data_8T7B # _entry.id 8T7B # _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 8T7B pdb_00008t7b 10.2210/pdb8t7b/pdb WWPDB D_1000275298 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8T7B _pdbx_database_status.recvd_initial_deposition_date 2023-06-20 _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 8T7B _cell.details ? _cell.formula_units_Z ? _cell.length_a 68.752 _cell.length_a_esd ? _cell.length_b 68.752 _cell.length_b_esd ? _cell.length_c 59.870 _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 8T7B _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*CP*AP*AP*TP*TP*A)-3') ; 6465.213 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(P*TP*CP*GP*TP*C)-3') ; 1470.998 1 ? ? ? ? 3 polymer syn ;DNA (5'-D(*TP*CP*TP*AP*AP*TP*TP*G)-3') ; 2416.615 1 ? ? ? ? 4 polymer syn ;DNA (5'-D(P*AP*GP*GP*TP*CP*TP*GP*C)-3') ; 2442.616 1 ? ? ? ? 5 non-polymer syn NETROPSIN 430.464 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)(DC)(DA)(DA)(DT)(DT) (DA) ; GAGCAGACCTGACGACAATTA A ? 2 polydeoxyribonucleotide no no '(DT)(DC)(DG)(DT)(DC)' TCGTC B ? 3 polydeoxyribonucleotide no no '(DT)(DC)(DT)(DA)(DA)(DT)(DT)(DG)' TCTAATTG C ? 4 polydeoxyribonucleotide no no '(DA)(DG)(DG)(DT)(DC)(DT)(DG)(DC)' AGGTCTGC 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 DC n 1 17 DA n 1 18 DA n 1 19 DT n 1 20 DT n 1 21 DA n 2 1 DT n 2 2 DC n 2 3 DG n 2 4 DT n 2 5 DC n 3 1 DT n 3 2 DC n 3 3 DT n 3 4 DA n 3 5 DA n 3 6 DT n 3 7 DT n 3 8 DG n 4 1 DA n 4 2 DG n 4 3 DG n 4 4 DT n 4 5 DC n 4 6 DT n 4 7 DG n 4 8 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 8 'synthetic construct' ? 32630 ? 4 1 sample 1 8 '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 8T7B 8T7B ? 1 ? 1 2 PDB 8T7B 8T7B ? 2 ? 1 3 PDB 8T7B 8T7B ? 3 ? 1 4 PDB 8T7B 8T7B ? 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 8T7B A 1 ? 21 ? 8T7B 0 ? 20 ? 0 20 2 2 8T7B B 1 ? 5 ? 8T7B 1 ? 5 ? 1 5 3 3 8T7B C 1 ? 8 ? 8T7B 2 ? 9 ? 2 9 4 4 8T7B D 1 ? 8 ? 8T7B 10 ? 17 ? 10 17 # 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 NT non-polymer . NETROPSIN ? 'C18 H26 N10 O3' 430.464 # _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 8T7B _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 6.38 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 80.73 _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 Na Cacodylate pH 6.5 with 20 mM MgCl2, 1.0 mM spermine, and 2.0 M (NH4)2SO4 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 2022-10-15 _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 8T7B _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 3.05 _reflns.d_resolution_low 59.54 _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 5931 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.8 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 10.1 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 7.8 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 0.670 _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 0.082 _reflns.pdbx_Rpim_I_all 0.025 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.954 _reflns.pdbx_CC_star 0.988 _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.078 _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 ? ? ? ? ? ? 