data_9VUN # _entry.id 9VUN # _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 9VUN pdb_00009vun 10.2210/pdb9vun/pdb WWPDB D_1300061165 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2026-02-11 _pdbx_audit_revision_history.part_number ? # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9VUN _pdbx_database_status.recvd_initial_deposition_date 2025-07-13 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBC _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 3 _pdbx_contact_author.email huanglin36@mail.sysu.edu.cn _pdbx_contact_author.name_first Lin _pdbx_contact_author.name_last Huang _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-2121-365X # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Ren, Y.' 1 0009-0006-0959-2008 'Huang, L.' 2 0000-0002-2121-365X # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Chem _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2451-9294 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Unlocking the potential of diarylmethane dyes for living systems' _citation.year 2026 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.chempr.2025.102883 _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wang, J.' 1 ? primary 'Ren, Y.' 2 ? primary 'Huang, Y.' 3 ? primary 'Qian, Z.' 4 ? primary 'Tang, J.' 5 ? primary 'Huang, Z.' 6 ? primary 'Chen, S.' 7 ? primary 'Huang, L.' 8 ? primary 'Tan, J.' 9 ? # 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 ;RNA (5'-R(*GP*UP*UP*GP*CP*CP*UP*GP*GP*AP*GP*AP*CP*G)-3') ; 4518.731 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*CP*GP*TP*CP*TP*CP*CP*AP*GP*GP*CP*AP*AP*C)-3') ; 4225.756 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 polyribonucleotide no no GUUGCCUGGAGACG GUUGCCUGGAGACG A ? 2 polydeoxyribonucleotide no no '(DC)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA)(DA)(DC)' CGTCTCCAGGCAAC B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 U n 1 3 U n 1 4 G n 1 5 C n 1 6 C n 1 7 U n 1 8 G n 1 9 G n 1 10 A n 1 11 G n 1 12 A n 1 13 C n 1 14 G n 2 1 DC n 2 2 DG n 2 3 DT n 2 4 DC n 2 5 DT n 2 6 DC n 2 7 DC n 2 8 DA n 2 9 DG n 2 10 DG n 2 11 DC n 2 12 DA n 2 13 DA n 2 14 DC n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 14 'synthetic construct' ? 32630 ? 2 1 sample 1 14 '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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 G 1 1 1 G G A . n A 1 2 U 2 2 2 U U A . n A 1 3 U 3 3 3 U U A . n A 1 4 G 4 4 4 G G A . n A 1 5 C 5 5 5 C C A . n A 1 6 C 6 6 6 C C A . n A 1 7 U 7 7 7 U U A . n A 1 8 G 8 8 8 G G A . n A 1 9 G 9 9 9 G G A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 A 12 12 12 A A A . n A 1 13 C 13 13 13 C C A . n A 1 14 G 14 14 14 G G A . n B 2 1 DC 1 1 1 DC DC B . n B 2 2 DG 2 2 2 DG DG B . n B 2 3 DT 3 3 3 DT DT B . n B 2 4 DC 4 4 4 DC DC B . n B 2 5 DT 5 5 5 DT DT B . n B 2 6 DC 6 6 6 DC DC B . n B 2 7 DC 7 7 7 DC DC B . n B 2 8 DA 8 8 8 DA DA B . n B 2 9 DG 9 9 9 DG DG B . n B 2 10 DG 10 10 10 DG DG B . n B 2 11 DC 11 11 11 DC DC B . n B 2 12 DA 12 12 12 DA DA B . n B 2 13 DA 13 13 13 DA DA B . n B 2 14 DC 14 14 14 DC DC B . 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_reference_DOI _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 ? 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 ? 