data_7YVX # _entry.id 7YVX # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 7YVX pdb_00007yvx 10.2210/pdb7yvx/pdb WWPDB D_1300031738 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2022-10-12 2 'Structure model' 1 1 2024-05-29 # _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_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Data collection' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7YVX _pdbx_database_status.recvd_initial_deposition_date 2022-08-19 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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 2 _pdbx_contact_author.email j.kondo@sophia.ac.jp _pdbx_contact_author.name_first Jiro _pdbx_contact_author.name_last Kondo _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-5682-3685 # _audit_author.name 'Kondo, J.' _audit_author.pdbx_ordinal 1 _audit_author.identifier_ORCID 0000-0002-5682-3685 # _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 'Left-handed DNA duplex containing consecutive G-G base pairs' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # _citation_author.citation_id primary _citation_author.name 'Kondo, J.' _citation_author.ordinal 1 _citation_author.identifier_ORCID 0000-0002-5682-3685 # 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(*CP*GP*(CBR)P*GP*GP*GP*CP*GP*CP*G)-3') ; 3165.900 1 ? ? ? ? 2 non-polymer syn 'COBALT (II) ION' 58.933 3 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(CBR)(DG)(DG)(DG)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGGGCGCG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 'COBALT (II) ION' _pdbx_entity_nonpoly.comp_id CO # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 CBR n 1 4 DG n 1 5 DG n 1 6 DG n 1 7 DC n 1 8 DG n 1 9 DC n 1 10 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 10 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # 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 CBR 'DNA linking' n "5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 Br N3 O7 P' 386.093 CO non-polymer . 'COBALT (II) ION' ? 'Co 2' 58.933 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 # 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 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 CBR 3 3 3 CBR CBR A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DC 7 7 7 DC DC A . n A 1 8 DG 8 8 8 DG DG A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DG 10 10 10 DG DG A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 CO 1 101 1 CO CO A . C 2 CO 1 102 2 CO CO A . D 2 CO 1 103 3 CO CO A . # 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 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.17.1 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.27 3 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 5 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 120.000 _cell.angle_gamma_esd ? _cell.entry_id 7YVX _cell.details ? _cell.formula_units_Z ? _cell.length_a 43.375 _cell.length_a_esd ? _cell.length_b 43.375 _cell.length_b_esd ? _cell.length_c 71.998 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 12 _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 7YVX _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' _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 7YVX _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 3.09 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 60.17 