287 ? ? ? ? ? ? ? ? ? ? ? 8.6 0.660 ? ? 0.791 0.273 ? 1 1 0.854 0.960 ? 96.3 ? 0.739 ? ? ? ? ? ? ? ? ? 3.10 3.16 ? ? ? ? ? ? 273 ? ? ? ? ? ? ? ? ? ? ? 8.7 0.578 ? ? 0.300 0.099 ? 2 1 0.991 0.998 ? 99.3 ? 0.283 ? ? ? ? ? ? ? ? ? 3.16 3.22 ? ? ? ? ? ? 311 ? ? ? ? ? ? ? ? ? ? ? 9.5 0.904 ? ? 0.155 0.049 ? 3 1 0.996 0.999 ? 99.7 ? 0.147 ? ? ? ? ? ? ? ? ? 3.22 3.29 ? ? ? ? ? ? 304 ? ? ? ? ? ? ? ? ? ? ? 9.9 0.949 ? ? 0.120 0.037 ? 4 1 0.998 1.000 ? 100.0 ? 0.114 ? ? ? ? ? ? ? ? ? 3.29 3.36 ? ? ? ? ? ? 292 ? ? ? ? ? ? ? ? ? ? ? 10.0 0.517 ? ? 0.263 0.083 ? 5 1 0.992 0.998 ? 100.0 ? 0.249 ? ? ? ? ? ? ? ? ? 3.36 3.43 ? ? ? ? ? ? 297 ? ? ? ? ? ? ? ? ? ? ? 10.0 0.613 ? ? 0.191 0.061 ? 6 1 0.996 0.999 ? 100.0 ? 0.181 ? ? ? ? ? ? ? ? ? 3.43 3.52 ? ? ? ? ? ? 290 ? ? ? ? ? ? ? ? ? ? ? 9.4 0.675 ? ? 0.168 0.055 ? 7 1 0.997 0.999 ? 100.0 ? 0.159 ? ? ? ? ? ? ? ? ? 3.52 3.62 ? ? ? ? ? ? 308 ? ? ? ? ? ? ? ? ? ? ? 10.1 0.637 ? ? 0.173 0.054 ? 8 1 0.997 0.999 ? 100.0 ? 0.164 ? ? ? ? ? ? ? ? ? 3.62 3.72 ? ? ? ? ? ? 284 ? ? ? ? ? ? ? ? ? ? ? 10.0 0.549 ? ? 0.206 0.065 ? 9 1 0.992 0.998 ? 100.0 ? 0.195 ? ? ? ? ? ? ? ? ? 3.72 3.84 ? ? ? ? ? ? 299 ? ? ? ? ? ? ? ? ? ? ? 10.6 0.600 ? ? 0.149 0.046 ? 10 1 0.995 0.999 ? 100.0 ? 0.142 ? ? ? ? ? ? ? ? ? 3.84 3.98 ? ? ? ? ? ? 304 ? ? ? ? ? ? ? ? ? ? ? 10.7 0.629 ? ? 0.123 0.037 ? 11 1 0.996 0.999 ? 100.0 ? 0.117 ? ? ? ? ? ? ? ? ? 3.98 4.14 ? ? ? ? ? ? 290 ? ? ? ? ? ? ? ? ? ? ? 10.6 0.618 ? ? 0.096 0.030 ? 12 1 0.997 0.999 ? 100.0 ? 0.091 ? ? ? ? ? ? ? ? ? 4.14 4.33 ? ? ? ? ? ? 309 ? ? ? ? ? ? ? ? ? ? ? 10.7 0.567 ? ? 0.088 0.027 ? 13 1 0.998 0.999 ? 100.0 ? 0.084 ? ? ? ? ? ? ? ? ? 4.33 4.56 ? ? ? ? ? ? 304 ? ? ? ? ? ? ? ? ? ? ? 9.9 0.541 ? ? 0.074 0.024 ? 14 1 0.998 1.000 ? 100.0 ? 0.071 ? ? ? ? ? ? ? ? ? 4.56 4.84 ? ? ? ? ? ? 280 ? ? ? ? ? ? ? ? ? ? ? 10.0 0.543 ? ? 0.060 0.019 ? 15 1 0.998 1.000 ? 100.0 ? 0.057 ? ? ? ? ? ? ? ? ? 4.84 5.21 ? ? ? ? ? ? 299 ? ? ? ? ? ? ? ? ? ? ? 10.7 0.577 ? ? 0.048 0.015 ? 16 1 0.999 1.000 ? 100.0 ? 0.046 ? ? ? ? ? ? ? ? ? 5.21 5.74 ? ? ? ? ? ? 309 ? ? ? ? ? ? ? ? ? ? ? 10.8 0.582 ? ? 0.040 0.012 ? 17 1 0.999 1.000 ? 100.0 ? 0.038 ? ? ? ? ? ? ? ? ? 5.74 6.57 ? ? ? ? ? ? 296 ? ? ? ? ? ? ? ? ? ? ? 10.4 0.524 ? ? 0.038 0.012 ? 18 1 0.999 1.000 ? 100.0 ? 0.036 ? ? ? ? ? ? ? ? ? 6.57 8.27 ? ? ? ? ? ? 303 ? ? ? ? ? ? ? ? ? ? ? 9.9 0.539 ? ? 0.029 0.009 ? 19 1 1.000 1.000 ? 100.0 ? 0.028 ? ? ? ? ? ? ? ? ? 8.27 50.00 ? ? ? ? ? ? 292 ? ? ? ? ? ? ? ? ? ? ? 10.3 1.604 ? ? 0.083 0.025 ? 20 1 0.998 0.999 ? 100.0 ? 0.079 ? ? ? ? ? ? ? ? ? # _refine.aniso_B[1][1] -0.23 _refine.aniso_B[1][2] -0.12 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][2] -0.23 _refine.aniso_B[2][3] 0.00 _refine.aniso_B[3][3] 0.75 _refine.B_iso_max ? _refine.B_iso_mean 119.897 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.974 _refine.correlation_coeff_Fo_to_Fc_free 0.980 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _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 8T7B _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 3.05 _refine.ls_d_res_low 59.54 _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 5535 _refine.ls_number_reflns_R_free 270 