data_8TC4 # _entry.id 8TC4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 8TC4 pdb_00008tc4 10.2210/pdb8tc4/pdb WWPDB D_1000275297 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8TC4 _pdbx_database_status.recvd_initial_deposition_date 2023-06-29 _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 'Simmons, C.R.' 1 0000-0002-2290-6132 'MacCulloch, T.' 2 0000-0001-5875-3361 'Stephanopoulos, N.' 3 0000-0001-7859-410X 'Yan, H.' 4 0000-0001-7397-9852 # _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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_id_ASTM JACSAT _citation.journal_id_CSD ? _citation.journal_id_ISSN 1520-5126 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 145 _citation.language ? _citation.page_first 26075 _citation.page_last 26085 _citation.title ;Site-Specific Arrangement and Structure Determination of Minor Groove Binding Molecules in Self-Assembled Three-Dimensional DNA Crystals. ; _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/jacs.3c07802 _citation.pdbx_database_id_PubMed 37987645 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Simmons, C.R.' 1 0000-0002-2290-6132 primary 'Buchberger, A.' 2 ? primary 'Henry, S.J.W.' 3 0000-0002-5132-3948 primary 'Novacek, A.' 4 ? primary 'Fahmi, N.E.' 5 ? primary 'MacCulloch, T.' 6 ? primary 'Stephanopoulos, N.' 7 0000-0001-7859-410X primary 'Yan, H.' 8 0000-0001-7397-9852 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 8TC4 _cell.details ? _cell.formula_units_Z ? _cell.length_a 68.653 _cell.length_a_esd ? _cell.length_b 68.653 _cell.length_b_esd ? _cell.length_c 62.183 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 3 _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 8TC4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' _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*AP*CP*CP*TP*GP*AP*CP*GP*AP*TP*GP*TP*CP*AP*C)-3') ; 6457.187 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(P*CP*GP*TP*CP*A)-3') ; 1480.012 1 ? ? ? ? 3 polymer syn ;DNA (5'-D(*TP*CP*GP*TP*GP*AP*CP*AP*T)-3') ; 2730.810 1 ? ? ? ? 4 polymer syn ;DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3') ; 2129.409 1 ? ? ? ? 5 non-polymer syn ;N-[5-({5-[(3-{[3-(dimethylamino)propyl]amino}-3-oxopropyl)carbamoyl]-1-methyl-1H-pyrrol-3-yl}carbamoyl)-1-methyl-1H-pyrrol-3-yl]-1-methyl-1H-imidazole-2-carboxamide ; 525.603 2 ? ? ? ? 6 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 7 water nat water 18.015 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)(DA)(DC)(DC)(DT)(DG)(DA)(DC)(DG)(DA)(DT)(DG)(DT)(DC)(DA) (DC) ; GAGCAGACCTGACGATGTCAC A ? 2 polydeoxyribonucleotide no no '(DC)(DG)(DT)(DC)(DA)' CGTCA B ? 3 polydeoxyribonucleotide no no '(DT)(DC)(DG)(DT)(DG)(DA)(DC)(DA)(DT)' TCGTGACAT C ? 4 polydeoxyribonucleotide no no '(DG)(DG)(DT)(DC)(DT)(DG)(DC)' GGTCTGC 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 DA n 1 8 DC n 1 9 DC n 1 10 DT n 1 11 DG n 1 12 DA n 1 13 DC n 1 14 DG n 1 15 DA n 1 16 DT n 1 17 DG n 1 18 DT n 1 19 DC n 1 20 DA n 1 21 DC n 2 1 DC n 2 2 DG n 2 3 DT n 2 4 DC n 2 5 DA n 3 1 DT n 3 2 DC n 3 3 DG n 3 4 DT n 3 5 DG n 3 6 DA n 3 7 DC n 3 8 DA n 3 9 DT n 4 1 DG n 4 2 DG n 4 3 DT n 4 4 DC n 4 5 DT n 4 6 DG n 4 7 DC 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 21 'synthetic construct' ? 32630 ? 2 1 sample 1 5 'synthetic construct' ? 32630 ? 3 1 sample 1 9 'synthetic construct' ? 