data_9YBK # _entry.id 9YBK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.406 _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 9YBK pdb_00009ybk 10.2210/pdb9ybk/pdb WWPDB D_1000300182 ? ? # _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 2025-10-22 _pdbx_audit_revision_history.part_number ? # _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 ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9YBK _pdbx_database_status.recvd_initial_deposition_date 2025-09-17 _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 # _pdbx_contact_author.id 4 _pdbx_contact_author.email rs17@nyu.edu _pdbx_contact_author.name_first Ruojie _pdbx_contact_author.name_last Sha _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-0807-734X # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Horvath, A.' 1 0009-0008-5770-8014 'Singh, V.R.' 2 0000-0002-6692-3532 'Vecchioni, S.' 3 0000-0001-8243-650X 'Ohayon, Y.P.' 4 0000-0001-7500-4282 'Sha, R.' 5 0000-0002-0807-734X # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Mobile Junction in Double Crossover-Like Tiles' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Singh, V.R.' 1 ? primary 'Horvath, A.' 2 0009-0008-5770-8014 primary 'Vecchioni, S.' 3 0000-0001-8243-650X primary 'Ohayon, Y.P.' 4 0000-0001-7500-4282 primary 'Sha, R.' 5 0000-0002-0807-734X # 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(*(0DT)P*(0DG)P*(0DA)P*(0DC)P*(0DG)P*(0DG)P*(0DC)P*(0DT)P*(0DG)P*(0DG)P*(0DA)P*(0DC)P*(0DT)P*(0DC)P*(0DG)P*(0DT))-3') ; 4930.189 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*(0DC)P*(0DA)P*(0DA)P*(0DG)P*(0DC)P*(0DC)P*(0DG)P*(0DT)P*(0DG)P*(0DA)P*(0DG)P*(0DT)P*(0DC)P*(0DC)P*(0DA)P*(0DC))-3') ; 4868.169 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no yes '(0DT)(0DG)(0DA)(0DC)(0DG)(0DG)(0DC)(0DT)(0DG)(0DG)(0DA)(0DC)(0DT)(0DC)(0DG)(0DT)' TGACGGCTGGACTCGT A ? 2 polydeoxyribonucleotide no yes '(0DC)(0DA)(0DA)(0DG)(0DC)(0DC)(0DG)(0DT)(0DG)(0DA)(0DG)(0DT)(0DC)(0DC)(0DA)(0DC)' CAAGCCGTGAGTCCAC B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name 'MAGNESIUM ION' _pdbx_entity_nonpoly.comp_id MG # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 0DT n 1 2 0DG n 1 3 0DA n 1 4 0DC n 1 5 0DG n 1 6 0DG n 1 7 0DC n 1 8 0DT n 1 9 0DG n 1 10 0DG n 1 11 0DA n 1 12 0DC n 1 13 0DT n 1 14 0DC n 1 15 0DG n 1 16 0DT n 2 1 0DC n 2 2 0DA n 2 3 0DA n 2 4 0DG n 2 5 0DC n 2 6 0DC n 2 7 0DG n 2 8 0DT n 2 9 0DG n 2 10 0DA n 2 11 0DG n 2 12 0DT n 2 13 0DC n 2 14 0DC n 2 15 0DA n 2 16 0DC 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 16 'synthetic construct' ? 32630 ? 2 1 sample 1 16 'synthetic construct' ? 32630 ? # 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 0DA 'L-DNA linking' . ;2'-DEOXY-L-RIBO-FURANOSYL ADENOSINE-5'-MONOPHOSPHATE ; ? 'C10 H14 N5 O6 P' 331.222 0DC 'L-DNA linking' . ;2'-DEOXY-L-RIBO-FURANOSYL CYTOSINE-5'-MONOPHOSPHATE ; ? 'C9 H14 N3 O7 P' 307.197 0DG 'L-DNA linking' . ;2'-DEOXY-L-RIBO-FURANOSYL GUANINE-5'-MONOPHOSPHATE ; ? 'C10 H14 N5 O7 P' 347.221 0DT 'L-DNA linking' . ;2'-DEOXY-L-RIBO-FURANOSYL THYMIDINE-5'-MONOPHOSPHATE ; ? 'C10 H15 N2 O8 P' 322.208 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # 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 0DT 1 1 1 0DT 0DT A . n A 1 2 0DG 2 2 2 0DG 0DG A . n A 1 3 0DA 3 3 3 0DA 0DA A . n A 1 4 0DC 4 4 4 0DC 0DC A . n A 1 5 0DG 5 5 5 0DG 0DG A . n A 1 6 0DG 6 6 6 0DG 0DG A . n A 1 7 0DC 7 7 7 0DC 0DC A . n A 1 8 0DT 8 8 8 0DT 0DT A . n A 1 9 0DG 9 9 9 0DG 0DG A . n A 1 10 0DG 10 10 10 0DG 0DG A . n A 1 11 0DA 11 11 11 0DA 0DA A . n A 1 12 0DC 12 12 12 0DC 0DC A . n A 1 13 0DT 13 13 13 0DT 0DT A . n A 1 14 