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 96.46 _refine.ls_percent_reflns_R_free 4.7 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.19260 _refine.ls_R_factor_R_free 0.21083 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.19173 _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 MASK _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 ? _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 'MAXIMUM LIKELIHOOD' _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.402 _refine.pdbx_overall_ESU_R_Free 0.265 _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _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 ? _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 11.630 _refine.overall_SU_ML 0.214 _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 1 _refine_hist.details ? _refine_hist.d_res_high 3.05 _refine_hist.d_res_low 59.54 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 886 _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 855 _refine_hist.pdbx_number_atoms_ligand 31 _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' ? 0.011 0.011 988 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.007 0.020 501 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 1.959 1.228 1511 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 2.124 3.000 1178 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_1_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_2_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_3_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_4_deg ? ? 'X-RAY DIFFRACTION' ? 0.100 0.200 126 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.017 0.020 553 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.008 0.020 230 ? r_gen_planes_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcbond_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcangle_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcangle_other ? ? 'X-RAY DIFFRACTION' ? 15.934 12.321 988 ? r_scbond_it ? ? 'X-RAY DIFFRACTION' ? 15.926 12.325 989 ? r_scbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_scangle_it ? ? 'X-RAY DIFFRACTION' ? 21.435 18.435 1512 ? r_scangle_other ? ? 'X-RAY DIFFRACTION' ? 22.815 ? 1450 ? r_long_range_B_refined ? ? 'X-RAY DIFFRACTION' ? 22.808 ? 1451 ? r_long_range_B_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_rigid_bond_restr ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_free ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 3.054 _refine_ls_shell.d_res_low 3.134 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 20 _refine_ls_shell.number_reflns_R_work 382 _refine_ls_shell.percent_reflns_obs 84.63 _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 0.306 _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 20 _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 0.369 # _struct.entry_id 8T7B _struct.title ;Sequence specific (AATT) orientation of netropsin molecules at a unique minor groove binding site (position2) 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 8T7B _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 ? # 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 8 N3 ? ? A DG 2 D DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 3 N2 ? ? ? 