32630 ? 4 1 sample 1 7 '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 8TC4 8TC4 ? 1 ? 1 2 PDB 8TC4 8TC4 ? 2 ? 1 3 PDB 8TC4 8TC4 ? 3 ? 1 4 PDB 8TC4 8TC4 ? 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 8TC4 A 1 ? 21 ? 8TC4 1 ? 21 ? 1 21 2 2 8TC4 B 1 ? 5 ? 8TC4 1 ? 5 ? 1 5 3 3 8TC4 C 1 ? 9 ? 8TC4 1 ? 9 ? 1 9 4 4 8TC4 D 1 ? 7 ? 8TC4 10 ? 16 ? 10 16 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 ZQQ non-polymer . ;N-[5-({5-[(3-{[3-(dimethylamino)propyl]amino}-3-oxopropyl)carbamoyl]-1-methyl-1H-pyrrol-3-yl}carbamoyl)-1-methyl-1H-pyrrol-3-yl]-1-methyl-1H-imidazole-2-carboxamide ; ? 'C25 H35 N9 O4' 525.603 # _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 8TC4 _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 6.61 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 81.40 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.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, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details 'temperature gradient generated from 60 to 25 C at 0.3 degrees per hour' _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;0.5 mL of 0.05 M HEPES pH 7.5 with 20 mM MgCl2, 1.0 mM spermine, and 5% PEG 8000 was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock. ; _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 298 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS3 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2019-09-21 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.92 _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 'ALS BEAMLINE 5.0.2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.92 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 5.0.2 _diffrn_source.pdbx_synchrotron_site ALS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 8TC4 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 3.05 _reflns.d_resolution_low 50.00 _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 5432 _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 87.2 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 9.2 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 5.5 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.064 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.094 _reflns.pdbx_Rpim_I_all 0.029 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 1.00 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.089 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_redundancy_anomalous _reflns_shell.pdbx_CC_half_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_percent_possible_anomalous 3.05 3.10 ? ? ? ? ? ? 181 ? ? ? ? ? ? ? ? ? ? ? 8.3 0.401 ? ? 1.764 0.576 ? 1 1 0.628 0.878 ? 54.2 ? 1.663 ? ? ? ? ? ? ? ? ? 3.10 3.16 ? ? ? ? ? ? 161 ? ? ? ? ? ? ? ? ? ? ? 8.3 0.441 ? ? 0.840 0.277 ? 2 1 0.894 0.972 ? 56.9 ? 0.791 ? ? ? ? ? ? ? ? ? 3.16 3.22 ? ? ? ? ? ? 205 ? ? ? ? ? ? ? ? ? ? ? 8.5 0.557 ? ? 0.253 0.082 ? 3 1 0.992 0.998 ? 64.5 ? 0.239 ? ? ? ? ? ? ? ? ? 3.22 3.29 ? ? ? ? ? ? 221 ? ? ? ? ? ? ? ? ? ? ? 8.3 0.691 ? ? 0.174 0.056 ? 4 1 0.996 0.999 ? 66.0 ? 0.164 ? ? ? ? ? ? ? ? ? 3.29 3.36 ? ? ? ? ? ? 202 ? ? ? ? ? ? ? ? ? ? ? 8.6 0.475 ? ? 0.399 0.130 ? 5 1 0.976 0.994 ? 69.4 ? 0.377 ? ? ? ? ? ? ? ? ? 3.36 3.43 ? ? ? ? ? ? 257 ? ? ? ? ? ? ? ? ? ? ? 7.7 0.496 ? ? 0.331 0.111 ? 6 1 0.977 0.994 ? 79.1 ? 0.312 ? ? ? ? ? ? ? ? ? 3.43 3.52 ? ? ? ? ? ? 227 ? ? ? ? ? ? ? ? ? ? ? 7.8 0.601 ? ? 