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'MPD, sodium chloride, hexammine cobalt chloride, sodium cacodylate' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2021-12-21 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.605 _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 'PHOTON FACTORY BEAMLINE BL-17A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.605 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-17A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate 54.539 _reflns.entry_id 7YVX _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.99 _reflns.d_resolution_low 37.560 _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 1553 _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 99.700 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 10.003 _reflns.pdbx_Rmerge_I_obs 0.101 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 18.640 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.163 _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 0.106 _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 0.998 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? _reflns.pdbx_CC_split_method ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _reflns_shell.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_redundancy_anomalous _reflns_shell.pdbx_CC_half_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_percent_possible_anomalous 3.000 3.160 ? 9.820 ? 2334 227 ? 227 100.000 ? ? ? ? 0.318 ? ? ? ? ? ? ? ? 10.282 ? ? ? ? 0.335 ? ? 1 1 0.988 ? ? ? ? ? ? ? ? ? ? 3.160 3.350 ? 12.360 ? 2286 217 ? 217 100.000 ? ? ? ? 0.197 ? ? ? ? ? ? ? ? 10.535 ? ? ? ? 0.207 ? ? 2 1 0.997 ? ? ? ? ? ? ? ? ? ? 3.350 3.580 ? 17.150 ? 2003 198 ? 198 100.000 ? ? ? ? 0.129 ? ? ? ? ? ? ? ? 10.116 ? ? ? ? 0.136 ? ? 3 1 0.997 ? ? ? ? ? ? ? ? ? ? 3.580 3.870 ? 18.060 ? 1714 183 ? 183 100.000 ? ? ? ? 0.107 ? ? ? ? ? ? ? ? 9.366 ? ? ? ? 0.114 ? ? 4 1 0.995 ? ? ? ? ? ? ? ? ? ? 3.870 4.240 ? 20.090 ? 1495 174 ? 174 100.000 ? ? ? ? 0.099 ? ? ? ? ? ? ? ? 8.592 ? ? ? ? 0.105 ? ? 5 1 0.995 ? ? ? ? ? ? ? ? ? ? 4.240 4.740 ? 22.360 ? 1699 157 ? 157 100.000 ? ? ? ? 0.110 ? ? ? ? ? ? ? ? 10.822 ? ? ? ? 0.116 ? ? 6 1 0.995 ? ? ? ? ? ? ? ? ? ? 4.740 5.470 ? 24.610 ? 1449 136 ? 135 99.300 ? ? ? ? 0.095 ? ? ? ? ? ? ? ? 10.733 ? ? ? ? 0.100 ? ? 7 1 0.995 ? ? ? ? ? ? ? ? ? ? 5.470 6.700 ? 27.040 ? 1156 113 ? 113 100.000 ? ? ? ? 0.086 ? ? ? ? ? ? ? ? 10.230 ? ? ? ? 0.090 ? ? 8 1 0.999 ? ? ? ? ? ? ? ? ? ? 6.700 9.470 ? 27.280 ? 949 96 ? 95 99.000 ? ? ? ? 0.079 ? ? ? ? ? ? ? ? 9.989 ? ? ? ? 0.083 ? ? 9 1 0.998 ? ? ? ? ? ? ? ? ? ? 9.470 37.560 ? 25.160 ? 450 56 ? 54 96.400 ? ? ? ? 0.060 ? ? ? ? ? ? ? ? 8.333 ? ? ? ? 0.064 ? ? 10 1 0.998 ? ? ? ? ? ? ? ? ? ? # _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 120.240 _refine.B_iso_mean 50.3472 _refine.B_iso_min 28.950 _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 7YVX _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 2.9900 _refine.ls_d_res_low 37.5600 _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 1538 _refine.ls_number_reflns_R_free 149 _refine.ls_number_reflns_R_work 1389 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.6100 _refine.ls_percent_reflns_R_free 9.6900 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2007 _refine.ls_R_factor_R_free 0.2550 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1953 