1_555 D DC 8 O2 ? ? A DG 2 D DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 3 O6 ? ? ? 1_555 D DC 8 N4 ? ? A DG 2 D DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 4 N3 ? ? ? 1_555 D DG 7 N1 ? ? A DC 3 D DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 4 N4 ? ? ? 1_555 D DG 7 O6 ? ? A DC 3 D DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 4 O2 ? ? ? 1_555 D DG 7 N2 ? ? A DC 3 D DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 5 N1 ? ? ? 1_555 D DT 6 N3 ? ? A DA 4 D DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 5 N6 ? ? ? 1_555 D DT 6 O4 ? ? A DA 4 D DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 6 N1 ? ? ? 1_555 D DC 5 N3 ? ? A DG 5 D DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 6 N2 ? ? ? 1_555 D DC 5 O2 ? ? A DG 5 D DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 6 O6 ? ? ? 1_555 D DC 5 N4 ? ? A DG 5 D DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 7 N1 ? ? ? 1_555 D DT 4 N3 ? ? A DA 6 D DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 7 N6 ? ? ? 1_555 D DT 4 O4 ? ? A DA 6 D DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 N3 ? ? ? 1_555 D DG 3 N1 ? ? A DC 7 D DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 N4 ? ? ? 1_555 D DG 3 O6 ? ? A DC 7 D DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 O2 ? ? ? 1_555 D DG 3 N2 ? ? A DC 7 D DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 9 N3 ? ? ? 1_555 D DG 2 N1 ? ? A DC 8 D DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 9 N4 ? ? ? 1_555 D DG 2 O6 ? ? A DC 8 D DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 O2 ? ? ? 1_555 D DG 2 N2 ? ? A DC 8 D DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 10 N3 ? ? ? 1_555 D DA 1 N1 ? ? A DT 9 D DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 10 O4 ? ? ? 1_555 D DA 1 N6 ? ? A DT 9 D DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 10 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 10 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 10 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DA 12 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 11 B DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DA 12 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 11 B DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 13 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 12 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 13 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 12 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 13 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 12 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 14 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 13 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 14 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 13 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 14 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 13 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DA 15 N1 ? ? ? 1_555 B DT 1 N3 ? ? A DA 14 B DT 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DA 15 N6 ? ? ? 