0.262 0.091 ? 7 1 0.987 0.997 ? 78.3 ? 0.245 ? ? ? ? ? ? ? ? ? 3.52 3.62 ? ? ? ? ? ? 288 ? ? ? ? ? ? ? ? ? ? ? 8.3 0.527 ? ? 0.242 0.080 ? 8 1 0.993 0.998 ? 86.2 ? 0.228 ? ? ? ? ? ? ? ? ? 3.62 3.72 ? ? ? ? ? ? 284 ? ? ? ? ? ? ? ? ? ? ? 8.6 0.485 ? ? 0.347 0.112 ? 9 1 0.981 0.995 ? 92.8 ? 0.328 ? ? ? ? ? ? ? ? ? 3.72 3.84 ? ? ? ? ? ? 300 ? ? ? ? ? ? ? ? ? ? ? 9.2 0.457 ? ? 0.351 0.110 ? 10 1 0.978 0.994 ? 98.4 ? 0.332 ? ? ? ? ? ? ? ? ? 3.84 3.98 ? ? ? ? ? ? 299 ? ? ? ? ? ? ? ? ? ? ? 9.5 0.511 ? ? 0.383 0.121 ? 11 1 0.977 0.994 ? 99.0 ? 0.363 ? ? ? ? ? ? ? ? ? 3.98 4.14 ? ? ? ? ? ? 314 ? ? ? ? ? ? ? ? ? ? ? 9.8 0.495 ? ? 0.313 0.098 ? 12 1 0.985 0.996 ? 100.0 ? 0.297 ? ? ? ? ? ? ? ? ? 4.14 4.33 ? ? ? ? ? ? 313 ? ? ? ? ? ? ? ? ? ? ? 9.8 0.540 ? ? 0.233 0.074 ? 13 1 0.987 0.997 ? 100.0 ? 0.221 ? ? ? ? ? ? ? ? ? 4.33 4.56 ? ? ? ? ? ? 323 ? ? ? ? ? ? ? ? ? ? ? 9.2 0.617 ? ? 0.204 0.067 ? 14 1 0.989 0.997 ? 100.0 ? 0.192 ? ? ? ? ? ? ? ? ? 4.56 4.84 ? ? ? ? ? ? 296 ? ? ? ? ? ? ? ? ? ? ? 9.7 0.790 ? ? 0.166 0.053 ? 15 1 0.991 0.998 ? 100.0 ? 0.158 ? ? ? ? ? ? ? ? ? 4.84 5.21 ? ? ? ? ? ? 317 ? ? ? ? ? ? ? ? ? ? ? 10.5 1.108 ? ? 0.124 0.038 ? 16 1 0.993 0.998 ? 100.0 ? 0.118 ? ? ? ? ? ? ? ? ? 5.21 5.74 ? ? ? ? ? ? 313 ? ? ? ? ? ? ? ? ? ? ? 10.5 1.681 ? ? 0.106 0.033 ? 17 1 0.995 0.999 ? 100.0 ? 0.101 ? ? ? ? ? ? ? ? ? 5.74 6.57 ? ? ? ? ? ? 308 ? ? ? ? ? ? ? ? ? ? ? 9.8 1.764 ? ? 0.100 0.032 ? 18 1 0.995 0.999 ? 100.0 ? 0.095 ? ? ? ? ? ? ? ? ? 6.57 8.27 ? ? ? ? ? ? 313 ? ? ? ? ? ? ? ? ? ? ? 9.9 2.571 ? ? 0.089 0.028 ? 19 1 0.997 0.999 ? 100.0 ? 0.084 ? ? ? ? ? ? ? ? ? 8.27 50.00 ? ? ? ? ? ? 310 ? ? ? ? ? ? ? ? ? ? ? 10.0 3.809 ? ? 0.072 0.023 ? 20 1 0.997 0.999 ? 100.0 ? 0.069 ? ? ? ? ? ? ? ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8TC4 _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 3.06 _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 5365 _refine.ls_number_reflns_R_free 583 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 86.52 _refine.ls_percent_reflns_R_free 10.87 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2318 _refine.ls_R_factor_R_free 0.2535 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2289 _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 THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 45.31 _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 0.18 _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.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 855 _refine_hist.pdbx_number_atoms_ligand 78 _refine_hist.number_atoms_solvent 1 _refine_hist.number_atoms_total 934 _refine_hist.d_res_high 3.06 _refine_hist.d_res_low 34.33 # 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' ? 0.006 ? 1036 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.813 ? 1577 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 34.394 ? 426 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.040 ? 166 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.004 ? 56 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 3.06 3.37 . . 108 818 59.00 . . . . 0.4159 . . . . . . . . . . . 0.3985 'X-RAY DIFFRACTION' 3.37 3.85 . . 102 1256 87.00 . . . . 0.3499 . . . . . . . . . . . 0.3965 'X-RAY DIFFRACTION' 3.85 4.84 . . 157 1374 100.00 . . . . 0.3372 . . . . . . . . . . . 0.3291 'X-RAY DIFFRACTION' 4.85 34.33 . . 216 1334 100.00 . . . . 0.1639 . . . . . . . . . . . 