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.540 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 16.9000 _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 0.3700 _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 final _refine_hist.details ? _refine_hist.d_res_high 2.9900 _refine_hist.d_res_low 37.5600 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 209 _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 10 _refine_hist.pdbx_B_iso_mean_ligand 103.14 _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 206 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 2.9900 _refine_ls_shell.d_res_low 3.1600 _refine_ls_shell.number_reflns_all 1538 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 149 _refine_ls_shell.number_reflns_R_work 1389 _refine_ls_shell.percent_reflns_obs 100.0000 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.2550 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.R_factor_R_work 0.1953 _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 1 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 7YVX _struct.title 'Left-handed DNA duplex containing consecutive G-G base pairs' _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 7YVX _struct_keywords.text 'Z-form, DNA nanotechnology, DNA' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7YVX _struct_ref.pdbx_db_accession 7YVX _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7YVX _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7YVX _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 10 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2480 ? 1 MORE -11 ? 1 'SSA (A^2)' 3480 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 8_555 x-y,-y,-z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # 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 DG 2 "O3'" ? ? ? 1_555 A CBR 3 P ? ? A DG 2 A CBR 3 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale2 covale both ? A CBR 3 "O3'" ? ? ? 1_555 A DG 4 P ? ? A CBR 3 A DG 4 1_555 ? ? ? ? ? ? ? 1.599 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 A DG 10 N1 ? ? A DC 1 A DG 10 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 A DG 10 O6 ? ? A DC 1 A DG 10 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 A DG 10 N2 ? ? A DC 1 A DG 10 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DC 9 N3 ? ? A DG 2 A DC 9 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DC 9 O2 ? ? A DG 2 A DC 9 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DC 9 N4 ? ? A DG 2 A DC 9 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A CBR 3 N3 ? ? ? 1_555 A DG 8 N1 ? ? A CBR 3 A DG 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A CBR 3 N4 ? ? ? 1_555 A DG 8 O6 ? ? A CBR 3 A DG 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A CBR 3 O2 ? ? ? 1_555 A DG 8 N2 ? ? A CBR 3 A DG 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DC 7 N3 ? ? A DG 4 A DC 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DC 7 O2 ? ? A DG 4 A DC 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DC 7 N4 ? ? A DG 4 A DC 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 O6 ? ? ? 1_555 A DG 6 N1 ? ? A DG 5 A DG 6 8_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 A DG 5 O6 ? ? A DG 6 A DG 5 8_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog15 hydrog ? ? A DC 7 N3 ? ? ? 1_555 A DG 4 N1 ? ? A DC 7 A DG 4 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 N4 ? ? ? 