1_555 B DT 1 O4 ? ? A DA 14 B DT 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A DC 16 N3 ? ? ? 1_555 C DG 8 N1 ? ? A DC 15 C DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A DC 16 N4 ? ? ? 1_555 C DG 8 O6 ? ? A DC 15 C DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A DC 16 O2 ? ? ? 1_555 C DG 8 N2 ? ? A DC 15 C DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A DA 17 N1 ? ? ? 1_555 C DT 7 N3 ? ? A DA 16 C DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A DA 17 N6 ? ? ? 1_555 C DT 7 O4 ? ? A DA 16 C DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A DA 18 N1 ? ? ? 1_555 C DT 6 N3 ? ? A DA 17 C DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A DA 18 N6 ? ? ? 1_555 C DT 6 O4 ? ? A DA 17 C DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A DT 19 N3 ? ? ? 1_555 C DA 5 N1 ? ? A DT 18 C DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A DT 19 O4 ? ? ? 1_555 C DA 5 N6 ? ? A DT 18 C DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A DT 20 N3 ? ? ? 1_555 C DA 4 N1 ? ? A DT 19 C DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A DT 20 O4 ? ? ? 1_555 C DA 4 N6 ? ? A DT 19 C DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A DA 21 N1 ? ? ? 1_555 C DT 3 N3 ? ? A DA 20 C DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A DA 21 N6 ? ? ? 1_555 C DT 3 O4 ? ? A DA 20 C DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 8T7B _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] 0.014545 _atom_sites.fract_transf_matrix[1][2] 0.008398 _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] 0.016795 _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] 0.016703 _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 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 0 0 DG DG A . n A 1 2 DA 2 1 1 DA DA A . n A 1 3 DG 3 2 2 DG DG A . n A 1 4 DC 4 3 3 DC DC A . n A 1 5 DA 5 4 4 DA DA A . n A 1 6 DG 6 5 5 DG DG A . n A 1 7 DA 7 6 6 DA DA A . n A 1 8 DC 8 7 7 DC DC A . n A 1 9 DC 9 8 8 DC DC A . n A 1 10 DT 10 9 9 DT DT A . n A 1 11 DG 11 10 10 DG DG A . n A 1 12 DA 12 11 11 DA DA A . n A 1 13 DC 13 12 12 DC DC A . n A 1 14 DG 14 13 13 DG DG A . n A 1 15 DA 15 14 14 DA DA A . n A 1 16 DC 16 15 15 DC DC A . n A 1 17 DA 17 16 16 DA DA A . n A 1 18 DA 18 17 17 DA DA A . n A 1 19 DT 19 18 18 DT DT A . n A 1 20 DT 20 19 19 DT DT A . n A 1 21 DA 21 20 20 DA DA A . n B 2 1 DT 1 1 1 DT DT B . n B 2 2 DC 2 2 2 DC DC B . n B 2 3 DG 3 3 3 DG DG B . n B 2 4 DT 4 4 4 DT DT B . n B 2 5 DC 5 5 5 DC DC B . n C 3 1 DT 1 2 2 DT DT C . n C 3 2 DC 2 3 3 DC DC C . n C 3 3 DT 3 4 4 DT DT C . n C 3 4 DA 4 5 5 DA DA C . n C 3 5 DA 5 6 6 DA DA C . n C 3 6 DT 6 7 7 DT DT C . n C 3 7 DT 7 8 8 DT DT C . n C 3 8 DG 8 9 9 DG DG C . n D 4 1 DA 1 10 10 DA DA D . n D 4 2 DG 2 11 11 DG DG D . n D 4 3 DG 3 12 12 DG DG D . n D 4 4 DT 4 13 13 DT DT D . n D 4 5 DC 5 14 14 DC DC D . n D 4 6 DT 6 15 15 DT DT D . n D 4 7 DG 7 16 16 DG DG D . n D 4 8 DC 8 17 17 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 # _pdbx_nonpoly_scheme.asym_id E _pdbx_nonpoly_scheme.entity_id 5 _pdbx_nonpoly_scheme.mon_id NT _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id NT _pdbx_nonpoly_scheme.auth_mon_id NT _pdbx_nonpoly_scheme.pdb_strand_id