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? autoPX ? ? ? . ? 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? Aimless ? ? ? . ? 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 90.000 _cell.angle_gamma_esd ? _cell.entry_id 9VUN _cell.details ? _cell.formula_units_Z ? _cell.length_a 46.239 _cell.length_a_esd ? _cell.length_b 47.998 _cell.length_b_esd ? _cell.length_c 50.876 _cell.length_c_esd ? _cell.volume 112913.153 _cell.volume_esd ? _cell.Z_PDB 4 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 9VUN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' _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 9VUN _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 3.23 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 61.90 _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 ;0.02 M Magnesium chloride hexahydrate, 0.002 M Cobalt(II) chloride hexahydrate 0.05 M HEPES sodium pH 7.5 2.0 M Ammonium sulfate 0.001 M Spermine ; _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 291 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS3 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2025-05-27 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97853 _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 'SSRF BEAMLINE BL18U1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.97853 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL18U1 _diffrn_source.pdbx_synchrotron_site SSRF # _reflns.B_iso_Wilson_estimate 62.38 _reflns.entry_id 9VUN _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.72 _reflns.d_resolution_low 34.91 _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 3308 _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 99.9 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 11.3 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 26.1 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _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 2.72 _reflns_shell.d_res_low 2.87 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 3.5 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 467 _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 0.951 _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 54.54 _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 9VUN _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 2.72 _refine.ls_d_res_low 27.86 _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 3138 _refine.ls_number_reflns_R_free 309 _refine.ls_number_reflns_R_work 2829 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 95.55 _refine.ls_percent_reflns_R_free 9.85 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1990 _refine.ls_R_factor_R_free 0.2429 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1943 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.correlation_coeff_I_to_Fcsqd_work ? _refine.correlation_coeff_I_to_Fcsqd_free ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.33 _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 29.1491 _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 0.2671 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 2.72 _refine_hist.d_res_low 27.86 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 579 _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 579 _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_Zscore _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.0128 ? 