1_555 A DG 4 O6 ? ? A DC 7 A DG 4 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 O2 ? ? ? 1_555 A DG 4 N2 ? ? A DC 7 A DG 4 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 8 N1 ? ? ? 1_555 A CBR 3 N3 ? ? A DG 8 A CBR 3 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 8 N2 ? ? ? 1_555 A CBR 3 O2 ? ? A DG 8 A CBR 3 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 8 O6 ? ? ? 1_555 A CBR 3 N4 ? ? A DG 8 A CBR 3 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 A DG 2 N1 ? ? A DC 9 A DG 2 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 A DG 2 O6 ? ? A DC 9 A DG 2 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 A DG 2 N2 ? ? A DC 9 A DG 2 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 A DC 1 N3 ? ? A DG 10 A DC 1 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 A DC 1 O2 ? ? A DG 10 A DC 1 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 A DC 1 N4 ? ? A DG 10 A DC 1 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 DC _pdbx_validate_rmsd_bond.auth_seq_id_1 7 _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 A _pdbx_validate_rmsd_bond.auth_comp_id_2 DC _pdbx_validate_rmsd_bond.auth_seq_id_2 7 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.364 _pdbx_validate_rmsd_bond.bond_target_value 1.419 _pdbx_validate_rmsd_bond.bond_deviation -0.055 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.006 _pdbx_validate_rmsd_bond.linker_flag N # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id CO _pdbx_struct_special_symmetry.auth_seq_id 101 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id B _pdbx_struct_special_symmetry.label_comp_id CO _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_entry_details.entry_id 7YVX _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # loop_ _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 CBR BR BR N N 1 CBR P P N N 2 CBR OP1 O N N 3 CBR OP2 O N N 4 CBR "O5'" O N N 5 CBR N1 N N N 6 CBR C6 C N N 7 CBR C2 C N N 8 CBR O2 O N N 9 CBR N3 N N N 10 CBR C4 C N N 11 CBR N4 N N N 12 CBR C5 C N N 13 CBR "C2'" C N N 14 CBR "C5'" C N N 15 CBR "C4'" C N R 16 CBR "O4'" O N N 17 CBR "C1'" C N R 18 CBR "C3'" C N S 19 CBR "O3'" O N N 20 CBR OP3 O N N 21 CBR HOP2 H N N 22 CBR H6 H N N 23 CBR H41 H N N 24 CBR H42 H N N 25 CBR "H2'" H N N 26 CBR "H2''" H N N 27 CBR "H5'" H N N 28 CBR "H5''" H N N 29 CBR "H4'" H N N 30 CBR "H1'" H N N 31 CBR "H3'" H N N 32 CBR "HO3'" H N N 33 CBR HOP3 H N N 34 CO CO CO N N 35 DC OP3 O N N 36 DC P P N N 37 DC OP1 O N N 38 DC OP2 O N N 39 DC "O5'" O N N 40 DC "C5'" C N N 41 DC "C4'" C N R 42 DC "O4'" O N N 43 DC "C3'" C N S 44 DC "O3'" O N N 45 DC "C2'" C N N 46 DC "C1'" C N R 47 DC N1 N N N 48 DC C2 C N N 49 DC O2 O N N 50 DC N3 N N N 51 DC C4 C N N 52 DC N4 N N N 53 DC C5 C N N 54 DC C6 C N N 55 DC HOP3 H N N 56 DC HOP2 H N N 57 DC "H5'" H N N 58 DC "H5''" H N N 59 DC "H4'" H N N 60 DC "H3'" H N N 61 DC "HO3'" H N N 62 DC "H2'" H N N 63 DC "H2''" H N N 64 DC "H1'" H N N 65 DC H41 H N N 66 DC H42 H N N 67 DC H5 H N N 68 DC H6 H N N 69 DG OP3 O N N 70 DG P P N N 71 DG OP1 O N N 72 DG OP2 O N N 73 DG "O5'" O N N 74 DG "C5'" C N N 75 DG "C4'" C N R 76 DG "O4'" O N N 77 DG "C3'" C N S 78 DG "O3'" O N N 79 DG "C2'" C N N 80 DG "C1'" C N R 81 DG N9 N Y N 82 DG C8 C Y N 83 DG N7 N Y N 84 DG C5 C Y N 85 DG C6 C N N 86 DG O6 O N N 87 DG N1 N N N 88 DG C2 C N N 89 DG N2 N N N 90 DG N3 N N N 91 DG C4 C Y N 92 DG HOP3 H N N 93 DG HOP2 H N N 94 DG "H5'" H N N 95 DG "H5''" H N N 96 DG "H4'" H N N 97 DG "H3'" H N N 98 DG "HO3'" H N N 99 DG "H2'" H N N 100 DG "H2''" H N N 101 DG "H1'" H N N 102 DG H8 H N N 103 DG H1 H N N 104 DG H21 H N N 105 DG H22 H N N 106 # 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 CBR BR C5 sing N N 1 CBR P OP1 doub N N 2 CBR P OP2 sing N N 3 CBR P "O5'" sing N N 4 CBR P OP3 sing N N 5 CBR OP2 HOP2 sing N N 6 CBR "O5'" "C5'" sing N N 7 CBR N1 C6 sing N N 8 CBR N1 C2 sing N N 9 CBR N1 "C1'" sing N N 10 CBR C6 C5 doub N N 11 CBR C6 H6 sing N N 12 CBR C2 O2 doub N N 13 CBR C2 N3 sing N N 14 CBR N3 C4 doub N N 15 CBR C4 N4 sing N N 16 CBR C4 C5 sing N N 17 CBR N4 H41 sing N N 18 CBR N4 H42 sing N N 19 CBR "C2'" "C1'" sing N N 20 CBR "C2'" "C3'" sing N N 21 CBR "C2'" "H2'" sing N N 22 CBR "C2'" "H2''" sing N N 23 CBR "C5'" "C4'" sing N N 24 CBR "C5'" "H5'" sing N N 25 CBR "C5'" "H5''" sing N N 26 CBR "C4'" "O4'" sing N N 27 CBR "C4'" "C3'" sing N N 28 CBR "C4'" "H4'" sing N N 29 CBR "O4'" "C1'" sing N N 30 CBR "C1'" "H1'" sing N N 31 CBR "C3'" "O3'" sing N N 32 CBR "C3'" "H3'" sing N N 33 CBR "O3'" "HO3'" sing N N 34 CBR OP3 HOP3 sing N N 35 DC OP3 P sing N N 36 DC OP3 HOP3 sing N N 37 DC P OP1 doub N N 38 DC P OP2 sing N N 39 DC P "O5'" sing N N 40 DC OP2 HOP2 sing N N 41 DC "O5'" "C5'" sing N N 42 DC "C5'" "C4'" sing N N 43 DC "C5'" "H5'" sing N N 44 DC "C5'" "H5''" sing N N 45 DC "C4'" "O4'" sing N N 46 DC "C4'" "C3'" sing N N 47 DC "C4'" "H4'" sing N N 48 DC "O4'" "C1'" sing N N 49 DC "C3'" "O3'" sing N N 50 DC "C3'" "C2'" sing N N 51 DC "C3'" "H3'" sing N N 52 DC "O3'" "HO3'" sing N N 53 DC "C2'" "C1'" sing N N 54 DC "C2'" "H2'" sing N N 55 DC "C2'" "H2''" sing N N 56 DC "C1'" N1 sing N N 57 DC "C1'" "H1'" sing N N 58 DC N1 C2 sing N N 59 DC N1 C6 sing N N 60 DC C2 O2 doub N N 61 DC C2 N3 sing N N 62 DC N3 C4 doub N N 63 DC C4 N4 sing N N 64 DC C4 C5 sing N N 65 DC N4 H41 sing N N 66 DC N4 H42 sing N N 67 DC C5 C6 doub N N 68 DC C5 H5 sing N N 69 DC C6 H6 sing N N 70 DG OP3 P sing N N 71 DG OP3 HOP3 sing N N 72 DG P OP1 doub N N 73 DG P OP2 sing N N 74 DG P "O5'" sing N N 75 DG OP2 HOP2 sing N N 76 DG "O5'" "C5'" sing N N 77 DG "C5'" "C4'" sing N N 78 DG "C5'" "H5'" sing N N 79 DG "C5'" "H5''" sing N N 80 DG "C4'" "O4'" sing N N 81 DG "C4'" "C3'" sing N N 82 DG "C4'" "H4'" sing N N 83 DG "O4'" "C1'" sing N N 84 DG "C3'" "O3'" sing N N 85 DG "C3'" "C2'" sing N N 86 DG "C3'" "H3'" sing N N 87 DG "O3'" "HO3'" sing N N 88 DG "C2'" "C1'" sing N N 89 DG "C2'" "H2'" sing N N 90 DG "C2'" "H2''" sing N N 91 DG "C1'" N9 sing N N 92 DG "C1'" "H1'" sing N N 93 DG N9 C8 sing Y N 94 DG N9 C4 sing Y N 95 DG C8 N7 doub Y N 96 DG C8 H8 sing N N 97 DG N7 C5 sing Y N 98 DG C5 C6 sing N N 99 DG C5 C4 doub Y N 100 DG C6 O6 doub N N 101 DG C6 N1 sing N N 102 DG N1 C2 sing N N 103 DG N1 H1 sing N N 104 DG C2 N2 sing N N 105 DG C2 N3 doub N N 106 DG N2 H21 sing N N 107 DG N2 H22 sing N N 108 DG N3 C4 sing N N 109 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7YVX 'double helix' 7YVX 'mismatched base pair' # 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 DC 1 1_555 A DG 10 8_555 -0.015 -0.611 0.024 -2.960 -4.268 -6.377 1 A_DC1:DG10_A A 1 ? A 10 ? 19 1 1 A DG 2 1_555 A DC 9 8_555 -0.247 -0.215 -0.006 8.306 0.754 -2.095 2 A_DG2:DC9_A A 2 ? A 9 ? 19 1 1 A CBR 3 1_555 A DG 8 8_555 0.191 -0.181 -0.102 -4.999 -2.934 -3.318 3 A_CBR3:DG8_A A 3 ? A 8 ? 19 1 1 A DG 4 1_555 A DC 7 8_555 -0.374 -0.224 -0.079 12.662 -4.526 -1.351 4 A_DG4:DC7_A A 4 ? A 7 ? 19 1 1 A DG 5 1_555 A DG 6 8_555 -3.652 1.618 0.330 10.943 -12.279 -64.781 5 A_DG5:DG6_A A 5 ? A 6 ? ? 1 1 A DG 6 1_555 A DG 5 8_555 3.652 1.618 0.330 -10.943 -12.279 -64.781 6 A_DG6:DG5_A A 6 ? A 5 ? ? 1 1 A DC 7 1_555 A DG 4 8_555 0.374 -0.224 -0.079 -12.662 -4.526 -1.351 7 A_DC7:DG4_A A 7 ? A 4 ? 19 1 1 A DG 8 1_555 A CBR 3 8_555 -0.191 -0.181 -0.102 4.999 -2.934 -3.318 8 A_DG8:CBR3_A A 8 ? A 3 ? 19 1 1 A DC 9 1_555 A DG 2 8_555 0.247 -0.215 -0.006 -8.306 0.754 -2.095 9 A_DC9:DG2_A A 9 ? A 2 ? 19 1 1 A DG 10 1_555 A DC 1 8_555 0.015 -0.611 0.024 2.960 -4.268 -6.377 10 A_DG10:DC1_A A 10 ? A 1 ? 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 DC 1 1_555 A DG 10 8_555 A DG 2 1_555 A DC 9 8_555 0.173 5.047 -3.810 -0.569 -3.041 10.734 19.632 0.289 -5.041 -15.831 2.960 11.170 1 AA_DC1DG2:DC9DG10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A DG 2 1_555 A DC 9 8_555 A CBR 3 1_555 A DG 8 8_555 0.242 -1.170 -3.142 0.359 -7.171 47.439 -1.971 -0.324 -2.944 -8.853 -0.443 47.948 2 AA_DG2CBR3:DG8DC9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A CBR 3 1_555 A DG 8 8_555 A DG 4 1_555 A DC 7 8_555 -0.094 5.448 -3.906 2.201 -5.332 8.912 14.812 -5.536 -6.033 -30.469 -12.578 10.613 3 AA_CBR3DG4:DC7DG8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DG 4 1_555 A DC 7 8_555 A DG 5 1_555 A DG 6 8_555 2.783 0.931 1.154 -34.754 164.713 70.634 -0.064 -1.508 0.943 84.756 17.883 170.491 4 AA_DG4DG5:DG6DC7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DG 5 1_555 A DG 6 8_555 A DG 6 1_555 A DG 5 8_555 0.000 -1.155 3.723 0.000 -7.881 60.442 -0.701 0.000 3.833 -7.793 0.000 60.906 5 AA_DG5DG6:DG5DG6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DG 6 1_555 A DG 5 8_555 A DC 7 1_555 A DG 4 8_555 -2.783 0.931 1.154 34.754 164.713 70.634 -0.064 1.508 0.943 84.756 -17.883 170.491 6 AA_DG6DC7:DG4DG5_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A DC 7 1_555 A DG 4 8_555 A DG 8 1_555 A CBR 3 8_555 0.094 5.448 -3.906 -2.201 -5.332 8.912 14.812 5.536 -6.033 -30.469 12.578 10.613 7 AA_DC7DG8:CBR3DG4_AA A 7 ? A 4 ? A 8 ? A 3 ? 1 A DG 8 1_555 A CBR 3 8_555 A DC 9 1_555 A DG 2 8_555 -0.242 -1.170 -3.142 -0.359 -7.171 47.439 -1.971 0.324 -2.944 -8.853 0.443 47.948 8 AA_DG8DC9:DG2CBR3_AA A 8 ? A 3 ? A 9 ? A 2 ? 1 A DC 9 1_555 A DG 2 8_555 A DG 10 1_555 A DC 1 8_555 -0.173 5.047 -3.810 0.569 -3.041 10.734 19.632 -0.289 -5.041 -15.831 -2.960 11.170 9 AA_DC9DG10:DC1DG2_AA A 9 ? A 2 ? A 10 ? A 1 ? # _pdbx_audit_support.funding_organization 'Ministry of Education, Culture, Sports, Science and Technology (Japan)' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number 21H01956 _pdbx_audit_support.ordinal 1 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id CBR _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id CBR _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _atom_sites.entry_id 7YVX _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] 0.023055 _atom_sites.fract_transf_matrix[1][2] 0.013311 _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] 0.026621 _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] 0.013889 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol BR C CO N O P # loop_