C _pdbx_nonpoly_scheme.pdb_ins_code . # _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 # _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 ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0131 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _pdbx_entry_details.entry_id 8T7B _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_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 "O3'" _pdbx_validate_symm_contact.auth_asym_id_1 C _pdbx_validate_symm_contact.auth_comp_id_1 DG _pdbx_validate_symm_contact.auth_seq_id_1 9 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 OP1 _pdbx_validate_symm_contact.auth_asym_id_2 D _pdbx_validate_symm_contact.auth_comp_id_2 DA _pdbx_validate_symm_contact.auth_seq_id_2 10 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 2_554 _pdbx_validate_symm_contact.dist 2.15 # 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 "O5'" A DT 9 ? ? P A DT 9 ? ? OP1 A DT 9 ? ? 99.23 105.70 -6.47 0.90 N 2 1 "C1'" A DG 13 ? ? "O4'" A DG 13 ? ? "C4'" A DG 13 ? ? 103.23 110.10 -6.87 1.00 N 3 1 "O5'" D DA 10 ? ? P D DA 10 ? ? OP1 D DA 10 ? ? 98.04 105.70 -7.66 0.90 N 4 1 "O4'" D DA 10 ? ? "C4'" D DA 10 ? ? "C3'" D DA 10 ? ? 100.61 104.50 -3.89 0.40 N 5 1 "O4'" D DG 11 ? ? "C4'" D DG 11 ? ? "C3'" D DG 11 ? ? 101.57 104.50 -2.93 0.40 N 6 1 "C1'" D DG 11 ? ? "O4'" D DG 11 ? ? "C4'" D DG 11 ? ? 104.00 110.10 -6.10 1.00 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 NT C1 C N N 144 NT N1 N N N 145 NT N2 N N N 146 NT N3 N N N 147 NT C2 C N N 148 NT C3 C N N 149 NT O1 O N N 150 NT N4 N N N 151 NT C4 C Y N 152 NT C5 C Y N 153 NT C6 C Y N 154 NT N5 N Y N 155 NT C8 C N N 156 NT C7 C Y N 157 NT C9 C N N 158 NT O2 O N N 159 NT N6 N N N 160 NT C10 C Y N 161 NT C11 C Y N 162 NT C12 C Y N 163 NT N7 N Y N 164 NT C14 C N N 165 NT C13 C Y N 166 NT C15 C N N 167 NT O3 O N N 168 NT N8 N N N 169 NT C16 C N N 170 NT C17 C N N 171 NT C18 C N N 172 NT N9 N N N 173 NT N10 N N N 174 NT HN1 H N N 175 NT HN21 H N N 176 NT HN22 H N N 177 NT HN3 H N N 178 NT H21 H N N 179 NT H22 H N N 180 NT HN4 H N N 181 NT H5 H N N 182 NT H81 H N N 183 NT H82 H N N 184 NT H83 H N N 185 NT H7 H N N 186 NT HN6 H N N 187 NT H11 H N N 188 NT H141 H N N 189 NT H142 H N N 190 NT H143 H N N 191 NT H13 H N N 192 NT HN8 H N N 193 NT H161 H N N 194 NT H162 H N N 195 NT H171 H N N 196 NT H172 H N N 197 NT HN9 H N N 198 NT HN01 H N N 199 NT HN02 H N N 200 # 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 NT C1 N1 doub N N 150 NT C1 N2 sing N N 151 NT C1 N3 sing N N 152 NT N1 HN1 sing N N 153 NT N2 HN21 sing N N 154 NT N2 HN22 sing N N 155 NT N3 C2 sing N N 156 NT N3 HN3 sing N N 157 NT C2 C3 sing N N 158 NT C2 H21 sing N N 159 NT C2 H22 sing N N 160 NT C3 O1 doub N N 161 NT C3 N4 sing N N 162 NT N4 C4 sing N N 163 NT N4 HN4 sing N N 164 NT C4 C5 sing Y N 165 NT C4 C7 doub Y N 166 NT C5 C6 doub Y N 167 NT C5 H5 sing N N 168 NT C6 N5 sing Y N 169 NT C6 C9 sing N N 170 NT N5 C8 sing N N 171 NT N5 C7 sing Y N 172 NT C8 H81 sing N N 173 NT C8 H82 sing N N 174 NT C8 H83 sing N N 175 NT C7 H7 sing N N 176 NT C9 O2 doub N N 177 NT C9 N6 sing N N 178 NT N6 C10 sing N N 179 NT N6 HN6 sing N N 180 NT C10 C11 sing Y N 181 NT C10 