0.2136 # _struct.entry_id 8TC4 _struct.title ;Sequence specific (TGTCA) orientation of ImPyPy molecules at a unique minor groove binding site within a self-assembled 3D DNA lattice (4x5) ; _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 8TC4 _struct_keywords.text ;Self-Assembly, DNA Nanotechnology, DNA Scaffold, Crystal Lattice, DNA, Minor Groove Binders, Netropsin, DAPI, Hoechst, ImPyPy, polyamide, host-guest ; _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 ? E N N 5 ? F N N 6 ? G N N 5 ? H N N 6 ? I N N 7 ? # 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 D DC 7 N3 ? ? A DG 3 D DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 3 N2 ? ? ? 1_555 D DC 7 O2 ? ? A DG 3 D DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 3 O6 ? ? ? 1_555 D DC 7 N4 ? ? A DG 3 D DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 4 O2 ? ? ? 1_555 D DG 6 N2 ? ? A DC 4 D DG 15 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog5 hydrog ? ? A DA 5 N1 ? ? ? 1_555 D DT 5 N3 ? ? A DA 5 D DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DA 5 N6 ? ? ? 1_555 D DT 5 O4 ? ? A DA 5 D DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 6 N1 ? ? ? 1_555 D DC 4 N3 ? ? A DG 6 D DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 6 N2 ? ? ? 1_555 D DC 4 O2 ? ? A DG 6 D DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 6 O6 ? ? ? 1_555 D DC 4 N4 ? ? A DG 6 D DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 7 N1 ? ? ? 1_555 D DT 3 N3 ? ? A DA 7 D DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 7 N6 ? ? ? 1_555 D DT 3 O4 ? ? A DA 7 D DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 8 N3 ? ? ? 1_555 D DG 2 N1 ? ? A DC 8 D DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 8 N4 ? ? ? 1_555 D DG 2 O6 ? ? A DC 8 D DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 O2 ? ? ? 1_555 D DG 2 N2 ? ? A DC 8 D DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 9 N3 ? ? ? 1_555 D DG 1 N1 ? ? A DC 9 D DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 9 N4 ? ? ? 1_555 D DG 1 O6 ? ? A DC 9 D DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 9 O2 ? ? ? 1_555 D DG 1 N2 ? ? A DC 9 D DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 10 B DA 5 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog19 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DA 12 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 12 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DA 12 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 12 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 13 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 13 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 13 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 13 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 13 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 13 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 14 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 14 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 14 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 14 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 14 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 14 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DA 15 N1 ? ? ? 1_555 C DT 9 N3 ? ? A DA 15 C DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DA 15 N6 ? ? ? 1_555 C DT 9 O4 ? ? A DA 15 C DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DT 16 N3 ? ? ? 1_555 C DA 8 N1 ? ? A DT 16 C DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DT 16 O4 ? ? ? 1_555 C DA 8 N6 ? ? A DT 16 C DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DG 17 N1 ? ? ? 1_555 C DA 6 N1 ? ? A DG 17 C DA 6 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog35 hydrog ? ? A DG 17 O6 ? ? ? 1_555 C DA 6 N6 ? ? A DG 17 C DA 6 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog36 hydrog ? ? A DG 17 N1 ? ? ? 1_555 C DC 7 N3 ? ? A DG 17 C DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A DG 17 N2 ? ? ? 1_555 C DC 7 O2 ? ? A DG 17 C DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A DG 17 O6 ? ? ? 1_555 C DC 7 N4 ? ? A DG 17 C DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A DT 18 N3 ? ? ? 1_555 C DA 6 N1 ? ? A DT 18 C DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A DT 18 O4 ? ? ? 1_555 C DA 6 N6 ? ? A DT 18 C DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A DC 19 N3 ? ? ? 1_555 C DG 5 N1 ? ? A DC 19 C DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A DC 19 N4 ? ? ? 1_555 C DG 5 O6 ? ? A DC 19 C DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A DC 19 O2 ? ? ? 1_555 C DG 5 N2 ? ? A DC 19 C DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A DA 20 N1 ? ? ? 1_555 C DG 3 N1 ? ? A DA 20 C DG 3 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog45 hydrog ? ? A DA 20 N6 ? ? ? 1_555 C DG 3 O6 ? ? A DA 20 C DG 3 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog46 hydrog ? ? A DC 21 N3 ? ? ? 1_555 C DG 3 N1 ? ? A DC 21 C DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A DC 21 N4 ? ? ? 1_555 C DG 3 O6 ? ? A DC 21 C DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A DC 21 O2 ? ? ? 1_555 C DG 3 N2 ? ? A DC 21 C DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 8TC4 _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] 0.014566 _atom_sites.fract_transf_matrix[1][2] 0.008410 _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] 0.016819 _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] 0.016082 _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 C MG N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG DG A . n A 1 2 DA 2 2 2 DA DA A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DA 7 7 7 DA DA A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DT 10 10 10 DT DT A . n A 1 11 DG 11 11 11 DG DG A . n A 1 12 DA 12 12 12 DA DA A . n A 1 13 DC 13 13 13 DC DC A . n A 1 14 DG 14 14 14 DG DG A . n A 1 15 DA 15 15 15 DA DA A . n A 1 16 DT 16 16 16 DT DT A . n A 1 17 DG 17 17 17 DG DG A . n A 1 18 DT 18 18 18 DT DT A . n A 1 19 DC 19 19 19 DC DC A . n A 1 20 DA 20 20 20 DA DA A . n A 1 21 DC 21 21 21 DC DC A . n B 2 1 DC 1 1 1 DC DC B . n B 2 2 DG 2 2 2 DG DG B . n B 2 3 DT 3 3 3 DT DT B . n B 2 4 DC 4 4 4 DC DC B . n B 2 5 DA 5 5 5 DA DA B . n C 3 1 DT 1 1 1 DT DT C . n C 3 2 DC 2 2 2 DC DC C . n C 3 3 DG 3 3 3 DG DG C . n C 3 4 DT 4 4 4 DT DT C . n C 3 5 DG 5 5 5 DG DG C . n C 3 6 DA 6 6 6 DA DA C . n C 3 7 DC 7 7 7 DC DC C . n C 3 8 DA 8 8 8 DA DA C . n C 3 9 DT 9 9 9 DT DT C . n D 4 1 DG 1 10 10 DG DG D . n D 4 2 DG 2 11 11 DG DG D . n D 4 3 DT 3 12 12 DT DT D . n D 4 4 DC 4 13 13 DC DC D . n D 4 5 DT 5 14 14 DT DT D . n D 4 6 DG 6 15 15 DG DG D . n D 4 7 DC 7 16 16 DC DC D . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email hao.yan@asu.edu _pdbx_contact_author.name_first Hao _pdbx_contact_author.name_last Yan _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0001-7397-9852 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 5 ZQQ 1 101 2 ZQQ DER A . F 6 MG 1 101 2 MG MG B . G 5 ZQQ 1 101 1 ZQQ DER C . H 6 MG 1 101 1 MG MG D . I 7 HOH 1 201 1 HOH HOH C . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2023-12-20 # _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_ _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 ? ? ? '(1.19.2_4158: ???)' 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _pdbx_entry_details.entry_id 8TC4 _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # loop_ _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 DT 16 ? ? "C1'" A DT 16 ? ? N1 A DT 16 ? ? 110.41 108.30 2.11 0.30 N 2 1 "O4'" C DT 9 ? ? "C1'" C DT 9 ? ? N1 C DT 9 ? ? 110.28 108.30 1.98 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 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 MG MG MG N N 147 ZQQ C01 C Y N 148 ZQQ C03 C Y N 149 ZQQ C04 C Y N 150 ZQQ C06 C N N 151 ZQQ C07 C N N 152 ZQQ C10 C Y N 153 ZQQ C11 C Y N 154 ZQQ C13 C Y N 155 ZQQ C14 C Y N 156 ZQQ C15 C N N 157 ZQQ C16 C N N 158 ZQQ C19 C Y N 159 ZQQ C20 C Y N 160 ZQQ C22 C Y N 161 ZQQ C23 C Y N 162 ZQQ C24 C N N 163 ZQQ C25 C N N 164 ZQQ C28 C N N 165 ZQQ C29 C N N 166 ZQQ C30 C N N 167 ZQQ C33 C N N 168 ZQQ C34 C N N 169 ZQQ C35 C N N 170 ZQQ C37 C N N 171 ZQQ C38 C N N 172 ZQQ N02 N Y N 173 ZQQ N05 N Y N 174 ZQQ N08 N N N 175 ZQQ N12 N Y N 176 ZQQ N17 N N N 177 ZQQ N21 N Y N 178 ZQQ N27 N N N 179 ZQQ N31 N N N 180 ZQQ N36 N N N 181 ZQQ O09 O N N 182 ZQQ O18 O N N 183 ZQQ O26 O N N 184 ZQQ O32 O N N 185 ZQQ H1 H N N 186 ZQQ H2 H N N 187 ZQQ H3 H N N 188 ZQQ H4 H N N 189 ZQQ H5 H N N 190 ZQQ H6 H N N 191 ZQQ H7 H N N 192 ZQQ H8 H N N 193 ZQQ H9 H N N 194 ZQQ H10 H N N 195 ZQQ H11 H N N 196 ZQQ H12 H N N 197 ZQQ H13 H N N 198 ZQQ H14 H N N 199 ZQQ H15 H N N 200 ZQQ H16 H N N 201 ZQQ H17 H N N 202 ZQQ H18 H N N 203 ZQQ H19 H N N 204 ZQQ H20 H N N 205 ZQQ H21 H N N 206 ZQQ H22 H N N 207 ZQQ H23 H N N 208 ZQQ H24 H N N 209 ZQQ H25 H N N 210 ZQQ H26 H N N 211 ZQQ H27 H N N 212 ZQQ H28 H N N 213 ZQQ H29 H N N 214 ZQQ H30 H N N 215 ZQQ H31 H N N 216 ZQQ H32 H N N 217 ZQQ H33 H N N 218 ZQQ H34 H N N 219 ZQQ H35 H N N 220 # 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 HOH O H1 sing N N 150 HOH O H2 sing N N 151 ZQQ C34 C33 sing N N 152 ZQQ C34 C35 sing N N 153 ZQQ C33 N31 sing N N 154 ZQQ N31 C30 sing N N 155 ZQQ C35 N36 sing N N 156 ZQQ C03 C04 doub Y N 157 ZQQ C03 N02 sing Y N 158 ZQQ C04 N05 sing Y N 159 ZQQ C37 N36 sing N N 160 ZQQ N36 C38 sing N N 161 ZQQ N02 C01 doub Y N 162 ZQQ C30 O32 doub N N 163 ZQQ C30 C29 sing N N 164 ZQQ N05 C01 sing Y N 165 ZQQ N05 C06 sing N N 166 ZQQ C01 C07 sing N N 167 ZQQ C29 C28 sing N N 168 ZQQ C28 N27 sing N N 169 ZQQ C07 N08 sing N N 170 ZQQ C07 O09 doub N N 171 ZQQ N08 C10 sing N N 172 ZQQ N27 C25 sing N N 173 ZQQ C10 C14 sing Y N 174 ZQQ C10 C11 doub Y N 175 ZQQ C14 C13 doub Y N 176 ZQQ C23 C22 doub Y N 177 ZQQ C23 C19 sing Y N 178 ZQQ C25 O26 doub N N 179 ZQQ C25 C22 sing N N 180 ZQQ C22 N21 sing Y N 181 ZQQ N17 C19 sing N N 182 ZQQ N17 C16 sing N N 183 ZQQ C11 N12 sing Y N 184 ZQQ C19 C20 doub Y N 185 ZQQ C13 C16 sing N N 186 ZQQ C13 N12 sing Y N 187 