0DC 14 14 14 0DC 0DC A . n A 1 15 0DG 15 15 15 0DG 0DG A . n A 1 16 0DT 16 16 16 0DT 0DT A . n B 2 1 0DC 1 1 1 0DC 0DC B . n B 2 2 0DA 2 2 2 0DA 0DA B . n B 2 3 0DA 3 3 3 0DA 0DA B . n B 2 4 0DG 4 4 4 0DG 0DG B . n B 2 5 0DC 5 5 5 0DC 0DC B . n B 2 6 0DC 6 6 6 0DC 0DC B . n B 2 7 0DG 7 7 7 0DG 0DG B . n B 2 8 0DT 8 8 8 0DT 0DT B . n B 2 9 0DG 9 9 9 0DG 0DG B . n B 2 10 0DA 10 10 10 0DA 0DA B . n B 2 11 0DG 11 11 11 0DG 0DG B . n B 2 12 0DT 12 12 12 0DT 0DT B . n B 2 13 0DC 13 13 13 0DC 0DC B . n B 2 14 0DC 14 14 14 0DC 0DC B . n B 2 15 0DA 15 15 15 0DA 0DA B . n B 2 16 0DC 16 16 16 0DC 0DC B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id MG _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 101 _pdbx_nonpoly_scheme.pdb_mon_id MG _pdbx_nonpoly_scheme.auth_mon_id MG _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # 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_reference_DOI _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.21.2_5419 ? 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . ? 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? STARANISO ? ? ? . ? 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . ? 4 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 9YBK _cell.details ? _cell.formula_units_Z ? _cell.length_a 35.985 _cell.length_a_esd ? _cell.length_b 35.985 _cell.length_b_esd ? _cell.length_c 102.023 _cell.length_c_esd ? _cell.volume 132111.646 _cell.volume_esd ? _cell.Z_PDB 4 _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 9YBK _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall 'P 4w' _symmetry.space_group_name_H-M 'P 41' _symmetry.pdbx_full_space_group_name_H-M ? # _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 9YBK _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 3.37 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 63.51 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details '338-293 at 0.4/hr' _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '100 mM MOPS, 1.25 M magnesium sulfate' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 9M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2024-03-02 _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 0.92012 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 17-ID' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.92012 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 17-ID _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate 52.64 _reflns.entry_id 9YBK _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.613 _reflns.d_resolution_low 29.405 _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 2012 _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 84.8 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 5.0 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 8.2 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.995 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs ? _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 2.613 3.075 ? ? ? ? ? ? 202 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 1 0.770 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 7.054 29.405 ? ? ? ? ? ? 