C13 doub Y N 182 NT C11 C12 doub Y N 183 NT C11 H11 sing N N 184 NT C12 N7 sing Y N 185 NT C12 C15 sing N N 186 NT N7 C14 sing N N 187 NT N7 C13 sing Y N 188 NT C14 H141 sing N N 189 NT C14 H142 sing N N 190 NT C14 H143 sing N N 191 NT C13 H13 sing N N 192 NT C15 O3 doub N N 193 NT C15 N8 sing N N 194 NT N8 C16 sing N N 195 NT N8 HN8 sing N N 196 NT C16 C17 sing N N 197 NT C16 H161 sing N N 198 NT C16 H162 sing N N 199 NT C17 C18 sing N N 200 NT C17 H171 sing N N 201 NT C17 H172 sing N N 202 NT C18 N9 doub N N 203 NT C18 N10 sing N N 204 NT N9 HN9 sing N N 205 NT N10 HN01 sing N N 206 NT N10 HN02 sing N N 207 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8T7B 'double helix' 8T7B 'a-form double helix' 8T7B '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 8 1_555 0.062 -0.374 0.032 -6.229 -6.604 -3.833 1 A_DG2:DC17_D A 2 ? D 17 ? 19 1 1 A DC 4 1_555 D DG 7 1_555 0.170 -0.158 0.250 1.463 -5.959 -2.785 2 A_DC3:DG16_D A 3 ? D 16 ? 19 1 1 A DA 5 1_555 D DT 6 1_555 0.322 0.213 0.731 2.702 -4.847 -3.285 3 A_DA4:DT15_D A 4 ? D 15 ? 20 1 1 A DG 6 1_555 D DC 5 1_555 -0.069 0.200 0.421 8.094 -8.807 2.770 4 A_DG5:DC14_D A 5 ? D 14 ? 19 1 1 A DA 7 1_555 D DT 4 1_555 0.426 -0.014 0.351 2.605 -5.042 -8.900 5 A_DA6:DT13_D A 6 ? D 13 ? 20 1 1 A DC 8 1_555 D DG 3 1_555 0.026 -0.423 0.315 7.799 -3.674 -1.963 6 A_DC7:DG12_D A 7 ? D 12 ? 19 1 1 A DC 9 1_555 D DG 2 1_555 -0.003 -0.381 0.539 1.245 -8.300 -1.490 7 A_DC8:DG11_D A 8 ? D 11 ? 19 1 1 A DT 10 1_555 D DA 1 1_555 -0.292 -0.375 0.276 -0.448 -10.624 0.869 8 A_DT9:DA10_D A 9 ? D 10 ? 20 1 1 A DG 11 1_555 B DC 5 1_555 0.076 -0.105 0.429 -0.631 -4.011 3.421 9 A_DG10:DC5_B A 10 ? B 5 ? 19 1 1 A DA 12 1_555 B DT 4 1_555 0.494 -0.132 0.595 6.980 -9.090 -3.787 10 A_DA11:DT4_B A 11 ? B 4 ? 20 1 1 A DC 13 1_555 B DG 3 1_555 0.099 -0.193 0.618 -5.459 -8.092 3.746 11 A_DC12:DG3_B A 12 ? B 3 ? 19 1 1 A DG 14 1_555 B DC 2 1_555 -0.245 -0.181 0.305 -0.934 -1.533 -2.375 12 A_DG13:DC2_B A 13 ? B 2 ? 19 1 1 A DA 15 1_555 B DT 1 1_555 0.247 -0.122 0.472 12.347 -12.311 -2.447 13 A_DA14:DT1_B A 14 ? B 1 ? 20 1 1 A DC 16 1_555 C DG 8 1_555 0.051 -0.085 0.214 -2.475 -4.268 -1.588 14 A_DC15:DG9_C A 15 ? C 9 ? 19 1 1 A DA 17 1_555 C DT 7 1_555 -0.092 -0.405 0.923 10.177 -5.350 1.869 15 A_DA16:DT8_C A 16 ? C 8 ? 20 1 1 A DA 18 1_555 C DT 6 1_555 0.103 -0.201 -0.055 -7.586 -9.900 3.643 16 A_DA17:DT7_C A 17 ? C 7 ? 20 1 1 A DT 19 1_555 C DA 5 1_555 -0.419 -0.251 0.333 -12.649 -10.672 1.982 17 A_DT18:DA6_C A 18 ? C 6 ? 20 1 1 A DT 20 1_555 C DA 4 1_555 -0.183 -0.366 0.283 -10.973 -10.971 -2.786 18 A_DT19:DA5_C A 19 ? C 5 ? 20 1 1 A DA 21 1_555 C DT 3 1_555 0.101 0.081 0.165 -1.469 -10.970 -0.570 19 A_DA20:DT4_C A 20 ? C 4 ? 20 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 8 1_555 A DC 4 1_555 D DG 7 1_555 0.568 -0.480 3.185 2.484 4.910 34.916 -1.495 -0.580 3.122 8.120 -4.107 35.333 1 AA_DG2DC3:DG16DC17_DD A 2 ? D 17 ? A 3 ? D 16 ? 1 A DC 4 1_555 D DG 7 1_555 A DA 5 1_555 D DT 6 1_555 0.061 1.577 3.301 -1.299 0.850 42.784 2.075 -0.216 3.327 1.165 1.780 42.811 2 AA_DC3DA4:DT15DG16_DD A 3 ? D 16 ? A 4 ? D 15 ? 