ZQQ C16 O18 doub N N 188 ZQQ N12 C15 sing N N 189 ZQQ N21 C20 sing Y N 190 ZQQ N21 C24 sing N N 191 ZQQ C03 H1 sing N N 192 ZQQ C04 H2 sing N N 193 ZQQ C06 H3 sing N N 194 ZQQ C06 H4 sing N N 195 ZQQ C06 H5 sing N N 196 ZQQ C11 H6 sing N N 197 ZQQ C14 H7 sing N N 198 ZQQ C15 H8 sing N N 199 ZQQ C15 H9 sing N N 200 ZQQ C15 H10 sing N N 201 ZQQ C20 H11 sing N N 202 ZQQ C23 H12 sing N N 203 ZQQ C24 H13 sing N N 204 ZQQ C24 H14 sing N N 205 ZQQ C24 H15 sing N N 206 ZQQ C28 H16 sing N N 207 ZQQ C28 H17 sing N N 208 ZQQ C29 H18 sing N N 209 ZQQ C29 H19 sing N N 210 ZQQ C33 H20 sing N N 211 ZQQ C33 H21 sing N N 212 ZQQ C34 H22 sing N N 213 ZQQ C34 H23 sing N N 214 ZQQ C35 H24 sing N N 215 ZQQ C35 H25 sing N N 216 ZQQ C37 H26 sing N N 217 ZQQ C37 H27 sing N N 218 ZQQ C37 H28 sing N N 219 ZQQ C38 H29 sing N N 220 ZQQ C38 H30 sing N N 221 ZQQ C38 H31 sing N N 222 ZQQ N08 H32 sing N N 223 ZQQ N17 H33 sing N N 224 ZQQ N27 H34 sing N N 225 ZQQ N31 H35 sing N N 226 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8TC4 'double helix' 8TC4 '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 D DC 7 1_555 -0.230 -0.191 -0.606 -4.916 -12.470 5.845 1 A_DG3:DC16_D A 3 ? D 16 ? 19 1 1 A DC 4 1_555 D DG 6 1_555 -0.399 1.322 -0.318 -5.017 -16.685 19.906 2 A_DC4:DG15_D A 4 ? D 15 ? ? 1 1 A DA 5 1_555 D DT 5 1_555 0.209 -0.131 -1.049 -11.345 1.741 -6.394 3 A_DA5:DT14_D A 5 ? D 14 ? 20 1 1 A DG 6 1_555 D DC 4 1_555 -0.279 0.003 -0.725 -6.688 -8.054 8.625 4 A_DG6:DC13_D A 6 ? D 13 ? 19 1 1 A DA 7 1_555 D DT 3 1_555 0.055 -0.121 -0.834 -7.205 -13.369 -2.355 5 A_DA7:DT12_D A 7 ? D 12 ? 20 1 1 A DC 8 1_555 D DG 2 1_555 0.231 -0.098 -0.213 -3.257 -7.957 2.698 6 A_DC8:DG11_D A 8 ? D 11 ? 19 1 1 A DC 9 1_555 D DG 1 1_555 0.143 -0.007 0.050 -4.554 -6.858 1.745 7 A_DC9:DG10_D A 9 ? D 10 ? 19 1 1 A DT 10 1_555 B DA 5 1_555 -1.491 0.266 0.534 -8.783 -15.317 8.727 8 A_DT10:DA5_B A 10 ? B 5 ? ? ? 1 A DG 11 1_555 B DC 4 1_555 -0.196 -0.115 -0.088 1.535 -11.114 0.184 9 A_DG11:DC4_B A 11 ? B 4 ? 19 1 1 A DA 12 1_555 B DT 3 1_555 0.074 -0.075 -0.392 -4.199 -12.974 -0.130 10 A_DA12:DT3_B A 12 ? B 3 ? 20 1 1 A DC 13 1_555 B DG 2 1_555 0.131 -0.159 -0.062 -7.109 -13.386 1.196 11 A_DC13:DG2_B A 13 ? B 2 ? 19 1 1 A DG 14 1_555 B DC 1 1_555 -0.107 -0.343 1.044 6.362 -3.468 -2.135 12 A_DG14:DC1_B A 14 ? B 1 ? 19 1 1 A DA 15 1_555 C DT 9 1_555 0.024 -0.097 0.386 -6.227 -1.325 -0.693 13 A_DA15:DT9_C A 15 ? C 9 ? 20 1 1 A DT 16 1_555 C DA 8 1_555 -0.158 -0.047 0.453 -2.445 0.129 -0.759 14 A_DT16:DA8_C A 16 ? C 8 ? 20 1 1 A DG 17 1_555 C DC 7 1_555 -0.135 -0.196 0.805 -1.128 -0.961 -2.254 15 A_DG17:DC7_C A 17 ? C 7 ? 19 1 1 A DT 18 1_555 C DA 6 1_555 -0.344 -0.066 0.783 2.633 -6.667 -17.231 16 A_DT18:DA6_C A 18 ? C 6 ? 20 1 1 A DC 19 1_555 C DG 5 1_555 0.065 -0.164 0.834 1.067 -8.191 -3.424 17 A_DC19:DG5_C A 19 ? C 5 ? 19 1 1 A DC 21 1_555 C DG 3 1_555 0.131 -0.213 0.968 -1.428 -8.430 -2.144 18 A_DC21:DG3_C A 21 ? C 3 ? 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 D DC 7 1_555 A DC 4 1_555 D DG 6 1_555 0.756 0.284 3.066 -0.512 1.618 30.980 0.239 -1.505 3.064 3.027 0.957 31.026 1 AA_DG3DC4:DG15DC16_DD A 3 ? D 16 ? A 4 ? D 15 ? 1 A DC 4 1_555 D DG 6 1_555 A DA 5 1_555 D DT 5 1_555 -2.114 1.384 3.276 -5.733 8.485 41.427 0.976 2.281 3.723 11.779 7.959 42.619 2 AA_DC4DA5:DT14DG15_DD A 4 ? D 15 ? A 5 ? D 14 ? 