202 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 0.995 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 53.85 _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 9YBK _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.63 _refine.ls_d_res_low 29.40 _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 1931 _refine.ls_number_reflns_R_free 113 _refine.ls_number_reflns_R_work 1818 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 49.61 _refine.ls_percent_reflns_R_free 5.85 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2262 _refine.ls_R_factor_R_free 0.2581 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2240 _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.correlation_coeff_I_to_Fcsqd_work ? _refine.correlation_coeff_I_to_Fcsqd_free ? _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 1.36 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 22.3662 _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 0.4405 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 2.63 _refine_hist.d_res_low 29.40 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 651 _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 650 _refine_hist.pdbx_number_atoms_ligand 1 _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_Zscore _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.0119 ? 728 ? f_bond_d ? ? ? 'X-RAY DIFFRACTION' ? 2.6376 ? 1120 ? f_angle_d ? ? ? 'X-RAY DIFFRACTION' ? 0.1638 ? 96 ? f_chiral_restr ? ? ? 'X-RAY DIFFRACTION' ? 0.0096 ? 32 ? f_plane_restr ? ? ? 'X-RAY DIFFRACTION' ? 37.9728 ? 306 ? f_dihedral_angle_d ? ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 2.63 _refine_ls_shell.d_res_low 29.40 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 113 _refine_ls_shell.number_reflns_R_work 1818 _refine_ls_shell.percent_reflns_obs 49.61 _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 0.2240 _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.correlation_coeff_Fo_to_Fc ? _refine_ls_shell.correlation_coeff_Fo_to_Fc_free ? _refine_ls_shell.correlation_coeff_I_to_Fcsqd_work ? _refine_ls_shell.correlation_coeff_I_to_Fcsqd_free ? _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 0.2581 # _struct.entry_id 9YBK _struct.title '[2ULA] Double crossover-like L-DNA motif containing a mobile junction' _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 9YBK _struct_keywords.text 'dna, dxl, crossover, mobile' _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 ? # 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 9YBK 9YBK ? 1 ? 1 2 PDB 9YBK 9YBK ? 2 ? 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 9YBK A 1 ? 16 ? 9YBK 1 ? 16 ? 1 16 2 2 9YBK B 1 ? 16 ? 9YBK 1 ? 16 ? 1 16 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'native gel electrophoresis' _pdbx_struct_assembly_auth_evidence.details ? # _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 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A 0DT 1 "O3'" ? ? ? 1_555 A 0DG 2 P ? ? A 0DT 1 A 0DG 2 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale2 covale both ? A 0DG 2 "O3'" ? ? ? 1_555 A 0DA 3 P ? ? A 0DG 2 A 0DA 3 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale3 covale both ? A 0DA 3 "O3'" ? ? ? 1_555 A 0DC 4 P ? ? A 0DA 3 A 0DC 4 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale4 covale both ? A 0DC 4 "O3'" ? ? ? 1_555 A 0DG 5 P ? ? A 0DC 4 A 0DG 5 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale5 covale both ? A 0DG 5 "O3'" ? ? ? 1_555 A 0DG 6 P ? ? A 0DG 5 A 0DG 6 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale6 covale both ? A 0DG 6 "O3'" ? ? ? 1_555 A 0DC 7 P ? ? A 0DG 6 A 0DC 7 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale7 covale both ? A 0DC 7 "O3'" ? ? ? 1_555 A 0DT 8 P ? ? A 0DC 7 A 0DT 8 1_555 ? ? ? ? ? ? ? 1.634 ? ? covale8 covale both ? A 0DT 8 "O3'" ? ? ? 1_555 A 0DG 9 P ? ? A 0DT 8 A 0DG 9 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale9 covale both ? A 0DG 9 "O3'" ? ? ? 1_555 A 0DG 10 P ? ? A 0DG 9 A 0DG 10 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale10 covale both ? A 0DG 10 "O3'" ? ? ? 