388 -3.638 3.055 42.043 -1.733 -0.353 3.300 4.242 5.051 42.299 5 AA_DC107DC108:DG109DG110_CC A 107 ? C 110 ? A 108 ? C 109 ? 1 A DC 8 1_555 C DG 9 1_555 A DT 9 1_555 B DA 3 1_555 -1.472 -1.363 3.496 -1.295 0.006 18.713 -4.184 3.771 3.588 0.019 3.978 18.758 6 AA_DC108DT109:DA107DG109_BC A 108 ? C 109 ? A 109 ? B 107 ? 1 A DT 9 1_555 B DA 3 1_555 A DG 10 1_555 B DC 2 1_555 -0.260 -0.072 3.459 1.171 2.640 25.911 -0.921 0.914 3.419 5.864 -2.601 26.068 7 AA_DT109DG110:DC106DA107_BB A 109 ? B 107 ? A 110 ? B 106 ? 1 A DG 10 1_555 B DC 2 1_555 A DT 11 1_555 B DA 1 1_555 -0.221 0.708 3.250 2.281 4.015 33.598 0.567 0.747 3.288 6.905 -3.922 33.905 8 AA_DG110DT111:DA105DC106_BB A 110 ? B 106 ? A 111 ? B 105 ? 1 C DT 3 1_555 D DA 9 1_555 C DG 4 1_555 D DC 8 1_555 0.468 -0.079 3.569 -7.524 3.831 38.543 -0.606 -1.652 3.399 5.721 11.234 39.423 9 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 -0.013 -0.570 3.304 -3.052 -2.654 37.086 -0.534 -0.390 3.326 -4.158 4.781 37.298 10 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 -0.122 -0.320 3.500 -1.336 -3.393 31.327 0.091 -0.042 3.516 -6.257 2.463 31.533 11 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 0.127 0.406 3.231 -0.599 -3.823 45.666 0.848 -0.215 3.187 -4.916 0.770 45.821 12 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 -0.090 -0.438 3.287 3.233 1.904 24.587 -1.589 1.179 3.207 4.439 -7.535 24.867 13 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 0.747 0.030 3.293 1.878 -3.827 29.296 0.879 -1.061 3.303 -7.517 -3.689 29.598 14 CB_DT108DC111:DG115DA116_DD C 108 ? D 116 ? B 111 ? D 115 ? 1 B DC 4 1_555 D DG 3 1_555 B DC 5 1_555 D DG 2 1_555 0.047 1.311 3.439 4.937 4.756 42.863 1.278 0.452 3.542 6.458 -6.704 43.382 15 BB_DC111DC112:DG114DG115_DD B 111 ? D 115 ? B 112 ? D 114 ? 1 B DC 5 1_555 D DG 2 1_555 B DG 6 1_555 D DC 1 1_555 -0.235 2.410 3.509 0.351 -0.082 42.770 3.313 0.360 3.503 -0.112 -0.481 42.772 16 BB_DC112DG113:DC113DG114_DD B 112 ? D 114 ? B 113 ? 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 'National Aeronautic Space Administration (NASA, United States)' 'United States' '2020 NASA Center Innovation Fund' 6 # _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 'R 3 :H' _space_group.name_Hall 'R 3' _space_group.IT_number 146 _space_group.crystal_system trigonal _space_group.id 1 #