647 ? f_bond_d ? ? ? 'X-RAY DIFFRACTION' ? 1.6114 ? 1000 ? f_angle_d ? ? ? 'X-RAY DIFFRACTION' ? 0.0667 ? 124 ? f_chiral_restr ? ? ? 'X-RAY DIFFRACTION' ? 0.0103 ? 28 ? f_plane_restr ? ? ? 'X-RAY DIFFRACTION' ? 11.9051 ? 300 ? f_dihedral_angle_d ? ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.correlation_coeff_Fo_to_Fc _refine_ls_shell.correlation_coeff_Fo_to_Fc_free _refine_ls_shell.correlation_coeff_I_to_Fcsqd_work _refine_ls_shell.correlation_coeff_I_to_Fcsqd_free _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 2.72 3.43 . . 150 1375 95.25 . . . . 0.2894 . . . . . . . . . . . . . . . 0.3573 'X-RAY DIFFRACTION' 3.43 27.86 . . 159 1454 95.84 . . . . 0.1614 . . . . . . . . . . . . . . . 0.2047 # _struct.entry_id 9VUN _struct.title 'Crystal structure of the DNA/RNA hybrid, D(CGTCTCCAGGCAAC)/R(GUUGCCUGGAGACG)' _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 9VUN _struct_keywords.text 'DNA/RNA hybrid, DNA-RNA HYBRID' _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' # 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 ? # 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 9VUN 9VUN ? 1 ? 1 2 PDB 9VUN 9VUN ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 9VUN A 1 ? 14 ? 9VUN 1 ? 14 ? 1 14 2 2 9VUN B 1 ? 14 ? 9VUN 1 ? 14 ? 1 14 # _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)' 1350 ? 1 MORE -6 ? 1 'SSA (A^2)' 5150 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B DC 14 N3 ? ? A G 1 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B DC 14 O2 ? ? A G 1 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B DC 14 N4 ? ? A G 1 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 B DA 13 N1 ? ? A U 2 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 B DA 13 N6 ? ? A U 2 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 3 N3 ? ? ? 1_555 B DA 12 N1 ? ? A U 3 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 O4 ? ? ? 1_555 B DA 12 N6 ? ? A U 3 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 B DC 11 N3 ? ? A G 4 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 B DC 11 O2 ? ? A G 4 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 B DC 11 N4 ? ? A G 4 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 B DG 10 N1 ? ? A C 5 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 B DG 10 O6 ? ? A C 5 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 B DG 10 N2 ? ? A C 5 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N3 ? ? ? 1_555 B DG 9 N1 ? ? A C 6 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 N4 ? ? ? 1_555 B DG 9 O6 ? ? A C 6 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 6 O2 ? ? ? 1_555 B DG 9 N2 ? ? A C 6 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 7 N3 ? ? ? 1_555 B DA 8 N1 ? ? A U 7 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 7 O4 ? ? ? 1_555 B DA 8 N6 ? ? A U 7 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 8 N1 ? ? ? 1_555 B DC 7 N3 ? ? A G 8 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 8 N2 ? ? ? 1_555 B DC 7 O2 ? ? A G 8 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 8 O6 ? ? ? 1_555 B DC 7 N4 ? ? A G 8 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 9 N1 ? ? ? 1_555 B DC 6 N3 ? ? A G 9 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 9 N2 ? ? ? 1_555 B DC 6 O2 ? ? A G 9 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 9 O6 ? ? ? 1_555 B DC 6 N4 ? ? A G 9 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A A 10 N1 ? ? ? 1_555 B DT 5 N3 ? ? A A 10 B DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A A 10 N6 ? ? ? 1_555 B DT 5 O4 ? ? A A 10 B DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 11 N1 ? ? ? 1_555 B DC 4 N3 ? ? A G 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 11 N2 ? ? ? 1_555 B DC 4 O2 ? ? A G 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 11 O6 ? ? ? 1_555 B DC 4 N4 ? ? A G 11 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 12 N1 ? ? ? 1_555 B DT 3 N3 ? ? A A 12 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 12 N6 ? ? ? 1_555 B DT 3 O4 ? ? A A 12 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 13 N3 ? ? ? 1_555 B DG 2 N1 ? ? A C 13 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 13 N4 ? ? ? 1_555 B DG 2 O6 ? ? A C 13 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 13 O2 ? ? ? 1_555 B DG 2 N2 ? ? A C 13 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 14 N1 ? ? ? 1_555 B DC 1 N3 ? ? A G 14 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 14 N2 ? ? ? 1_555 B DC 1 O2 ? ? A G 14 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 14 O6 ? ? ? 1_555 B DC 1 N4 ? ? A G 14 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_entry_details.entry_id 9VUN _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 # 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'" B DG 2 ? ? "C3'" B DG 2 ? ? 1.368 1.419 -0.051 0.006 N 2 1 "O3'" B DC 4 ? ? "C3'" B DC 4 ? ? 1.372 1.419 -0.047 0.006 N 3 1 "O3'" B DC 6 ? ? "C3'" B DC 6 ? ? 1.357 1.419 -0.062 0.006 N 4 1 "O3'" B DA 13 ? ? "C3'" B DA 13 ? ? 1.382 1.419 -0.037 0.006 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 C6 A C 6 ? ? N1 A C 6 ? ? C2 A C 6 ? ? 117.12 120.30 -3.18 0.40 N 2 1 C5 A C 6 ? ? C6 A C 6 ? ? N1 A C 6 ? ? 124.23 121.00 3.23 0.50 N 3 1 C8 A A 12 ? ? N9 A A 12 ? ? C4 A A 12 ? ? 108.50 105.80 2.70 0.40 N 4 1 "O3'" B DT 5 ? ? P B DC 6 ? ? OP2 B DC 6 ? ? 118.12 110.50 7.62 1.10 Y 5 1 "O4'" B DA 13 ? ? "C1'" B DA 13 ? ? N9 B DA 13 ? ? 110.86 108.30 2.56 0.30 N # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 x+1/2,-y+1/2,-z 3 -x,y+1/2,-z+1/2 4 -x+1/2,-y,z+1/2 # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 DA OP3 O N N 73 DA P P N N 74 DA OP1 O N N 75 DA OP2 O N N 76 DA "O5'" O N N 77 DA "C5'" C N N 78 DA "C4'" C N R 79 DA "O4'" O N N 80 DA "C3'" C N S 81 DA "O3'" O N N 82 DA "C2'" C N N 83 DA "C1'" C N R 84 DA N9 N Y N 85 DA C8 C Y N 86 DA N7 N Y N 87 DA C5 C Y N 88 DA C6 C Y N 89 DA N6 N N N 90 DA N1 N Y N 91 DA C2 C Y N 92 DA N3 N Y N 93 DA C4 C Y N 94 DA HOP3 H N N 95 DA HOP2 H N N 96 DA "H5'" H N N 97 DA "H5''" H N N 98 DA "H4'" H N N 99 DA "H3'" H N N 100 DA "HO3'" H N N 101 DA "H2'" H N N 102 DA "H2''" H N N 103 DA "H1'" H N N 104 DA H8 H N N 105 DA H61 H N N 106 DA H62 H N N 107 DA H2 H N N 108 DC OP3 O N N 109 DC P P N N 110 DC OP1 O N N 111 DC OP2 O N N 112 DC "O5'" O N N 113 DC "C5'" C N N 114 DC "C4'" C N R 115 DC "O4'" O N N 116 DC "C3'" C N S 117 DC "O3'" O N N 118 DC "C2'" C N N 119 DC "C1'" C N R 120 DC N1 N N N 121 DC C2 C N N 122 DC O2 O N N 123 DC N3 N N N 124 DC C4 C N N 125 DC N4 N N N 126 DC C5 C N N 127 DC C6 C N N 128 DC HOP3 H N N 129 DC HOP2 H N N 130 DC "H5'" H N N 131 DC "H5''" H N N 132 DC "H4'" H N N 133 DC "H3'" H N N 134 DC "HO3'" H N N 135 DC "H2'" H N N 136 DC "H2''" H N N 137 DC "H1'" H N N 138 DC H41 H N N 139 DC H42 H N N 140 DC H5 H N N 141 DC H6 H N N 142 DG OP3 O N N 143 DG P P N N 144 DG OP1 O N N 145 DG OP2 O N N 146 DG "O5'" O N N 147 DG "C5'" C N N 148 DG "C4'" C N R 149 DG "O4'" O N N 150 DG "C3'" C N S 151 DG "O3'" O N N 152 DG "C2'" C N N 153 DG "C1'" C N R 154 DG N9 N Y N 155 DG C8 C Y N 156 DG N7 N Y N 157 DG C5 C Y N 158 DG C6 C N N 159 DG O6 O N N 160 DG N1 N N N 161 DG C2 C N N 162 DG N2 N N N 163 DG N3 N N N 164 DG C4 C Y N 165 DG HOP3 H N N 166 DG HOP2 H N N 167 DG "H5'" H N N 168 DG "H5''" H N N 169 DG "H4'" H N N 170 DG "H3'" H N N 171 DG "HO3'" H N N 172 DG "H2'" H N N 173 DG "H2''" H N N 174 DG "H1'" H N N 175 DG H8 H N N 176 DG H1 H N N 177 DG H21 H N N 178 DG H22 H N N 179 DT OP3 O N N 180 DT P P N N 181 DT OP1 O N N 182 DT OP2 O N N 183 DT "O5'" O N N 184 DT "C5'" C N N 185 DT "C4'" C N R 186 DT "O4'" O N N 187 DT "C3'" C N S 188 DT "O3'" O N N 189 DT "C2'" C N N 190 DT "C1'" C N R 191 DT N1 N N N 192 DT C2 C N N 193 DT O2 O N N 194 DT N3 N N N 195 DT C4 C N N 196 DT O4 O N N 197 DT C5 C N N 198 DT C7 C N N 199 DT C6 C N N 200 DT HOP3 H N N 201 DT HOP2 H N N 202 DT "H5'" H N N 203 DT "H5''" H N N 204 DT "H4'" H N N 205 DT "H3'" H N N 206 DT "HO3'" H N N 207 DT "H2'" H N N 208 DT "H2''" H N N 209 DT "H1'" H N N 210 DT H3 H N N 211 DT H71 H N N 212 DT H72 H N N 213 DT H73 H N N 214 DT H6 H N N 215 G OP3 O N N 216 G P P N N 217 G OP1 O N N 218 G OP2 O N N 219 G "O5'" O N N 220 G "C5'" C N N 221 G "C4'" C N R 222 G "O4'" O N N 223 G "C3'" C N S 224 G "O3'" O N N 225 G "C2'" C N R 226 G "O2'" O N N 227 G "C1'" C N R 228 G N9 N Y N 229 G C8 C Y N 230 G N7 N Y N 231 G C5 C Y N 232 G C6 C N N 233 G O6 O N N 234 G N1 N N N 235 G C2 C N N 236 G N2 N N N 237 G N3 N N N 238 G C4 C Y N 239 G HOP3 H N N 240 G HOP2 H N N 241 G "H5'" H N N 242 G "H5''" H N N 243 G "H4'" H N N 244 G "H3'" H N N 245 G "HO3'" H N N 246 G "H2'" H N N 247 G "HO2'" H N N 248 G "H1'" H N N 249 G H8 H N N 250 G H1 H N N 251 G H21 H N N 252 G H22 H N N 253 U OP3 O N N 254 U P P N N 255 U OP1 O N N 256 U OP2 O N N 257 U "O5'" O N N 258 U "C5'" C N N 259 U "C4'" C N R 260 U "O4'" O N N 261 U "C3'" C N S 262 U "O3'" O N N 263 U "C2'" C N R 264 U "O2'" O N N 265 U "C1'" C N R 266 U N1 N N N 267 U C2 C N N 268 U O2 O N N 269 U N3 N N N 270 U C4 C N N 271 U O4 O N N 272 U C5 C N N 273 U C6 C N N 274 U HOP3 H N N 275 U HOP2 H N N 276 U "H5'" H N N 277 U "H5''" H N N 278 U "H4'" H N N 279 U "H3'" H N N 280 U "HO3'" H N N 281 U "H2'" H N N 282 U "HO2'" H N N 283 U "H1'" H N N 284 U H3 H N N 285 U H5 H N N 286 U H6 H N N 287 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 DA OP3 P sing N N 76 DA OP3 HOP3 sing N N 77 DA P OP1 doub N N 78 DA P OP2 sing N N 79 DA P "O5'" sing N N 80 DA OP2 HOP2 sing N N 81 DA "O5'" "C5'" sing N N 82 DA "C5'" "C4'" sing N N 83 DA "C5'" "H5'" sing N N 84 DA "C5'" "H5''" sing N N 85 DA "C4'" "O4'" sing N N 86 DA "C4'" "C3'" sing N N 87 DA "C4'" "H4'" sing N N 88 DA "O4'" "C1'" sing N N 89 DA "C3'" "O3'" sing N N 90 DA "C3'" "C2'" sing N N 91 DA "C3'" "H3'" sing N N 92 DA "O3'" "HO3'" sing N N 93 DA "C2'" "C1'" sing N N 94 DA "C2'" "H2'" sing N N 95 DA "C2'" "H2''" sing N N 96 DA "C1'" N9 sing N N 97 DA "C1'" "H1'" sing N N 98 DA N9 C8 sing Y N 99 DA N9 C4 sing Y N 100 DA C8 N7 doub Y N 101 DA C8 H8 sing N N 102 DA N7 C5 sing Y N 103 DA C5 C6 sing Y N 104 DA C5 C4 doub Y N 105 DA C6 N6 sing N N 106 DA C6 N1 doub Y N 107 DA N6 H61 sing N N 108 DA N6 H62 sing N N 109 DA N1 C2 sing Y N 110 DA C2 N3 doub Y N 111 DA C2 H2 sing N N 112 DA N3 C4 sing Y N 113 DC OP3 P sing N N 114 DC OP3 HOP3 sing N N 115 DC P OP1 doub N N 116 DC P OP2 sing N N 117 DC P "O5'" sing N N 118 DC OP2 HOP2 sing N N 119 DC "O5'" "C5'" sing N N 120 DC "C5'" "C4'" sing N N 121 DC "C5'" "H5'" sing N N 122 DC "C5'" "H5''" sing N N 123 DC "C4'" "O4'" sing N N 124 DC "C4'" "C3'" sing N N 125 DC "C4'" "H4'" sing N N 126 DC "O4'" "C1'" sing N N 127 DC "C3'" "O3'" sing N N 128 DC "C3'" "C2'" sing N N 129 DC "C3'" "H3'" sing N N 130 DC "O3'" "HO3'" sing N N 131 DC "C2'" "C1'" sing N N 132 DC "C2'" "H2'" sing N N 133 DC "C2'" "H2''" sing N N 134 DC "C1'" N1 sing N N 135 DC "C1'" "H1'" sing N N 136 DC N1 C2 sing N N 137 DC N1 C6 sing N N 138 DC C2 O2 doub N N 139 DC C2 N3 sing N N 140 DC N3 C4 doub N N 141 DC C4 N4 sing N N 142 DC C4 C5 sing N N 143 DC N4 H41 sing N N 144 DC N4 H42 sing N N 145 DC C5 C6 doub N N 146 DC C5 H5 sing N N 147 DC C6 H6 sing N N 148 DG OP3 P sing N N 149 DG OP3 HOP3 sing N N 150 DG P OP1 doub N N 151 DG P OP2 sing N N 152 DG P "O5'" sing N N 153 DG OP2 HOP2 sing N N 154 DG "O5'" "C5'" sing N N 155 DG "C5'" "C4'" sing N N 156 DG "C5'" "H5'" sing N N 157 DG "C5'" "H5''" sing N N 158 DG "C4'" "O4'" sing N N 159 DG "C4'" "C3'" sing N N 160 DG "C4'" "H4'" sing N N 161 DG "O4'" "C1'" sing N N 162 DG "C3'" "O3'" sing N N 163 DG "C3'" "C2'" sing N N 164 DG "C3'" "H3'" sing N N 165 DG "O3'" "HO3'" sing N N 166 DG "C2'" "C1'" sing N N 167 DG "C2'" "H2'" sing N N 168 DG "C2'" "H2''" sing N N 169 DG "C1'" N9 sing N N 170 DG "C1'" "H1'" sing N N 171 DG N9 C8 sing Y N 172 DG N9 C4 sing Y N 173 DG C8 N7 doub Y N 174 DG C8 H8 sing N N 175 DG N7 C5 sing Y N 176 DG C5 C6 sing N N 177 DG C5 C4 doub Y N 178 DG C6 O6 doub N N 179 DG C6 N1 sing N N 180 DG N1 C2 sing N N 181 DG N1 H1 sing N N 182 DG C2 N2 sing N N 183 DG C2 N3 doub N N 184 DG N2 H21 sing N N 185 DG N2 H22 sing N N 186 DG N3 C4 sing N N 187 DT OP3 P sing N N 188 DT OP3 HOP3 sing N N 189 DT P OP1 doub N N 190 DT P OP2 sing N N 191 DT P "O5'" sing N N 192 DT OP2 HOP2 sing N N 193 DT "O5'" "C5'" sing N N 194 DT "C5'" "C4'" sing N N 195 DT "C5'" "H5'" sing N N 196 DT "C5'" "H5''" sing N N 197 DT "C4'" "O4'" sing N N 198 DT "C4'" "C3'" sing N N 199 DT "C4'" "H4'" sing N N 200 DT "O4'" "C1'" sing N N 201 DT "C3'" "O3'" sing N N 202 DT "C3'" "C2'" sing N N 203 DT "C3'" "H3'" sing N N 204 DT "O3'" "HO3'" sing N N 205 DT "C2'" "C1'" sing N N 206 DT "C2'" "H2'" sing N N 207 DT "C2'" "H2''" sing N N 208 DT "C1'" N1 sing N N 209 DT "C1'" "H1'" sing N N 210 DT N1 C2 sing N N 211 DT N1 C6 sing N N 212 DT C2 O2 doub N N 213 DT C2 N3 sing N N 214 DT N3 C4 sing N N 215 DT N3 H3 sing N N 216 DT C4 O4 doub N N 217 DT C4 C5 sing N N 218 DT C5 C7 sing N N 219 DT C5 C6 doub N N 220 DT C7 H71 sing N N 221 DT C7 H72 sing N N 222 DT C7 H73 sing N N 223 DT C6 H6 sing N N 224 G OP3 P sing N N 225 G OP3 HOP3 sing N N 226 G P OP1 doub N N 227 G P OP2 sing N N 228 G P "O5'" sing N N 229 G OP2 HOP2 sing N N 230 G "O5'" "C5'" sing N N 231 G "C5'" "C4'" sing N N 232 G "C5'" "H5'" sing N N 233 G "C5'" "H5''" sing N N 234 G "C4'" "O4'" sing N N 235 G "C4'" "C3'" sing N N 236 G "C4'" "H4'" sing N N 237 G "O4'" "C1'" sing N N 238 G "C3'" "O3'" sing N N 239 G "C3'" "C2'" sing N N 240 G "C3'" "H3'" sing N N 241 G "O3'" "HO3'" sing N N 242 G "C2'" "O2'" sing N N 243 G "C2'" "C1'" sing N N 244 G "C2'" "H2'" sing N N 245 G "O2'" "HO2'" sing N N 246 G "C1'" N9 sing N N 247 G "C1'" "H1'" sing N N 248 G N9 C8 sing Y N 249 G N9 C4 sing Y N 250 G C8 N7 doub Y N 251 G C8 H8 sing N N 252 G N7 C5 sing Y N 253 G C5 C6 sing N N 254 G C5 C4 doub Y N 255 G C6 O6 doub N N 256 G C6 N1 sing N N 257 G N1 C2 sing N N 258 G N1 H1 sing N N 259 G C2 N2 sing N N 260 G C2 N3 doub N N 261 G N2 H21 sing N N 262 G N2 H22 sing N N 263 G N3 C4 sing N N 264 U OP3 P sing N N 265 U OP3 HOP3 sing N N 266 U P OP1 doub N N 267 U P OP2 sing N N 268 U P "O5'" sing N N 269 U OP2 HOP2 sing N N 270 U "O5'" "C5'" sing N N 271 U "C5'" "C4'" sing N N 272 U "C5'" "H5'" sing N N 273 U "C5'" "H5''" sing N N 274 U "C4'" "O4'" sing N N 275 U "C4'" "C3'" sing N N 276 U "C4'" "H4'" sing N N 277 U "O4'" "C1'" sing N N 278 U "C3'" "O3'" sing N N 279 U "C3'" "C2'" sing N N 280 U "C3'" "H3'" sing N N 281 U "O3'" "HO3'" sing N N 282 U "C2'" "O2'" sing N N 283 U "C2'" "C1'" sing N N 284 U "C2'" "H2'" sing N N 285 U "O2'" "HO2'" sing N N 286 U "C1'" N1 sing N N 287 U "C1'" "H1'" sing N N 288 U N1 C2 sing N N 289 U N1 C6 sing N N 290 U C2 O2 doub N N 291 U C2 N3 sing N N 292 U N3 C4 sing N N 293 U N3 H3 sing N N 294 U C4 O4 doub N N 295 U C4 C5 sing N N 296 U C5 C6 doub N N 297 U C5 H5 sing N N 298 U C6 H6 sing N N 299 # _ndb_struct_conf_na.entry_id 9VUN _ndb_struct_conf_na.feature 'a-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 G 1 1_555 B DC 14 1_555 -0.173 -0.181 0.268 -4.731 -12.126 1.413 1 A_G1:DC14_B A 1 ? B 14 ? 19 1 1 A U 2 1_555 B DA 13 1_555 -0.257 -0.191 0.208 -3.804 -11.674 3.663 2 A_U2:DA13_B A 2 ? B 13 ? 20 1 1 A U 3 1_555 B DA 12 1_555 -0.330 -0.181 0.249 0.529 -8.021 -3.229 3 A_U3:DA12_B A 3 ? B 12 ? 20 1 1 A G 4 1_555 B DC 11 1_555 -0.061 -0.336 0.280 3.731 -6.214 -1.753 4 A_G4:DC11_B A 4 ? B 11 ? 19 1 1 A C 5 1_555 B DG 10 1_555 0.103 -0.212 0.099 2.270 -7.404 2.613 5 A_C5:DG10_B A 5 ? B 10 ? 19 1 1 A C 6 1_555 B DG 9 1_555 0.202 -0.139 0.075 2.602 -9.203 3.073 6 A_C6:DG9_B A 6 ? B 9 ? 19 1 1 A U 7 1_555 B DA 8 1_555 -0.040 -0.105 -0.071 -4.614 -3.566 5.039 7 A_U7:DA8_B A 7 ? B 8 ? 20 1 1 A G 8 1_555 B DC 7 1_555 -0.237 -0.146 0.062 -7.457 -8.813 2.218 8 A_G8:DC7_B A 8 ? B 7 ? 19 1 1 A G 9 1_555 B DC 6 1_555 -0.112 -0.136 0.151 -8.369 -11.929 0.570 9 A_G9:DC6_B A 9 ? B 6 ? 19 1 1 A A 10 1_555 B DT 5 1_555 0.213 -0.334 0.165 -7.242 -4.765 -1.274 10 A_A10:DT5_B A 10 ? B 5 ? 20 1 1 A G 11 1_555 B DC 4 1_555 -0.145 -0.268 -0.063 -4.431 -7.863 1.038 11 A_G11:DC4_B A 11 ? B 4 ? 19 1 1 A A 12 1_555 B DT 3 1_555 0.049 -0.150 0.170 -3.274 -12.446 2.373 12 A_A12:DT3_B A 12 ? B 3 ? 20 1 1 A C 13 1_555 B DG 2 1_555 0.350 -0.113 0.301 0.983 -11.683 1.271 13 A_C13:DG2_B A 13 ? B 2 ? 19 1 1 A G 14 1_555 B DC 1 1_555 -0.120 -0.139 0.175 0.794 -2.497 1.525 14 A_G14:DC1_B A 14 ? B 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 G 1 1_555 B DC 14 1_555 A U 2 1_555 B DA 13 1_555 -0.432 -1.357 3.176 1.078 3.229 32.708 -2.920 0.938 3.016 5.715 -1.908 32.880 1 AA_G1U2:DA13DC14_BB A 1 ? B 14 ? A 2 ? B 13 ? 1 A U 2 1_555 B DA 13 1_555 A U 3 1_555 B DA 12 1_555 -0.139 -1.029 3.174 -1.671 4.922 31.181 -2.753 -0.039 2.983 9.078 3.081 31.601 2 AA_U2U3:DA12DA13_BB A 2 ? B 13 ? A 3 ? B 12 ? 1 A U 3 1_555 B DA 12 1_555 A G 4 1_555 B DC 11 1_555 -0.051 -1.228 3.107 -2.524 5.334 32.503 -2.994 -0.304 2.870 9.433 4.463 33.020 3 AA_U3G4:DC11DA12_BB A 3 ? B 12 ? A 4 ? B 11 ? 1 A G 4 1_555 B DC 11 1_555 A C 5 1_555 B DG 10 1_555 0.264 -1.877 3.298 1.506 -0.652 29.602 -3.528 -0.192 3.347 -1.275 -2.945 29.647 4 AA_G4C5:DG10DC11_BB A 4 ? B 11 ? A 5 ? B 10 ? 1 A C 5 1_555 B DG 10 1_555 A C 6 1_555 B DG 9 1_555 0.039 -2.065 3.166 -0.196 7.691 32.386 -4.759 -0.098 2.620 13.551 0.345 33.264 5 AA_C5C6:DG9DG10_BB A 5 ? B 10 ? A 6 ? B 9 ? 1 A C 6 1_555 B DG 9 1_555 A U 7 1_555 B DA 8 1_555 -0.341 -1.507 3.365 1.419 7.023 29.909 -4.185 0.914 2.925 13.367 -2.700 30.737 6 AA_C6U7:DA8DG9_BB A 6 ? B 9 ? A 7 ? B 8 ? 1 A U 7 1_555 B DA 8 1_555 A G 8 1_555 B DC 7 1_555 0.390 -1.511 3.280 -1.114 10.180 29.678 -4.572 -0.915 2.615 19.170 2.097 31.358 7 AA_U7G8:DC7DA8_BB A 7 ? B 8 ? A 8 ? B 7 ? 1 A G 8 1_555 B DC 7 1_555 A G 9 1_555 B DC 6 1_555 -0.795 -1.749 3.188 -2.832 7.225 34.990 -3.813 0.913 2.836 11.838 4.640 35.814 8 AA_G8G9:DC6DC7_BB A 8 ? B 7 ? A 9 ? B 6 ? 1 A G 9 1_555 B DC 6 1_555 A A 10 1_555 B DT 5 1_555 0.331 -2.138 3.230 3.768 14.255 29.655 -5.817 -0.038 2.042 25.931 -6.854 33.045 9 AA_G9A10:DT5DC6_BB A 9 ? B 6 ? A 10 ? B 5 ? 1 A A 10 1_555 B DT 5 1_555 A G 11 1_555 B DC 4 1_555 0.471 -1.941 3.291 3.554 5.803 25.584 -5.706 -0.132 2.827 12.817 -7.851 26.459 10 AA_A10G11:DC4DT5_BB A 10 ? B 5 ? A 11 ? B 4 ? 1 A G 11 1_555 B DC 4 1_555 A A 12 1_555 B DT 3 1_555 0.178 -1.776 3.278 -0.599 4.808 30.973 -4.159 -0.438 2.971 8.935 1.113 31.341 11 AA_G11A12:DT3DC4_BB A 11 ? B 4 ? A 12 ? B 3 ? 1 A A 12 1_555 B DT 3 1_555 A C 13 1_555 B DG 2 1_555 -0.195 -1.462 3.162 -1.295 2.485 32.430 -3.021 0.133 3.050 4.440 2.314 32.547 12 AA_A12C13:DG2DT3_BB A 12 ? B 3 ? A 13 ? B 2 ? 1 A C 13 1_555 B DG 2 1_555 A G 14 1_555 B DC 1 1_555 0.323 -1.821 3.194 2.894 5.730 31.517 -4.245 -0.100 2.845 10.413 -5.260 32.148 13 AA_C13G14:DC1DG2_BB A 13 ? B 2 ? A 14 ? B 1 ? # _pdbx_audit_support.funding_organization 'National Natural Science Foundation of China (NSFC)' _pdbx_audit_support.country China _pdbx_audit_support.grant_number 32171191 _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 AlphaFold _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.details ? # _space_group.name_H-M_alt 'P 21 21 21' _space_group.name_Hall 'P 2ac 2ab' _space_group.IT_number 19 _space_group.crystal_system orthorhombic _space_group.id 1 # _atom_sites.entry_id 9VUN _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] 0.021627 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.020834 _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] 0.019656 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 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 ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_ #