1_555 A 0DA 11 P ? ? A 0DG 10 A 0DA 11 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale11 covale both ? A 0DA 11 "O3'" ? ? ? 1_555 A 0DC 12 P ? ? A 0DA 11 A 0DC 12 1_555 ? ? ? ? ? ? ? 1.619 ? ? covale12 covale both ? A 0DC 12 "O3'" ? ? ? 1_555 A 0DT 13 P ? ? A 0DC 12 A 0DT 13 1_555 ? ? ? ? ? ? ? 1.636 ? ? covale13 covale both ? A 0DT 13 "O3'" ? ? ? 1_555 A 0DC 14 P ? ? A 0DT 13 A 0DC 14 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale14 covale both ? A 0DC 14 "O3'" ? ? ? 1_555 A 0DG 15 P ? ? A 0DC 14 A 0DG 15 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale15 covale both ? A 0DG 15 "O3'" ? ? ? 1_555 A 0DT 16 P ? ? A 0DG 15 A 0DT 16 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale16 covale both ? B 0DC 1 "O3'" ? ? ? 1_555 B 0DA 2 P ? ? B 0DC 1 B 0DA 2 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale17 covale both ? B 0DA 2 "O3'" ? ? ? 1_555 B 0DA 3 P ? ? B 0DA 2 B 0DA 3 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale18 covale both ? B 0DA 3 "O3'" ? ? ? 1_555 B 0DG 4 P ? ? B 0DA 3 B 0DG 4 1_555 ? ? ? ? ? ? ? 1.620 ? ? covale19 covale both ? B 0DG 4 "O3'" ? ? ? 1_555 B 0DC 5 P ? ? B 0DG 4 B 0DC 5 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale20 covale both ? B 0DC 5 "O3'" ? ? ? 1_555 B 0DC 6 P ? ? B 0DC 5 B 0DC 6 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale21 covale both ? B 0DC 6 "O3'" ? ? ? 1_555 B 0DG 7 P ? ? B 0DC 6 B 0DG 7 1_555 ? ? ? ? ? ? ? 1.617 ? ? covale22 covale both ? B 0DG 7 "O3'" ? ? ? 1_555 B 0DT 8 P ? ? B 0DG 7 B 0DT 8 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale23 covale both ? B 0DT 8 "O3'" ? ? ? 1_555 B 0DG 9 P ? ? B 0DT 8 B 0DG 9 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale24 covale both ? B 0DG 9 "O3'" ? ? ? 1_555 B 0DA 10 P ? ? B 0DG 9 B 0DA 10 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale25 covale both ? B 0DA 10 "O3'" ? ? ? 1_555 B 0DG 11 P ? ? B 0DA 10 B 0DG 11 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale26 covale both ? B 0DG 11 "O3'" ? ? ? 1_555 B 0DT 12 P ? ? B 0DG 11 B 0DT 12 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale27 covale both ? B 0DT 12 "O3'" ? ? ? 1_555 B 0DC 13 P ? ? B 0DT 12 B 0DC 13 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale28 covale both ? B 0DC 13 "O3'" ? ? ? 1_555 B 0DC 14 P ? ? B 0DC 13 B 0DC 14 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale29 covale both ? B 0DC 14 "O3'" ? ? ? 1_555 B 0DA 15 P ? ? B 0DC 14 B 0DA 15 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale30 covale both ? B 0DA 15 "O3'" ? ? ? 1_555 B 0DC 16 P ? ? B 0DA 15 B 0DC 16 1_555 ? ? ? ? ? ? ? 1.612 ? ? hydrog1 hydrog ? ? A 0DC 4 N3 ? ? ? 1_555 B 0DG 7 N1 ? ? A 0DC 4 B 0DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A 0DC 4 N4 ? ? ? 1_555 B 0DG 7 O6 ? ? A 0DC 4 B 0DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A 0DC 4 O2 ? ? ? 1_555 B 0DG 7 N2 ? ? A 0DC 4 B 0DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A 0DG 5 N1 ? ? ? 1_555 B 0DC 6 N3 ? ? A 0DG 5 B 0DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A 0DG 5 N2 ? ? ? 1_555 B 0DC 6 O2 ? ? A 0DG 5 B 0DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A 0DG 5 O6 ? ? ? 1_555 B 0DC 6 N4 ? ? A 0DG 5 B 0DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A 0DG 6 N1 ? ? ? 1_555 B 0DC 5 N3 ? ? A 0DG 6 B 0DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A 0DG 6 N2 ? ? ? 1_555 B 0DC 5 O2 ? ? A 0DG 6 B 0DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A 0DG 6 O6 ? ? ? 1_555 B 0DC 5 N4 ? ? A 0DG 6 B 0DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A 0DC 7 N3 ? ? ? 