1 A DA 5 1_555 D DT 6 1_555 A DG 6 1_555 D DC 5 1_555 0.250 0.199 3.362 1.094 2.351 30.665 -0.099 -0.250 3.374 4.435 -2.064 30.771 3 AA_DA4DG5:DC14DT15_DD A 4 ? D 15 ? A 5 ? D 14 ? 1 A DG 6 1_555 D DC 5 1_555 A DA 7 1_555 D DT 4 1_555 -0.640 0.066 3.395 -3.700 1.487 38.915 -0.089 0.490 3.440 2.225 5.537 39.111 4 AA_DG5DA6:DT13DC14_DD A 5 ? D 14 ? A 6 ? D 13 ? 1 A DA 7 1_555 D DT 4 1_555 A DC 8 1_555 D DG 3 1_555 0.559 -1.206 3.189 -1.350 2.841 29.486 -2.929 -1.364 3.034 5.562 2.642 29.650 5 AA_DA6DC7:DG12DT13_DD A 6 ? D 13 ? A 7 ? D 12 ? 1 A DC 8 1_555 D DG 3 1_555 A DC 9 1_555 D DG 2 1_555 0.429 -0.671 3.339 -1.609 0.793 36.071 -1.197 -0.922 3.303 1.280 2.597 36.115 6 AA_DC7DC8:DG11DG12_DD A 7 ? D 12 ? A 8 ? D 11 ? 1 A DC 9 1_555 D DG 2 1_555 A DT 10 1_555 D DA 1 1_555 -0.113 -1.356 3.331 0.925 -0.023 35.663 -2.210 0.320 3.328 -0.038 -1.510 35.675 7 AA_DC8DT9:DA10DG11_DD A 8 ? D 11 ? A 9 ? D 10 ? 1 A DT 10 1_555 D DA 1 1_555 A DG 11 1_555 B DC 5 1_555 -0.682 0.092 3.282 0.427 2.615 30.449 -0.346 1.379 3.269 4.968 -0.812 30.561 8 AA_DT9DG10:DC5DA10_BD A 9 ? D 10 ? A 10 ? B 5 ? 1 A DG 11 1_555 B DC 5 1_555 A DA 12 1_555 B DT 4 1_555 -1.076 0.224 3.237 -1.330 5.669 33.732 -0.515 1.619 3.269 9.680 2.271 34.217 9 AA_DG10DA11:DT4DC5_BB A 10 ? B 5 ? A 11 ? B 4 ? 1 A DA 12 1_555 B DT 4 1_555 A DC 13 1_555 B DG 3 1_555 0.900 -0.621 3.636 1.533 -1.817 26.290 -0.815 -1.512 3.715 -3.985 -3.362 26.396 10 AA_DA11DC12:DG3DT4_BB A 11 ? B 4 ? A 12 ? B 3 ? 1 A DC 13 1_555 B DG 3 1_555 A DG 14 1_555 B DC 2 1_555 0.548 -0.378 3.076 3.019 2.707 33.049 -1.086 -0.482 3.073 4.737 -5.282 33.290 11 AA_DC12DG13:DC2DG3_BB A 12 ? B 3 ? A 13 ? B 2 ? 1 A DG 14 1_555 B DC 2 1_555 A DA 15 1_555 B DT 1 1_555 -0.347 -0.201 2.917 -2.465 1.039 43.938 -0.356 0.255 2.926 1.387 3.291 44.015 12 AA_DG13DA14:DT1DC2_BB A 13 ? B 2 ? A 14 ? B 1 ? 1 A DA 15 1_555 B DT 1 1_555 A DC 16 1_555 C DG 8 1_555 -0.738 -0.876 3.503 -0.841 4.091 28.253 -2.758 1.294 3.366 8.322 1.711 28.554 13 AA_DA14DC15:DG9DT1_CB A 14 ? B 1 ? A 15 ? C 9 ? 1 A DC 16 1_555 C DG 8 1_555 A DA 17 1_555 C DT 7 1_555 0.014 0.222 3.083 -5.488 5.433 31.290 -0.520 -0.954 3.032 9.885 9.986 32.205 14 AA_DC15DA16:DT8DG9_CC A 15 ? C 9 ? A 16 ? C 8 ? 1 A DA 17 1_555 C DT 7 1_555 A DA 18 1_555 C DT 6 1_555 -0.386 -0.138 3.770 2.287 2.857 37.767 -0.631 0.929 3.722 4.402 -3.522 37.938 15 AA_DA16DA17:DT7DT8_CC A 16 ? C 8 ? A 17 ? C 7 ? 1 A DA 18 1_555 C DT 6 1_555 A DT 19 1_555 C DA 5 1_555 -0.237 -0.843 3.341 -4.942 -3.088 32.028 -0.943 -0.474 3.403 -5.540 8.865 32.540 16 AA_DA17DT18:DA6DT7_CC A 17 ? C 7 ? A 18 ? C 6 ? 1 A DT 19 1_555 C DA 5 1_555 A DT 20 1_555 C DA 4 1_555 0.362 -0.087 3.166 0.798 -4.153 38.651 0.360 -0.449 3.164 -6.251 -1.202 38.873 17 AA_DT18DT19:DA5DA6_CC A 18 ? C 6 ? A 19 ? C 5 ? 1 A DT 20 1_555 C DA 4 1_555 A DA 21 1_555 C DT 3 1_555 -0.816 0.065 3.093 0.574 -1.074 40.046 0.211 1.253 3.079 -1.568 -0.839 40.064 18 AA_DT19DA20:DT4DA5_CC A 19 ? C 5 ? A 20 ? C 4 ? # 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 # _pdbx_entity_nonpoly.entity_id 5 _pdbx_entity_nonpoly.name NETROPSIN _pdbx_entity_nonpoly.comp_id NT # _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 5VY6 _pdbx_initial_refinement_model.details ? # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #