data_9DG0 # _entry.id 9DG0 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.409 _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 9DG0 pdb_00009dg0 10.2210/pdb9dg0/pdb WWPDB D_1000288033 ? ? # 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 _pdbx_audit_revision_history.part_number 1 'Structure model' 1 0 2025-11-12 ? 2 'Structure model' 1 1 2025-12-24 ? # _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 'Database references' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category citation # _pdbx_audit_revision_item.ordinal 1 _pdbx_audit_revision_item.revision_ordinal 2 _pdbx_audit_revision_item.data_content_type 'Structure model' _pdbx_audit_revision_item.item '_citation.journal_volume' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9DG0 _pdbx_database_status.recvd_initial_deposition_date 2024-09-01 _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 2 _pdbx_contact_author.email mao@purdue.edu _pdbx_contact_author.name_first Chengde _pdbx_contact_author.name_last Mao _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0001-7516-8666 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Koomullam, N.' 1 0009-0000-3495-8434 'Mao, C.' 2 0000-0001-7516-8666 # _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 GE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_id_ASTM ACIEAY _citation.journal_id_CSD 0179 _citation.journal_id_ISSN 1521-3773 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 64 _citation.language ? _citation.page_first e18174 _citation.page_last e18174 _citation.title 'Crystallographic Study of DNA T-Junction via Crystal Engineering.' _citation.year 2025 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/anie.202518174 _citation.pdbx_database_id_PubMed 41165523 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Li, X.' 1 ? primary 'Siraj, N.' 2 ? primary 'Sha, R.' 3 ? primary 'Mao, C.' 4 0000-0001-7516-8666 # 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*AP*GP*CP*AP*GP*CP*CP*TP*GP*AP*AP*TP*AP*C)-3') ; 4562.988 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3') ; 1825.216 1 ? ? ? ? 3 polymer syn 'DNA (49-MER)' 15084.606 1 ? ? ? 'The four T bases from 24 to 27 are not modeled in the structure.' 4 polymer syn ;DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*T)-3') ; 2433.602 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DC)(DA)(DG)(DC)(DA)(DG)(DC)(DC)(DT)(DG)(DA)(DA)(DT)(DA)(DC)' CAGCAGCCTGAATAC A ? 2 polydeoxyribonucleotide no no '(DG)(DG)(DC)(DT)(DG)(DC)' GGCTGC B ? 3 polydeoxyribonucleotide no no ;(DT)(DG)(DC)(DG)(DA)(DG)(DT)(DA)(DT)(DT)(DC)(DA)(DC)(DC)(DG)(DG)(DC)(DC)(DC)(DG) (DC)(DG)(DG)(DT)(DT)(DT)(DT)(DC)(DC)(DG)(DC)(DG)(DG)(DT)(DC)(DG)(DC)(DA)(DG)(DC) (DC)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG) ; TGCGAGTATTCACCGGCCCGCGGTTTTCCGCGGTCGCAGCCGGACAGCG C ? 4 polydeoxyribonucleotide no no '(DT)(DG)(DC)(DG)(DC)(DT)(DG)(DT)' TGCGCTGT E ? # 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 DA n 1 3 DG n 1 4 DC n 1 5 DA n 1 6 DG n 1 7 DC n 1 8 DC n 1 9 DT n 1 10 DG n 1 11 DA n 1 12 DA n 1 13 DT n 1 14 DA n 1 15 DC n 2 1 DG n 2 2 DG n 2 3 DC n 2 4 DT n 2 5 DG n 2 6 DC n 3 1 DT n 3 2 DG n 3 3 DC n 3 4 DG n 3 5 DA n 3 6 DG n 3 7 DT n 3 8 DA n 3 9 DT n 3 10 DT n 3 11 DC n 3 12 DA n 3 13 DC n 3 14 DC n 3 15 DG n 3 16 DG n 3 17 DC n 3 18 DC n 3 19 DC n 3 20 DG n 3 21 DC n 3 22 DG n 3 23 DG n 3 24 DT n 3 25 DT n 3 26 DT n 3 27 DT n 3 28 DC n 3 29 DC n 3 30 DG n 3 31 DC n 3 32 DG n 3 33 DG n 3 34 DT n 3 35 DC n 3 36 DG n 3 37 DC n 3 38 DA n 3 39 DG n 3 40 DC n 3 41 DC n 3 42 DG n 3 43 DG n 3 44 DA n 3 45 DC n 3 46 DA n 3 47 DG n 3 48 DC n 3 49 DG n 4 1 DT n 4 2 DG n 4 3 DC n 4 4 DG n 4 5 DC n 4 6 DT n 4 7 DG n 4 8 DT 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 15 'synthetic construct' ? 32630 ? 2 1 sample 1 6 'synthetic construct' ? 32630 ? 3 1 sample 1 49 'synthetic construct' ? 32630 ? 4 1 sample 1 8 '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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # 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 DA 2 2 2 DA DA A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DC 7 7 7 DC DC A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DT 9 9 9 DT DT A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DA 11 11 11 DA DA A . n A 1 12 DA 12 12 12 DA DA A . n A 1 13 DT 13 13 13 DT DT A . n A 1 14 DA 14 14 14 DA DA A . n A 1 15 DC 15 15 15 DC DC A . n B 2 1 DG 1 9 9 DG DG B . n B 2 2 DG 2 10 10 DG DG B . n B 2 3 DC 3 11 11 DC DC B . n B 2 4 DT 4 12 12 DT DT B . n B 2 5 DG 5 13 13 DG DG B . n B 2 6 DC 6 14 14 DC DC B . n C 3 1 DT 1 1 1 DT DT C . n C 3 2 DG 2 2 2 DG DG C . n C 3 3 DC 3 3 3 DC DC C . n C 3 4 DG 4 4 4 DG DG C . n C 3 5 DA 5 5 5 DA DA C . n C 3 6 DG 6 6 6 DG DG C . n C 3 7 DT 7 7 7 DT DT C . n C 3 8 DA 8 8 8 DA DA C . n C 3 9 DT 9 9 9 DT DT C . n C 3 10 DT 10 10 10 DT DT C . n C 3 11 DC 11 11 11 DC DC C . n C 3 12 DA 12 12 12 DA DA C . n C 3 13 DC 13 13 13 DC DC C . n C 3 14 DC 14 14 14 DC DC C . n C 3 15 DG 15 15 15 DG DG C . n C 3 16 DG 16 16 16 DG DG C . n C 3 17 DC 17 17 17 DC DC C . n C 3 18 DC 18 18 18 DC DC C . n C 3 19 DC 19 19 19 DC DC C . n C 3 20 DG 20 20 20 DG DG C . n C 3 21 DC 21 21 21 DC DC C . n C 3 22 DG 22 22 22 DG DG C . n C 3 23 DG 23 23 23 DG DG C . n C 3 24 DT 24 24 ? ? ? C . n C 3 25 DT 25 25 ? ? ? C . n C 3 26 DT 26 26 ? ? ? C . n C 3 27 DT 27 27 ? ? ? C . n C 3 28 DC 28 28 28 DC DC C . n C 3 29 DC 29 29 29 DC DC C . n C 3 30 DG 30 30 30 DG DG C . n C 3 31 DC 31 31 31 DC DC C . n C 3 32 DG 32 32 32 DG DG C . n C 3 33 DG 33 33 33 DG DG C . n C 3 34 DT 34 34 34 DT DT C . n C 3 35 DC 35 35 35 DC DC C . n C 3 36 DG 36 36 36 DG DG C . n C 3 37 DC 37 37 37 DC DC C . n C 3 38 DA 38 38 38 DA DA C . n C 3 39 DG 39 39 39 DG DG C . n C 3 40 DC 40 40 40 DC DC C . n C 3 41 DC 41 41 41 DC DC C . n C 3 42 DG 42 42 42 DG DG C . n C 3 43 DG 43 43 43 DG DG C . n C 3 44 DA 44 44 44 DA DA C . n C 3 45 DC 45 45 45 DC DC C . n C 3 46 DA 46 46 46 DA DA C . n C 3 47 DG 47 47 47 DG DG C . n C 3 48 DC 48 48 48 DC DC C . n C 3 49 DG 49 49 49 DG DG C . n D 4 1 DT 1 1 1 DT DT E . n D 4 2 DG 2 2 2 DG DG E . n D 4 3 DC 3 3 3 DC DC E . n D 4 4 DG 4 4 4 DG DG E . n D 4 5 DC 5 5 5 DC DC E . n D 4 6 DT 6 6 6 DT DT E . n D 4 7 DG 7 7 7 DG DG E . n D 4 8 DT 8 8 8 DT DT E . n # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 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 120.000 _cell.angle_gamma_esd ? _cell.entry_id 9DG0 _cell.details ? _cell.formula_units_Z ? _cell.length_a 167.218 _cell.length_a_esd ? _cell.length_b 167.218 _cell.length_b_esd ? _cell.length_c 80.113 _cell.length_c_esd ? _cell.volume 1939990.827 _cell.volume_esd ? _cell.Z_PDB 9 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9DG0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall 'R 3' _symmetry.space_group_name_H-M 'H 3' _symmetry.pdbx_full_space_group_name_H-M ? # _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 9DG0 _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 ? _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol ? _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 ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;DNA strands mixed with TAE/Mg2+ and 0.001 M Magnesium chloride hexahydrate, 0.005 M Tris hydrochloride, pH=7.5, 0.16 M Ammonium sulfate, 0.23 M sucrose and crystallized against (NH4)2SO4 ; _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 298 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'RIGAKU RAXIS IV++' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2016-08-18 _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 1.54 _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 'ROTATING ANODE' _diffrn_source.target ? _diffrn_source.type 'RIGAKU R-AXIS IV' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.54 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_synchrotron_site ? # _reflns.B_iso_Wilson_estimate 154.52 _reflns.entry_id 9DG0 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 6.4 _reflns.d_resolution_low 50 _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 1703 _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 99.26 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.6 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 13.5 _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 0.041 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _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 ? # _reflns_shell.d_res_high 6.4 _reflns_shell.d_res_low 6.63 _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 173 _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 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.932 _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 ? # _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 311.61 _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 9DG0 _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 6.53 _refine.ls_d_res_low 32.32 _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 1604 _refine.ls_number_reflns_R_free 164 _refine.ls_number_reflns_R_work 1440 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.63 _refine.ls_percent_reflns_R_free 10.22 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1715 _refine.ls_R_factor_R_free 0.2184 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1664 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.96 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _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 21.0024 _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 0.6441 _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 6.53 _refine_hist.d_res_low 32.32 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1511 _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 1511 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.0165 ? 1691 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.5373 ? 2599 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0914 ? 294 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0072 ? 74 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 36.6408 ? 723 ? f_dihedral_angle_d ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 6.53 _refine_ls_shell.d_res_low 32.32 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 164 _refine_ls_shell.number_reflns_R_work 1440 _refine_ls_shell.percent_reflns_obs 99.63 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.1664 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_R_complete ? _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? _refine_ls_shell.R_factor_R_free 0.2184 # _struct.entry_id 9DG0 _struct.title 'T-junction triangle 7-6' _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 9DG0 _struct_keywords.text 'Structure of DNA tensegrity triangle with T junctions, Design T-7-6, DNA' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? # loop_ _struct_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 9DG0 9DG0 ? 1 ? 1 2 PDB 9DG0 9DG0 ? 2 ? 1 3 PDB 9DG0 9DG0 ? 3 ? 1 4 PDB 9DG0 9DG0 ? 4 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 9DG0 A 1 ? 15 ? 9DG0 1 ? 15 ? 1 15 2 2 9DG0 B 1 ? 6 ? 9DG0 9 ? 14 ? 9 14 3 3 9DG0 C 1 ? 49 ? 9DG0 1 ? 49 ? 1 49 4 4 9DG0 E 1 ? 8 ? 9DG0 1 ? 8 ? 1 8 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D 1 2 A,B,C,D 1 3 A,B,C,D # _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 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DG 5 N1 ? ? A DG 3 B DG 13 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog2 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 6 O2 ? ? A DG 3 B DC 14 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog3 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 5 N1 ? ? A DC 4 B DG 13 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog4 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 5 B DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 5 B DT 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 6 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 6 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 6 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 7 B DG 10 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog10 hydrog ? ? C DC 13 N3 ? ? ? 1_555 C DG 43 N1 ? ? C DC 13 C DG 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? C DC 13 N4 ? ? ? 1_555 C DG 43 O6 ? ? C DC 13 C DG 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? C DC 13 O2 ? ? ? 1_555 C DG 43 N2 ? ? C DC 13 C DG 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? C DC 14 O2 ? ? ? 1_555 C DG 43 N2 ? ? C DC 14 C DG 43 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog14 hydrog ? ? C DG 15 N1 ? ? ? 1_555 C DC 41 N3 ? ? C DG 15 C DC 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? C DG 15 N2 ? ? ? 1_555 C DC 41 O2 ? ? C DG 15 C DC 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? C DG 15 O6 ? ? ? 1_555 C DC 41 N4 ? ? C DG 15 C DC 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? C DG 16 N2 ? ? ? 1_555 C DC 40 N3 ? ? C DG 16 C DC 40 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog18 hydrog ? ? C DC 17 O2 ? ? ? 1_555 C DG 39 N2 ? ? C DC 17 C DG 39 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog19 hydrog ? ? C DC 18 N4 ? ? ? 1_555 C DG 32 O6 ? ? C DC 18 C DG 32 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog20 hydrog ? ? C DC 19 N3 ? ? ? 1_555 C DG 32 N1 ? ? C DC 19 C DG 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? C DC 19 N4 ? ? ? 1_555 C DG 32 O6 ? ? C DC 19 C DG 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? C DC 19 O2 ? ? ? 1_555 C DG 32 N2 ? ? C DC 19 C DG 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? C DG 20 N1 ? ? ? 1_555 C DC 31 N3 ? ? C DG 20 C DC 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C DG 20 N2 ? ? ? 1_555 C DC 31 O2 ? ? C DG 20 C DC 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? C DG 20 O6 ? ? ? 1_555 C DC 31 N4 ? ? C DG 20 C DC 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? C DC 21 N3 ? ? ? 1_555 C DG 30 N1 ? ? C DC 21 C DG 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C DC 21 N4 ? ? ? 1_555 C DG 30 O6 ? ? C DC 21 C DG 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C DC 21 O2 ? ? ? 1_555 C DG 30 N2 ? ? C DC 21 C DG 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C DG 22 N1 ? ? ? 1_555 C DC 29 N3 ? ? C DG 22 C DC 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C DG 22 N2 ? ? ? 1_555 C DC 29 O2 ? ? C DG 22 C DC 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C DG 22 O6 ? ? ? 1_555 C DC 29 N4 ? ? C DG 22 C DC 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C DG 23 N1 ? ? ? 1_555 C DC 28 O2 ? ? C DG 23 C DC 28 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog33 hydrog ? ? C DA 44 N1 ? ? ? 1_555 D DT 8 N3 ? ? C DA 44 E DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C DA 44 N6 ? ? ? 1_555 D DT 8 O4 ? ? C DA 44 E DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C DC 45 N3 ? ? ? 1_555 D DG 7 N1 ? ? C DC 45 E DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C DC 45 N4 ? ? ? 1_555 D DG 7 O6 ? ? C DC 45 E DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C DC 45 O2 ? ? ? 1_555 D DG 7 N2 ? ? C DC 45 E DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C DA 46 N1 ? ? ? 1_555 D DT 6 N3 ? ? C DA 46 E DT 6 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog39 hydrog ? ? C DG 47 N1 ? ? ? 1_555 D DC 5 N3 ? ? C DG 47 E DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C DG 47 N2 ? ? ? 1_555 D DC 5 O2 ? ? C DG 47 E DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C DG 47 O6 ? ? ? 1_555 D DC 5 N4 ? ? C DG 47 E DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C DC 48 O2 ? ? ? 1_555 D DG 4 N2 ? ? C DC 48 E DG 4 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog43 hydrog ? ? C DG 49 N1 ? ? ? 1_555 D DC 3 O2 ? ? C DG 49 E DC 3 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_entry_details.entry_id 9DG0 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification N # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O6 _pdbx_validate_close_contact.auth_asym_id_1 C _pdbx_validate_close_contact.auth_comp_id_1 DG _pdbx_validate_close_contact.auth_seq_id_1 49 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 N3 _pdbx_validate_close_contact.auth_asym_id_2 E _pdbx_validate_close_contact.auth_comp_id_2 DC _pdbx_validate_close_contact.auth_seq_id_2 3 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.13 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 N2 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 DG _pdbx_validate_symm_contact.auth_seq_id_1 10 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O2 _pdbx_validate_symm_contact.auth_asym_id_2 C _pdbx_validate_symm_contact.auth_comp_id_2 DC _pdbx_validate_symm_contact.auth_seq_id_2 11 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 3_555 _pdbx_validate_symm_contact.dist 2.09 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A DC 1 ? ? "C3'" A DC 1 ? ? 1.516 1.435 0.081 0.013 N 2 1 "C1'" A DC 1 ? ? N1 A DC 1 ? ? 1.599 1.488 0.111 0.013 N 3 1 "C5'" A DA 5 ? ? "C4'" A DA 5 ? ? 1.558 1.512 0.046 0.007 N 4 1 "C1'" A DT 9 ? ? N1 A DT 9 ? ? 1.567 1.488 0.079 0.013 N 5 1 "O3'" A DA 11 ? ? "C3'" A DA 11 ? ? 1.382 1.419 -0.037 0.006 N 6 1 N9 A DA 12 ? ? C4 A DA 12 ? ? 1.337 1.374 -0.037 0.006 N 7 1 "O3'" B DG 10 ? ? "C3'" B DG 10 ? ? 1.375 1.419 -0.044 0.006 N 8 1 "O3'" C DC 3 ? ? "C3'" C DC 3 ? ? 1.537 1.435 0.102 0.013 N 9 1 "O3'" C DT 7 ? ? "C3'" C DT 7 ? ? 1.363 1.419 -0.056 0.006 N 10 1 "O3'" C DT 34 ? ? "C3'" C DT 34 ? ? 1.371 1.419 -0.048 0.006 N 11 1 "O3'" C DC 45 ? ? "C3'" C DC 45 ? ? 1.379 1.419 -0.040 0.006 N 12 1 "O3'" C DA 46 ? ? "C3'" C DA 46 ? ? 1.381 1.419 -0.038 0.006 N 13 1 "O3'" C DC 48 ? ? "C3'" C DC 48 ? ? 1.357 1.419 -0.062 0.006 N 14 1 "O3'" E DC 3 ? ? "C3'" E DC 3 ? ? 1.365 1.419 -0.054 0.006 N 15 1 "C1'" E DT 6 ? ? N1 E DT 6 ? ? 1.376 1.468 -0.092 0.014 N 16 1 N9 E DG 7 ? ? C4 E DG 7 ? ? 1.325 1.375 -0.050 0.008 N 17 1 "C1'" E DT 8 ? ? N1 E DT 8 ? ? 1.379 1.468 -0.089 0.014 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.31 108.30 3.01 0.30 N 2 1 "O5'" A DC 8 ? ? P A DC 8 ? ? OP1 A DC 8 ? ? 99.46 105.70 -6.24 0.90 N 3 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 110.80 108.30 2.50 0.30 N 4 1 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.29 108.30 2.99 0.30 N 5 1 "O4'" A DT 13 ? ? "C1'" A DT 13 ? ? N1 A DT 13 ? ? 110.63 108.30 2.33 0.30 N 6 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? N9 B DG 13 ? ? 111.67 108.30 3.37 0.30 N 7 1 "O4'" B DC 14 ? ? "C1'" B DC 14 ? ? N1 B DC 14 ? ? 112.08 108.30 3.78 0.30 N 8 1 "O4'" C DG 2 ? ? "C1'" C DG 2 ? ? N9 C DG 2 ? ? 110.22 108.30 1.92 0.30 N 9 1 "O5'" C DA 5 ? ? P C DA 5 ? ? OP1 C DA 5 ? ? 98.64 105.70 -7.06 0.90 N 10 1 "O5'" C DG 6 ? ? P C DG 6 ? ? OP2 C DG 6 ? ? 99.00 105.70 -6.70 0.90 N 11 1 "O4'" C DG 6 ? ? "C1'" C DG 6 ? ? N9 C DG 6 ? ? 110.89 108.30 2.59 0.30 N 12 1 "C3'" C DT 7 ? ? "C2'" C DT 7 ? ? "C1'" C DT 7 ? ? 97.54 102.40 -4.86 0.80 N 13 1 "O4'" C DT 7 ? ? "C1'" C DT 7 ? ? N1 C DT 7 ? ? 111.59 108.30 3.29 0.30 N 14 1 "O4'" C DT 9 ? ? "C1'" C DT 9 ? ? N1 C DT 9 ? ? 111.05 108.30 2.75 0.30 N 15 1 "O4'" C DT 10 ? ? "C1'" C DT 10 ? ? N1 C DT 10 ? ? 110.11 108.30 1.81 0.30 N 16 1 "O4'" C DC 14 ? ? "C1'" C DC 14 ? ? N1 C DC 14 ? ? 110.78 108.30 2.48 0.30 N 17 1 "O4'" C DG 32 ? ? "C1'" C DG 32 ? ? N9 C DG 32 ? ? 111.28 108.30 2.98 0.30 N 18 1 "O4'" C DG 33 ? ? "C1'" C DG 33 ? ? N9 C DG 33 ? ? 110.21 108.30 1.91 0.30 N 19 1 "O4'" C DA 44 ? ? "C1'" C DA 44 ? ? N9 C DA 44 ? ? 111.93 108.30 3.63 0.30 N 20 1 "C3'" C DG 47 ? ? "C2'" C DG 47 ? ? "C1'" C DG 47 ? ? 95.46 102.40 -6.94 0.80 N 21 1 "O4'" C DG 47 ? ? "C1'" C DG 47 ? ? N9 C DG 47 ? ? 111.78 108.30 3.48 0.30 N 22 1 "O4'" E DG 2 ? ? "C1'" E DG 2 ? ? N9 E DG 2 ? ? 110.64 108.30 2.34 0.30 N 23 1 "C3'" E DT 6 ? ? "C2'" E DT 6 ? ? "C1'" E DT 6 ? ? 97.48 102.40 -4.92 0.80 N # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y,x-y,z 3 -x+y,-x,z 4 x+1/3,y+2/3,z+2/3 5 -y+1/3,x-y+2/3,z+2/3 6 -x+y+1/3,-x+2/3,z+2/3 7 x+2/3,y+1/3,z+1/3 8 -y+2/3,x-y+1/3,z+1/3 9 -x+y+2/3,-x+1/3,z+1/3 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 C DT 24 ? C DT 24 2 1 Y 1 C DT 25 ? C DT 25 3 1 Y 1 C DT 26 ? C DT 26 4 1 Y 1 C DT 27 ? C DT 27 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9DG0 'double helix' 9DG0 'a-form double helix' 9DG0 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 3 1_555 B DC 6 1_555 -2.022 0.196 -1.541 -28.188 2.030 -2.201 1 A_DG3:DC14_B A 3 ? B 14 ? ? ? 1 A DC 4 1_555 B DG 5 1_555 2.065 0.077 -0.280 31.256 -6.209 12.035 2 A_DC4:DG13_B A 4 ? B 13 ? ? 1 1 A DA 5 1_555 B DT 4 1_555 -1.380 -0.897 -0.801 2.308 -13.269 -3.288 3 A_DA5:DT12_B A 5 ? B 12 ? 20 1 1 A DG 6 1_555 B DC 3 1_555 -0.005 -0.082 0.759 3.474 -6.467 9.801 4 A_DG6:DC11_B A 6 ? B 11 ? 19 1 1 A DC 7 1_555 B DG 2 1_555 1.509 -0.498 2.086 -17.598 -6.899 20.493 5 A_DC7:DG10_B A 7 ? B 10 ? ? 1 1 C DG 39 1_555 C DC 17 1_555 -0.274 0.894 0.430 -0.442 -14.154 18.717 6 C_DG39:DC17_C C 39 ? C 17 ? ? 1 1 C DC 40 1_555 C DG 16 1_555 -2.550 -0.095 1.003 3.334 -26.736 -4.873 7 C_DC40:DG16_C C 40 ? C 16 ? ? 1 1 C DC 41 1_555 C DG 15 1_555 0.463 -0.257 1.076 5.741 -19.607 -14.005 8 C_DC41:DG15_C C 41 ? C 15 ? 19 1 1 C DG 43 1_555 C DC 13 1_555 0.361 -0.493 -0.808 3.193 -4.817 -8.859 9 C_DG43:DC13_C C 43 ? C 13 ? 19 1 1 C DA 44 1_555 D DT 8 1_555 1.172 -0.188 -0.700 5.179 -9.686 5.874 10 C_DA44:DT8_E C 44 ? E 8 ? 20 1 1 C DC 45 1_555 D DG 7 1_555 1.281 -0.207 -0.965 20.872 -8.927 4.479 11 C_DC45:DG7_E C 45 ? E 7 ? 19 1 1 C DA 46 1_555 D DT 6 1_555 0.677 0.594 1.636 19.644 -14.904 14.644 12 C_DA46:DT6_E C 46 ? E 6 ? ? ? 1 C DG 47 1_555 D DC 5 1_555 -1.982 -0.533 0.550 3.524 -19.340 8.287 13 C_DG47:DC5_E C 47 ? E 5 ? 19 1 1 C DC 48 1_555 D DG 4 1_555 0.268 0.449 1.959 -7.708 -17.284 21.036 14 C_DC48:DG4_E C 48 ? E 4 ? ? 1 1 C DG 49 1_555 D DC 3 1_555 -2.717 -1.443 -0.915 -8.795 -31.849 -6.499 15 C_DG49:DC3_E C 49 ? E 3 ? ? 1 1 C DC 19 1_555 C DG 32 1_555 1.683 -0.794 0.289 11.658 -20.255 -9.115 16 C_DC19:DG32_C C 19 ? C 32 ? 19 1 1 C DG 20 1_555 C DC 31 1_555 -2.271 -1.013 -0.996 -2.613 -9.261 3.955 17 C_DG20:DC31_C C 20 ? C 31 ? 19 1 1 C DC 21 1_555 C DG 30 1_555 1.949 -0.785 -1.334 26.025 -11.471 6.829 18 C_DC21:DG30_C C 21 ? C 30 ? 19 1 1 C DG 22 1_555 C DC 29 1_555 -1.454 -0.640 0.139 16.822 -2.675 7.523 19 C_DG22:DC29_C C 22 ? C 29 ? 19 1 1 C DG 23 1_555 C DC 28 1_555 -2.917 -0.775 1.147 -57.082 -21.699 -4.052 20 C_DG23:DC28_C C 23 ? C 28 ? ? ? # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 3 1_555 B DC 6 1_555 A DC 4 1_555 B DG 5 1_555 0.832 1.162 1.444 -10.297 9.396 47.962 1.070 -1.325 1.438 11.284 12.366 49.832 1 AA_DG3DC4:DG13DC14_BB A 3 ? B 14 ? A 4 ? B 13 ? 1 A DC 4 1_555 B DG 5 1_555 A DA 5 1_555 B DT 4 1_555 -2.004 -0.443 3.377 -7.092 6.651 20.996 -3.683 2.252 3.553 17.117 18.252 23.115 2 AA_DC4DA5:DT12DG13_BB A 4 ? B 13 ? A 5 ? B 12 ? 1 A DA 5 1_555 B DT 4 1_555 A DG 6 1_555 B DC 3 1_555 0.987 -1.134 3.324 -9.644 -7.520 47.331 -0.790 -1.942 3.211 -9.189 11.784 48.797 3 AA_DA5DG6:DC11DT12_BB A 5 ? B 12 ? A 6 ? B 11 ? 1 A DG 6 1_555 B DC 3 1_555 A DC 7 1_555 B DG 2 1_555 -0.297 -0.167 4.171 -6.664 -14.399 49.357 1.070 -0.244 4.074 -16.749 7.752 51.692 4 AA_DG6DC7:DG10DC11_BB A 6 ? B 11 ? A 7 ? B 10 ? 1 C DG 39 1_555 C DC 17 1_555 C DC 40 1_555 C DG 16 1_555 -0.744 -1.214 2.927 -6.101 -8.338 27.330 -0.640 0.182 3.238 -16.899 12.365 29.183 5 CC_DG39DC40:DG16DC17_CC C 39 ? C 17 ? C 40 ? C 16 ? 1 C DC 40 1_555 C DG 16 1_555 C DC 41 1_555 C DG 15 1_555 0.026 -1.500 3.273 1.373 5.505 43.613 -2.510 0.092 3.070 7.373 -1.839 43.963 6 CC_DC40DC41:DG15DG16_CC C 40 ? C 16 ? C 41 ? C 15 ? 1 C DC 41 1_555 C DG 15 1_555 C DG 43 1_555 C DC 13 1_555 -0.278 -0.632 6.829 10.973 -17.625 78.364 0.484 0.820 6.752 -13.727 -8.546 80.638 7 CC_DC41DG43:DC13DG15_CC C 41 ? C 15 ? C 43 ? C 13 ? 1 C DG 43 1_555 C DC 13 1_555 C DA 44 1_555 D DT 8 1_555 -1.053 -0.778 3.044 -4.192 4.647 25.240 -2.926 1.261 2.987 10.431 9.410 25.992 8 CC_DG43DA44:DT8DC13_EC C 43 ? C 13 ? C 44 ? E 8 ? 1 C DA 44 1_555 D DT 8 1_555 C DC 45 1_555 D DG 7 1_555 -0.068 -0.890 2.888 8.652 4.482 34.019 -2.038 1.216 2.657 7.473 -14.425 35.347 9 CC_DA44DC45:DG7DT8_EE C 44 ? E 8 ? C 45 ? E 7 ? 1 C DC 45 1_555 D DG 7 1_555 C DA 46 1_555 D DT 6 1_555 1.508 1.464 3.313 -5.168 5.033 37.071 1.606 -3.007 3.245 7.825 8.035 37.742 10 CC_DC45DA46:DT6DG7_EE C 45 ? E 7 ? C 46 ? E 6 ? 1 C DA 46 1_555 D DT 6 1_555 C DG 47 1_555 D DC 5 1_555 -0.261 -0.805 3.970 -1.271 -11.348 20.567 2.930 0.091 3.880 -29.069 3.255 23.495 11 CC_DA46DG47:DC5DT6_EE C 46 ? E 6 ? C 47 ? E 5 ? 1 C DG 47 1_555 D DC 5 1_555 C DC 48 1_555 D DG 4 1_555 0.755 0.510 3.768 -7.764 -17.218 56.951 1.480 -1.194 3.382 -17.532 7.906 59.752 12 CC_DG47DC48:DG4DC5_EE C 47 ? E 5 ? C 48 ? E 4 ? 1 C DC 48 1_555 D DG 4 1_555 C DG 49 1_555 D DC 3 1_555 -1.226 -1.728 2.742 3.902 18.472 24.377 -5.589 2.804 1.008 37.395 -7.898 30.746 13 CC_DC48DG49:DC3DG4_EE C 48 ? E 4 ? C 49 ? E 3 ? 1 C DC 19 1_555 C DG 32 1_555 C DG 20 1_555 C DC 31 1_555 0.833 -0.214 3.490 4.197 7.025 13.829 -6.308 0.330 3.131 26.371 -15.755 16.058 14 CC_DC19DG20:DC31DG32_CC C 19 ? C 32 ? C 20 ? C 31 ? 1 C DG 20 1_555 C DC 31 1_555 C DC 21 1_555 C DG 30 1_555 0.860 1.313 2.528 7.755 2.125 51.886 1.373 -0.567 2.670 2.412 -8.803 52.463 15 CC_DG20DC21:DG30DC31_CC C 20 ? C 31 ? C 21 ? C 30 ? 1 C DC 21 1_555 C DG 30 1_555 C DG 22 1_555 C DC 29 1_555 0.266 0.343 3.741 -8.111 7.899 22.284 -1.919 -3.401 3.366 18.945 19.455 24.963 16 CC_DC21DG22:DC29DG30_CC C 21 ? C 30 ? C 22 ? C 29 ? 1 C DG 22 1_555 C DC 29 1_555 C DG 23 1_555 C DC 28 1_555 -0.519 0.000 6.967 -9.614 7.146 37.543 -1.828 -1.688 6.782 10.773 14.493 39.342 17 CC_DG22DG23:DC28DC29_CC C 22 ? C 29 ? C 23 ? C 28 ? # _pdbx_audit_support.funding_organization 'National Science Foundation (NSF, United States)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number 'CCF 2107393' _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.details 'B DNA duplex with 31 base pairs' # _space_group.name_H-M_alt 'R 3 :H' _space_group.name_Hall 'R 3' _space_group.IT_number 146 _space_group.crystal_system trigonal _space_group.id 1 # _atom_sites.entry_id 9DG0 _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] 0.005980 _atom_sites.fract_transf_matrix[1][2] 0.003453 _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] 0.006905 _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] 0.012482 _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 ? ? 5.96793 ? ? ? 14.89577 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 6.96715 ? ? ? 11.43723 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 7.96527 ? ? ? 9.05267 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 14.90797 ? ? ? 11.91318 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_ #