1_555 B 0DG 4 N1 ? ? A 0DC 7 B 0DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A 0DC 7 N4 ? ? ? 1_555 B 0DG 4 O6 ? ? A 0DC 7 B 0DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A 0DC 7 O2 ? ? ? 1_555 B 0DG 4 N2 ? ? A 0DC 7 B 0DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A 0DT 8 O4 ? ? ? 1_555 B 0DC 14 N4 ? ? A 0DT 8 B 0DC 14 1_555 ? ? ? ? ? ? '0DT-0DC MISPAIR' ? ? ? hydrog14 hydrog ? ? A 0DG 9 N1 ? ? ? 1_555 B 0DC 14 N3 ? ? A 0DG 9 B 0DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A 0DG 9 N2 ? ? ? 1_555 B 0DC 14 O2 ? ? A 0DG 9 B 0DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A 0DG 9 O6 ? ? ? 1_555 B 0DC 14 N4 ? ? A 0DG 9 B 0DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A 0DG 10 N1 ? ? ? 1_555 B 0DC 13 N3 ? ? A 0DG 10 B 0DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A 0DG 10 N2 ? ? ? 1_555 B 0DC 13 O2 ? ? A 0DG 10 B 0DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A 0DG 10 O6 ? ? ? 1_555 B 0DC 13 N4 ? ? A 0DG 10 B 0DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A 0DC 12 N3 ? ? ? 1_555 B 0DG 11 N1 ? ? A 0DC 12 B 0DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A 0DC 12 N4 ? ? ? 1_555 B 0DG 11 O6 ? ? A 0DC 12 B 0DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A 0DC 12 O2 ? ? ? 1_555 B 0DG 11 N2 ? ? A 0DC 12 B 0DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A 0DC 14 N3 ? ? ? 1_555 B 0DG 9 N1 ? ? A 0DC 14 B 0DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A 0DC 14 N4 ? ? ? 1_555 B 0DG 9 O6 ? ? A 0DC 14 B 0DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A 0DC 14 O2 ? ? ? 1_555 B 0DG 9 N2 ? ? A 0DC 14 B 0DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_entry_details.entry_id 9YBK _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.has_protein_modification N # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "C4'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 0DA _pdbx_validate_rmsd_bond.auth_seq_id_1 3 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C3'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 0DA _pdbx_validate_rmsd_bond.auth_seq_id_2 3 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.597 _pdbx_validate_rmsd_bond.bond_target_value 1.529 _pdbx_validate_rmsd_bond.bond_deviation 0.068 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.010 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O3'" A 0DG 2 ? ? P A 0DA 3 ? ? OP1 A 0DA 3 ? ? 117.42 110.50 6.92 1.10 Y 2 1 "O3'" A 0DC 7 ? ? P A 0DT 8 ? ? OP2 A 0DT 8 ? ? 122.79 110.50 12.29 1.10 Y 3 1 "C4'" B 0DC 1 ? ? "C3'" B 0DC 1 ? ? "C2'" B 0DC 1 ? ? 108.76 103.10 5.66 0.90 N # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y,x,z+1/4 3 y,-x,z+3/4 4 -x,-y,z+1/2 # _pdbx_refine_tls.id 1 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 9.85870994167 _pdbx_refine_tls.origin_y 9.74538571832 _pdbx_refine_tls.origin_z -0.558281489368 _pdbx_refine_tls.T[1][1] 0.568779368356 _pdbx_refine_tls.T[1][1]_esd ? _pdbx_refine_tls.T[1][2] 0.1941763597 _pdbx_refine_tls.T[1][2]_esd ? _pdbx_refine_tls.T[1][3] 0.0364624376564 _pdbx_refine_tls.T[1][3]_esd ? _pdbx_refine_tls.T[2][2] 0.416968325053 _pdbx_refine_tls.T[2][2]_esd ? _pdbx_refine_tls.T[2][3] -0.00936807091669 _pdbx_refine_tls.T[2][3]_esd ? _pdbx_refine_tls.T[3][3] 0.335872864379 _pdbx_refine_tls.T[3][3]_esd ? _pdbx_refine_tls.L[1][1] 1.31608444025 _pdbx_refine_tls.L[1][1]_esd ? _pdbx_refine_tls.L[1][2] -0.359199189539 _pdbx_refine_tls.L[1][2]_esd ? _pdbx_refine_tls.L[1][3] 0.362945200459 _pdbx_refine_tls.L[1][3]_esd ? _pdbx_refine_tls.L[2][2] 1.24423397691 _pdbx_refine_tls.L[2][2]_esd ? _pdbx_refine_tls.L[2][3] 0.150427862065 _pdbx_refine_tls.L[2][3]_esd ? _pdbx_refine_tls.L[3][3] 1.9601892378 _pdbx_refine_tls.L[3][3]_esd ? _pdbx_refine_tls.S[1][1] -0.253884115892 _pdbx_refine_tls.S[1][1]_esd ? _pdbx_refine_tls.S[1][2] 0.144238602541 _pdbx_refine_tls.S[1][2]_esd ? _pdbx_refine_tls.S[1][3] 0.0469161073161 _pdbx_refine_tls.S[1][3]_esd ? _pdbx_refine_tls.S[2][1] 0.266258876988 _pdbx_refine_tls.S[2][1]_esd ? _pdbx_refine_tls.S[2][2] -0.345707361643 _pdbx_refine_tls.S[2][2]_esd ? _pdbx_refine_tls.S[2][3] 0.0787097907636 _pdbx_refine_tls.S[2][3]_esd ? _pdbx_refine_tls.S[3][1] 0.0725851158969 _pdbx_refine_tls.S[3][1]_esd ? _pdbx_refine_tls.S[3][2] -0.188845534618 _pdbx_refine_tls.S[3][2]_esd ? _pdbx_refine_tls.S[3][3] -0.0890451496494 _pdbx_refine_tls.S[3][3]_esd ? # _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 1 _pdbx_refine_tls_group.beg_PDB_ins_code ? _pdbx_refine_tls_group.end_label_asym_id C _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id B _pdbx_refine_tls_group.end_auth_seq_id 16 _pdbx_refine_tls_group.end_PDB_ins_code ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details all # 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 0DA C8A C Y N 1 0DA N9A N Y N 2 0DA C4A C Y N 3 0DA C5A C Y N 4 0DA N7A N Y N 5 0DA N3A N Y N 6 0DA C2A C Y N 7 0DA N1A N Y N 8 0DA C6A C Y N 9 0DA N6A N N N 10 0DA "C4'" C N S 11 0DA "O4'" O N N 12 0DA "C3'" C N R 13 0DA "C2'" C N N 14 0DA "C1'" C N S 15 0DA "O3'" O N N 16 0DA "C5'" C N N 17 0DA "O5'" O N N 18 0DA P P N N 19 0DA OP2 O N N 20 0DA OP3 O N N 21 0DA OP1 O N N 22 0DA H8A H N N 23 0DA H2A H N N 24 0DA HN61 H N N 25 0DA HN62 H N N 26 0DA "H4'" H N N 27 0DA "H3'" H N N 28 0DA "H2'" H N N 29 0DA "H2''" H N N 30 0DA "H1'" H N N 31 0DA "HO3'" H N N 32 0DA "H5'" H N N 33 0DA "H5''" H N N 34 0DA H2P H N N 35 0DA HOP3 H N N 36 0DC OP3 O N N 37 0DC P P N N 38 0DC OP1 O N N 39 0DC OP2 O N N 40 0DC "O5'" O N N 41 0DC "C5'" C N N 42 0DC "C4'" C N S 43 0DC "O4'" O N N 44 0DC "C3'" C N R 45 0DC "O3'" O N N 46 0DC "C2'" C N N 47 0DC "C1'" C N S 48 0DC N1 N N N 49 0DC C2 C N N 50 0DC O2 O N N 51 0DC N3 N N N 52 0DC C4 C N N 53 0DC N4 N N N 54 0DC C5 C N N 55 0DC C6 C N N 56 0DC HOP3 H N N 57 0DC HOP2 H N N 58 0DC "H5'" H N N 59 0DC "H5''" H N N 60 0DC "H4'" H N N 61 0DC "H3'" H N N 62 0DC "HO3'" H N N 63 0DC "H2'" H N N 64 0DC "H2''" H N N 65 0DC "H1'" H N N 66 0DC H41 H N N 67 0DC H42 H N N 68 0DC H5 H N N 69 0DC H6 H N N 70 0DG OP3 O N N 71 0DG P P N N 72 0DG OP1 O N N 73 0DG OP2 O N N 74 0DG "O5'" O N N 75 0DG "C5'" C N N 76 0DG "C4'" C N S 77 0DG "O4'" O N N 78 0DG "C3'" C N R 79 0DG "O3'" O N N 80 0DG "C2'" C N N 81 0DG "C1'" C N S 82 0DG N9 N Y N 83 0DG C8 C Y N 84 0DG N7 N Y N 85 0DG C5 C Y N 86 0DG C6 C N N 87 0DG O6 O N N 88 0DG N1 N N N 89 0DG C2 C N N 90 0DG N2 N N N 91 0DG N3 N N N 92 0DG C4 C Y N 93 0DG HOP3 H N N 94 0DG HOP2 H N N 95 0DG "H5'" H N N 96 0DG "H5''" H N N 97 0DG "H4'" H N N 98 0DG "H3'" H N N 99 0DG "HO3'" H N N 100 0DG "H2'" H N N 101 0DG "H2''" H N N 102 0DG "H1'" H N N 103 0DG H8 H N N 104 0DG H1 H N N 105 0DG H21 H N N 106 0DG H22 H N N 107 0DT OP3 O N N 108 0DT P P N N 109 0DT OP1 O N N 110 0DT OP2 O N N 111 0DT "O5'" O N N 112 0DT "C5'" C N N 113 0DT "C4'" C N S 114 0DT "O4'" O N N 115 0DT "C3'" C N R 116 0DT "O3'" O N N 117 0DT "C2'" C N N 118 0DT "C1'" C N S 119 0DT N1 N N N 120 0DT C2 C N N 121 0DT O2 O N N 122 0DT N3 N N N 123 0DT C4 C N N 124 0DT O4 O N N 125 0DT C5 C N N 126 0DT C5M C N N 127 0DT C6 C N N 128 0DT HOP3 H N N 129 0DT HOP2 H N N 130 0DT "H5'" H N N 131 0DT "H5''" H N N 132 0DT "H4'" H N N 133 0DT "H3'" H N N 134 0DT "HO3'" H N N 135 0DT "H2'" H N N 136 0DT "H2''" H N N 137 0DT "H1'" H N N 138 0DT H3 H N N 139 0DT H71 H N N 140 0DT H72 H N N 141 0DT H73 H N N 142 0DT H6 H N N 143 MG MG MG N N 144 # 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 0DA C8A N9A sing Y N 1 0DA C8A N7A doub Y N 2 0DA N9A C4A sing Y N 3 0DA N9A "C1'" sing N N 4 0DA C4A C5A doub Y N 5 0DA C4A N3A sing Y N 6 0DA C5A N7A sing Y N 7 0DA C5A C6A sing Y N 8 0DA N3A C2A doub Y N 9 0DA C2A N1A sing Y N 10 0DA N1A C6A doub Y N 11 0DA C6A N6A sing N N 12 0DA "C4'" "O4'" sing N N 13 0DA "C4'" "C3'" sing N N 14 0DA "O4'" "C1'" sing N N 15 0DA "C3'" "C2'" sing N N 16 0DA "C2'" "C1'" sing N N 17 0DA "C3'" "O3'" sing N N 18 0DA "C4'" "C5'" sing N N 19 0DA "C5'" "O5'" sing N N 20 0DA "O5'" P sing N N 21 0DA P OP2 sing N N 22 0DA P OP3 sing N N 23 0DA P OP1 doub N N 24 0DA C8A H8A sing N N 25 0DA C2A H2A sing N N 26 0DA N6A HN61 sing N N 27 0DA N6A HN62 sing N N 28 0DA "C4'" "H4'" sing N N 29 0DA "C3'" "H3'" sing N N 30 0DA "C2'" "H2'" sing N N 31 0DA "C2'" "H2''" sing N N 32 0DA "C1'" "H1'" sing N N 33 0DA "O3'" "HO3'" sing N N 34 0DA "C5'" "H5'" sing N N 35 0DA "C5'" "H5''" sing N N 36 0DA OP2 H2P sing N N 37 0DA OP3 HOP3 sing N N 38 0DC OP3 P sing N N 39 0DC OP3 HOP3 sing N N 40 0DC P OP1 doub N N 41 0DC P OP2 sing N N 42 0DC P "O5'" sing N N 43 0DC OP2 HOP2 sing N N 44 0DC "O5'" "C5'" sing N N 45 0DC "C5'" "C4'" sing N N 46 0DC "C5'" "H5'" sing N N 47 0DC "C5'" "H5''" sing N N 48 0DC "C4'" "O4'" sing N N 49 0DC "C4'" "C3'" sing N N 50 0DC "C4'" "H4'" sing N N 51 0DC "O4'" "C1'" sing N N 52 0DC "C3'" "O3'" sing N N 53 0DC "C3'" "C2'" sing N N 54 0DC "C3'" "H3'" sing N N 55 0DC "O3'" "HO3'" sing N N 56 0DC "C2'" "C1'" sing N N 57 0DC "C2'" "H2'" sing N N 58 0DC "C2'" "H2''" sing N N 59 0DC "C1'" N1 sing N N 60 0DC "C1'" "H1'" sing N N 61 0DC N1 C2 sing N N 62 0DC N1 C6 sing N N 63 0DC C2 O2 doub N N 64 0DC C2 N3 sing N N 65 0DC N3 C4 doub N N 66 0DC C4 N4 sing N N 67 0DC C4 C5 sing N N 68 0DC N4 H41 sing N N 69 0DC N4 H42 sing N N 70 0DC C5 C6 doub N N 71 0DC C5 H5 sing N N 72 0DC C6 H6 sing N N 73 0DG OP3 P sing N N 74 0DG OP3 HOP3 sing N N 75 0DG P OP1 doub N N 76 0DG P OP2 sing N N 77 0DG P "O5'" sing N N 78 0DG OP2 HOP2 sing N N 79 0DG "O5'" "C5'" sing N N 80 0DG "C5'" "C4'" sing N N 81 0DG "C5'" "H5'" sing N N 82 0DG "C5'" "H5''" sing N N 83 0DG "C4'" "O4'" sing N N 84 0DG "C4'" "C3'" sing N N 85 0DG "C4'" "H4'" sing N N 86 0DG "O4'" "C1'" sing N N 87 0DG "C3'" "O3'" sing N N 88 0DG "C3'" "C2'" sing N N 89 0DG "C3'" "H3'" sing N N 90 0DG "O3'" "HO3'" sing N N 91 0DG "C2'" "C1'" sing N N 92 0DG "C2'" "H2'" sing N N 93 0DG "C2'" "H2''" sing N N 94 0DG "C1'" N9 sing N N 95 0DG "C1'" "H1'" sing N N 96 0DG N9 C8 sing Y N 97 0DG N9 C4 sing Y N 98 0DG C8 N7 doub Y N 99 0DG C8 H8 sing N N 100 0DG N7 C5 sing Y N 101 0DG C5 C6 sing N N 102 0DG C5 C4 doub Y N 103 0DG C6 O6 doub N N 104 0DG C6 N1 sing N N 105 0DG N1 C2 sing N N 106 0DG N1 H1 sing N N 107 0DG C2 N2 sing N N 108 0DG C2 N3 doub N N 109 0DG N2 H21 sing N N 110 0DG N2 H22 sing N N 111 0DG N3 C4 sing N N 112 0DT OP3 P sing N N 113 0DT OP3 HOP3 sing N N 114 0DT P OP1 doub N N 115 0DT P OP2 sing N N 116 0DT P "O5'" sing N N 117 0DT OP2 HOP2 sing N N 118 0DT "O5'" "C5'" sing N N 119 0DT "C5'" "C4'" sing N N 120 0DT "C5'" "H5'" sing N N 121 0DT "C5'" "H5''" sing N N 122 0DT "C4'" "O4'" sing N N 123 0DT "C4'" "C3'" sing N N 124 0DT "C4'" "H4'" sing N N 125 0DT "O4'" "C1'" sing N N 126 0DT "C3'" "O3'" sing N N 127 0DT "C3'" "C2'" sing N N 128 0DT "C3'" "H3'" sing N N 129 0DT "O3'" "HO3'" sing N N 130 0DT "C2'" "C1'" sing N N 131 0DT "C2'" "H2'" sing N N 132 0DT "C2'" "H2''" sing N N 133 0DT "C1'" N1 sing N N 134 0DT "C1'" "H1'" sing N N 135 0DT N1 C2 sing N N 136 0DT N1 C6 sing N N 137 0DT C2 O2 doub N N 138 0DT C2 N3 sing N N 139 0DT N3 C4 sing N N 140 0DT N3 H3 sing N N 141 0DT C4 O4 doub N N 142 0DT C4 C5 sing N N 143 0DT C5 C5M sing N N 144 0DT C5 C6 doub N N 145 0DT C5M H71 sing N N 146 0DT C5M H72 sing N N 147 0DT C5M H73 sing N N 148 0DT C6 H6 sing N N 149 # _ndb_struct_conf_na.entry_id 9YBK _ndb_struct_conf_na.feature 'z-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 0DC 4 1_555 B 0DG 7 1_555 -0.313 -0.114 -0.085 -0.783 -2.051 -0.130 1 A_0DC4:0DG7_B A 4 ? B 7 ? 19 1 1 A 0DG 5 1_555 B 0DC 6 1_555 0.113 -0.386 -0.076 3.239 -3.637 1.285 2 A_0DG5:0DC6_B A 5 ? B 6 ? 19 1 1 A 0DG 6 1_555 B 0DC 5 1_555 0.329 -0.287 -0.080 -1.283 -4.758 4.006 3 A_0DG6:0DC5_B A 6 ? B 5 ? 19 1 1 A 0DC 7 1_555 B 0DG 4 1_555 -0.175 0.079 -0.188 0.658 0.115 -2.848 4 A_0DC7:0DG4_B A 7 ? B 4 ? 19 1 1 A 0DG 9 1_555 B 0DC 14 1_555 0.099 -0.305 0.507 10.846 -3.223 0.039 5 A_0DG9:0DC14_B A 9 ? B 14 ? 19 1 1 A 0DG 10 1_555 B 0DC 13 1_555 0.140 -0.096 0.060 2.742 2.347 1.061 6 A_0DG10:0DC13_B A 10 ? B 13 ? 19 1 1 A 0DC 12 1_555 B 0DG 11 1_555 -0.060 -0.118 -0.138 2.640 -0.085 0.238 7 A_0DC12:0DG11_B A 12 ? B 11 ? 19 1 1 A 0DC 14 1_555 B 0DG 9 1_555 -0.191 0.159 0.419 -2.397 3.144 -5.117 8 A_0DC14:0DG9_B A 14 ? B 9 ? 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 0DC 4 1_555 B 0DG 7 1_555 A 0DG 5 1_555 B 0DC 6 1_555 -0.033 0.863 3.231 0.991 -3.349 -32.761 -0.950 0.110 3.300 5.917 1.751 -32.942 1 AA_0DC40DG5:0DC60DG7_BB A 4 ? B 7 ? A 5 ? B 6 ? 1 A 0DG 5 1_555 B 0DC 6 1_555 A 0DG 6 1_555 B 0DC 5 1_555 0.648 0.093 3.375 -3.111 -5.103 -32.832 0.723 0.591 3.396 8.937 -5.447 -33.357 2 AA_0DG50DG6:0DC50DC6_BB A 5 ? B 6 ? A 6 ? B 5 ? 1 A 0DG 6 1_555 B 0DC 5 1_555 A 0DC 7 1_555 B 0DG 4 1_555 -0.210 -0.005 3.178 0.598 -5.030 -36.103 0.686 -0.255 3.152 8.066 0.960 -36.445 3 AA_0DG60DC7:0DG40DC5_BB A 6 ? B 5 ? A 7 ? B 4 ? 1 A 0DG 9 1_555 B 0DC 14 1_555 A 0DG 10 1_555 B 0DC 13 1_555 0.024 -0.262 3.553 2.164 -4.727 -30.970 1.444 0.484 3.466 8.775 4.017 -31.393 4 AA_0DG90DG10:0DC130DC14_BB A 9 ? B 14 ? A 10 ? B 13 ? 1 A 0DG 10 1_555 B 0DC 13 1_555 A 0DC 12 1_555 B 0DG 11 1_555 -0.231 -0.940 6.536 -0.707 -1.632 -73.697 0.887 -0.238 6.515 1.360 -0.590 -73.715 5 AA_0DG100DC12:0DG110DC13_BB A 10 ? B 13 ? A 12 ? B 11 ? 1 A 0DC 12 1_555 B 0DG 11 1_555 A 0DC 14 1_555 B 0DG 9 1_555 0.220 -1.183 6.695 -2.857 -3.889 -66.060 1.401 -0.033 6.628 3.562 -2.617 -66.216 6 AA_0DC120DC14:0DG90DG11_BB A 12 ? B 11 ? A 14 ? B 9 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Office of Naval Research (ONR)' 'United States' N000141912596 1 'Department of Energy (DOE, United States)' 'United States' DE-SC0007991 2 'National Science Foundation (NSF, United States)' 'United States' CCF-2106790 3 'National Science Foundation (NSF, United States)' 'United States' GCR-2317843 4 # _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 8EPF _pdbx_initial_refinement_model.details ? # _space_group.name_H-M_alt 'P 41' _space_group.name_Hall 'P 4w' _space_group.IT_number 76 _space_group.crystal_system tetragonal _space_group.id 1 # _atom_sites.entry_id 9YBK _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.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.027789 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.027789 _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] 0.009802 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? MG ? ? 9.41153 2.53737 ? ? 2.59044 63.03566 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 ? ? 15.80542 1.70748 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_ # loop_ #