1 A DA 5 1_555 D DT 5 1_555 A DG 6 1_555 D DC 4 1_555 1.546 -0.885 3.201 -2.626 11.228 26.235 -4.092 -3.667 2.459 23.355 5.461 28.616 3 AA_DA5DG6:DC13DT14_DD A 5 ? D 14 ? A 6 ? D 13 ? 1 A DG 6 1_555 D DC 4 1_555 A DA 7 1_555 D DT 3 1_555 -1.943 0.882 3.240 -9.329 0.512 38.529 1.239 1.708 3.606 0.762 13.890 39.603 4 AA_DG6DA7:DT12DC13_DD A 6 ? D 13 ? A 7 ? D 12 ? 1 A DA 7 1_555 D DT 3 1_555 A DC 8 1_555 D DG 2 1_555 0.657 -0.694 3.040 -6.354 -1.185 34.986 -0.978 -1.925 2.901 -1.951 10.459 35.560 5 AA_DA7DC8:DG11DT12_DD A 7 ? D 12 ? A 8 ? D 11 ? 1 A DC 8 1_555 D DG 2 1_555 A DC 9 1_555 D DG 1 1_555 -0.606 -0.960 3.574 -7.220 -1.370 34.948 -1.345 -0.179 3.656 -2.251 11.861 35.689 6 AA_DC8DC9:DG10DG11_DD A 8 ? D 11 ? A 9 ? D 10 ? 1 A DC 9 1_555 D DG 1 1_555 A DT 10 1_555 B DA 5 1_555 -0.652 -1.686 3.440 -4.915 -2.625 18.267 -3.587 -0.837 3.689 -8.030 15.035 19.091 7 AA_DC9DT10:DA5DG10_BD A 9 ? D 10 ? A 10 ? B 5 ? 1 A DT 10 1_555 B DA 5 1_555 A DG 11 1_555 B DC 4 1_555 -1.062 1.395 3.250 -0.548 7.428 41.462 1.150 1.420 3.452 10.391 0.766 42.096 8 AA_DT10DG11:DC4DA5_BB A 10 ? B 5 ? A 11 ? B 4 ? 1 A DG 11 1_555 B DC 4 1_555 A DA 12 1_555 B DT 3 1_555 -0.255 -0.223 3.408 -2.583 1.654 35.548 -0.614 0.026 3.404 2.703 4.221 35.676 9 AA_DG11DA12:DT3DC4_BB A 11 ? B 4 ? A 12 ? B 3 ? 1 A DA 12 1_555 B DT 3 1_555 A DC 13 1_555 B DG 2 1_555 0.450 -0.891 3.312 -0.679 -2.755 32.611 -1.096 -0.918 3.364 -4.894 1.207 32.731 10 AA_DA12DC13:DG2DT3_BB A 12 ? B 3 ? A 13 ? B 2 ? 1 A DC 13 1_555 B DG 2 1_555 A DG 14 1_555 B DC 1 1_555 0.266 -0.054 3.057 -8.714 -4.675 38.798 0.419 -1.318 2.919 -6.901 12.865 39.992 11 AA_DC13DG14:DC1DG2_BB A 13 ? B 2 ? A 14 ? B 1 ? 1 A DG 14 1_555 B DC 1 1_555 A DA 15 1_555 C DT 9 1_555 -0.851 -1.140 3.538 3.010 2.536 31.880 -2.540 2.109 3.347 4.595 -5.453 32.115 12 AA_DG14DA15:DT9DC1_CB A 14 ? B 1 ? A 15 ? C 9 ? 1 A DA 15 1_555 C DT 9 1_555 A DT 16 1_555 C DA 8 1_555 -0.018 -1.047 3.326 -0.799 3.939 29.897 -2.811 -0.127 3.164 7.592 1.540 30.160 13 AA_DA15DT16:DA8DT9_CC A 15 ? C 9 ? A 16 ? C 8 ? 1 A DT 16 1_555 C DA 8 1_555 A DG 17 1_555 C DC 7 1_555 -1.170 0.136 3.278 -6.264 4.588 40.629 -0.315 0.965 3.409 6.535 8.923 41.333 14 AA_DT16DG17:DC7DA8_CC A 16 ? C 8 ? A 17 ? C 7 ? 1 A DG 17 1_555 C DC 7 1_555 A DT 18 1_555 C DA 6 1_555 -1.198 -0.829 3.109 -1.186 2.226 32.923 -1.817 1.917 3.087 3.921 2.089 33.017 15 AA_DG17DT18:DA6DC7_CC A 17 ? C 7 ? A 18 ? C 6 ? 1 A DT 18 1_555 C DA 6 1_555 A DC 19 1_555 C DG 5 1_555 0.309 -0.217 3.261 1.001 -1.641 36.627 -0.121 -0.355 3.275 -2.609 -1.592 36.675 16 AA_DT18DC19:DG5DA6_CC A 18 ? C 6 ? A 19 ? C 5 ? 1 A DC 19 1_555 C DG 5 1_555 A DC 21 1_555 C DG 3 1_555 0.959 -1.164 7.099 -5.418 2.267 68.732 -1.208 -1.276 6.980 2.004 4.790 68.952 17 AA_DC19DC21:DG3DG5_CC A 19 ? C 5 ? A 21 ? C 3 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Science Foundation (NSF, United States)' 'United States' 1360635 1 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' R01GM104960 2 'National Science Foundation (NSF, United States)' 'United States' NSF2004250 3 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 5 ;N-[5-({5-[(3-{[3-(dimethylamino)propyl]amino}-3-oxopropyl)carbamoyl]-1-methyl-1H-pyrrol-3-yl}carbamoyl)-1-methyl-1H-pyrrol-3-yl]-1-methyl-1H-imidazole-2-carboxamide ; ZQQ 6 'MAGNESIUM ION' MG 7 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 5KEK _pdbx_initial_refinement_model.details ? #