data_9VUO # _entry.id 9VUO # _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 9VUO pdb_00009vuo 10.2210/pdb9vuo/pdb WWPDB D_1300061166 ? ? # _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 9VUO _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 N # _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 ;DNA (5'-D(*CP*GP*TP*CP*TP*CP*CP*AP*GP*GP*CP*AP*AP*C)-3') ; 4225.756 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*GP*UP*UP*GP*CP*CP*UP*GP*GP*AP*GP*AP*CP*G)-3') ; 4518.731 1 ? ? ? GUUGCCUGGAGACG 3 non-polymer syn '5-[[5-(dimethylamino)thiophen-2-yl]methyl]-N,N-dimethyl-thiophen-2-amine' 266.425 1 ? ? ? ? 4 water nat water 18.015 9 ? ? ? ? # 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)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA)(DA)(DC)' CGTCTCCAGGCAAC A ? 2 polyribonucleotide no no GUUGCCUGGAGACG GUUGCCUGGAGACG B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 '5-[[5-(dimethylamino)thiophen-2-yl]methyl]-N,N-dimethyl-thiophen-2-amine' A1ETT 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DT n 1 4 DC n 1 5 DT n 1 6 DC n 1 7 DC n 1 8 DA n 1 9 DG n 1 10 DG n 1 11 DC n 1 12 DA n 1 13 DA n 1 14 DC n 2 1 G n 2 2 U n 2 3 U n 2 4 G n 2 5 C n 2 6 C n 2 7 U n 2 8 G n 2 9 G n 2 10 A n 2 11 G n 2 12 A n 2 13 C n 2 14 G 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 A1ETT non-polymer . '5-[[5-(dimethylamino)thiophen-2-yl]methyl]-N,N-dimethyl-thiophen-2-amine' ? 'C13 H18 N2 S2' 266.425 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 HOH non-polymer . WATER ? 'H2 O' 18.015 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 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DT 5 5 5 DT DT A . n A 1 6 DC 6 6 6 DC DC A . n A 1 7 DC 7 7 7 DC DC A . n A 1 8 DA 8 8 8 DA DA A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DA 12 12 12 DA DA A . n A 1 13 DA 13 13 13 DA DA A . n A 1 14 DC 14 14 14 DC DC A . n B 2 1 G 1 1 1 G G B . n B 2 2 U 2 2 2 U U B . n B 2 3 U 3 3 3 U U B . n B 2 4 G 4 4 4 G G B . n B 2 5 C 5 5 5 C C B . n B 2 6 C 6 6 6 C C B . n B 2 7 U 7 7 7 U U B . n B 2 8 G 8 8 8 G G B . n B 2 9 G 9 9 9 G G B . n B 2 10 A 10 10 10 A A B . n B 2 11 G 11 11 11 G G B . n B 2 12 A 12 12 12 A A B . n B 2 13 C 13 13 13 C C B . n B 2 14 G 14 14 14 G G B . n # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id A1ETT _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id A1ETT _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 A1ETT 1 101 101 A1ETT TIC A . D 4 HOH 1 201 7 HOH HOH A . D 4 HOH 2 202 5 HOH HOH A . D 4 HOH 3 203 1 HOH HOH A . D 4 HOH 4 204 3 HOH HOH A . D 4 HOH 5 205 4 HOH HOH A . D 4 HOH 6 206 6 HOH HOH A . D 4 HOH 7 207 8 HOH HOH A . E 4 HOH 1 101 9 HOH HOH B . E 4 HOH 2 102 2 HOH HOH B . # 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' ? ? ? ? ? ? ? ? ? ? ? xia2 ? ? ? . ? 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? xia2 ? ? ? . ? 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . ? 5 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 120.000 _cell.angle_gamma_esd ? _cell.entry_id 9VUO _cell.details ? _cell.formula_units_Z ? _cell.length_a 46.630 _cell.length_a_esd ? _cell.length_b 46.630 _cell.length_b_esd ? _cell.length_c 94.240 _cell.length_c_esd ? _cell.volume 177458.473 _cell.volume_esd ? _cell.Z_PDB 6 _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 9VUO _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ;P 31 2" ; _symmetry.space_group_name_H-M 'P 31 2 1' _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 9VUO _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 3.38 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 63.63 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 8.5 _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 ;0.002 M Copper(II) chloride dihydrate 0.05 M TRIS hydrochloride pH 8.5 1.8 M Lithium sulfate monohydrate 0.0005 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 2025-06-21 _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 53.25 _reflns.entry_id 9VUO _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.19 _reflns.d_resolution_low 20.90 _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 6408 _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 98.2 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 17.4 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 20.5 _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 ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 1.000 _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 2.19 _reflns_shell.d_res_low 2.25 _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 485 _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 0.633 _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 52.51 _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 9VUO _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 2.19 _refine.ls_d_res_low 20.90 _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 6388 _refine.ls_number_reflns_R_free 636 _refine.ls_number_reflns_R_work 5752 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.17 _refine.ls_percent_reflns_R_free 9.96 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2268 _refine.ls_R_factor_R_free 0.2524 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2237 _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 1.34 _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 35.9318 _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 0.3684 _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 2.19 _refine_hist.d_res_low 20.90 _refine_hist.number_atoms_solvent 9 _refine_hist.number_atoms_total 605 _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 17 _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' ? 0.0025 ? 665 ? f_bond_d ? ? ? 'X-RAY DIFFRACTION' ? 0.4607 ? 1025 ? f_angle_d ? ? ? 'X-RAY DIFFRACTION' ? 0.0167 ? 124 ? f_chiral_restr ? ? ? 'X-RAY DIFFRACTION' ? 0.0019 ? 32 ? f_plane_restr ? ? ? 'X-RAY DIFFRACTION' ? 13.4381 ? 302 ? 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' 2.19 2.36 . . 126 1125 98.35 . . . . 0.4254 . . . . . . . . . . . . . . . 0.4457 'X-RAY DIFFRACTION' 2.36 2.60 . . 122 1105 96.24 . . . . 0.3818 . . . . . . . . . . . . . . . 0.4415 'X-RAY DIFFRACTION' 2.60 2.97 . . 126 1141 99.76 . . . . 0.3547 . . . . . . . . . . . . . . . 0.3939 'X-RAY DIFFRACTION' 2.97 3.74 . . 130 1153 98.31 . . . . 0.2203 . . . . . . . . . . . . . . . 0.2779 'X-RAY DIFFRACTION' 3.74 20.90 . . 132 1228 98.27 . . . . 0.1579 . . . . . . . . . . . . . . . 0.1657 # _struct.entry_id 9VUO _struct.title 'Crystal structure of the DNA/RNA hybrid with Tica' _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 9VUO _struct_keywords.text 'DNA/RNA hybrid, Tica, 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 ? C N N 3 ? D N N 4 ? E 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 9VUO 9VUO ? 1 ? 1 2 PDB 9VUO 9VUO ? 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 9VUO A 1 ? 14 ? 9VUO 1 ? 14 ? 1 14 2 2 9VUO B 1 ? 14 ? 9VUO 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)' 1550 ? 1 MORE -6 ? 1 'SSA (A^2)' 5280 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_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 DC 1 N3 ? ? ? 1_555 B G 14 N1 ? ? A DC 1 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B G 14 O6 ? ? A DC 1 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B G 14 N2 ? ? A DC 1 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B C 13 N3 ? ? A DG 2 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B C 13 O2 ? ? A DG 2 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B C 13 N4 ? ? A DG 2 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B A 12 N1 ? ? A DT 3 B A 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B A 12 N6 ? ? A DT 3 B A 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B G 11 N1 ? ? A DC 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B G 11 O6 ? ? A DC 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B G 11 N2 ? ? A DC 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B A 10 N1 ? ? A DT 5 B A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B A 10 N6 ? ? A DT 5 B A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B G 9 N1 ? ? A DC 6 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B G 9 O6 ? ? A DC 6 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B G 9 N2 ? ? A DC 6 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B G 8 N1 ? ? A DC 7 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B G 8 O6 ? ? A DC 7 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B G 8 N2 ? ? A DC 7 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B U 7 N3 ? ? A DA 8 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B U 7 O4 ? ? A DA 8 B U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B C 6 N3 ? ? A DG 9 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B C 6 O2 ? ? A DG 9 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B C 6 N4 ? ? A DG 9 B C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B C 5 N3 ? ? A DG 10 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B C 5 O2 ? ? A DG 10 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B C 5 N4 ? ? A DG 10 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B G 4 N1 ? ? A DC 11 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B G 4 O6 ? ? A DC 11 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B G 4 N2 ? ? A DC 11 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DA 12 N1 ? ? ? 1_555 B U 3 N3 ? ? A DA 12 B U 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DA 12 N6 ? ? ? 1_555 B U 3 O4 ? ? A DA 12 B U 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DA 13 N1 ? ? ? 1_555 B U 2 N3 ? ? A DA 13 B U 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DA 13 N6 ? ? ? 1_555 B U 2 O4 ? ? A DA 13 B U 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A DC 14 N3 ? ? ? 1_555 B G 1 N1 ? ? A DC 14 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A DC 14 N4 ? ? ? 1_555 B G 1 O6 ? ? A DC 14 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A DC 14 O2 ? ? ? 1_555 B G 1 N2 ? ? A DC 14 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_entry_details.entry_id 9VUO _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification N # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O2 B C 5 ? ? O B HOH 101 ? ? 1.97 2 1 O A HOH 205 ? ? O A HOH 206 ? ? 2.04 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 "O2'" B C 5 ? ? 1_555 "O3'" B G 14 ? ? 4_545 1.98 2 1 "O3'" B G 14 ? ? 1_555 O B HOH 101 ? ? 4_655 2.01 # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y,x-y,z+1/3 3 -x+y,-x,z+2/3 4 x-y,-y,-z+2/3 5 -x,-x+y,-z+1/3 6 y,x,-z # 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 A1ETT S1 S Y N 38 A1ETT C2 C Y N 39 A1ETT C3 C Y N 40 A1ETT C4 C Y N 41 A1ETT C5 C Y N 42 A1ETT C6 C N N 43 A1ETT C7 C Y N 44 A1ETT C8 C Y N 45 A1ETT C9 C Y N 46 A1ETT C10 C Y N 47 A1ETT C13 C N N 48 A1ETT C14 C N N 49 A1ETT C16 C N N 50 A1ETT C17 C N N 51 A1ETT N12 N N N 52 A1ETT N15 N N N 53 A1ETT S11 S Y N 54 A1ETT H3 H N N 55 A1ETT H4 H N N 56 A1ETT H1 H N N 57 A1ETT H6 H N N 58 A1ETT H8 H N N 59 A1ETT H9 H N N 60 A1ETT H13A H N N 61 A1ETT H13C H N N 62 A1ETT H13B H N N 63 A1ETT H14A H N N 64 A1ETT H14B H N N 65 A1ETT H14C H N N 66 A1ETT H16C H N N 67 A1ETT H16A H N N 68 A1ETT H16B H N N 69 A1ETT H17C H N N 70 A1ETT H17B H N N 71 A1ETT H17A H N N 72 C OP3 O N N 73 C P P N N 74 C OP1 O N N 75 C OP2 O N N 76 C "O5'" O N N 77 C "C5'" C N N 78 C "C4'" C N R 79 C "O4'" O N N 80 C "C3'" C N S 81 C "O3'" O N N 82 C "C2'" C N R 83 C "O2'" O N N 84 C "C1'" C N R 85 C N1 N N N 86 C C2 C N N 87 C O2 O N N 88 C N3 N N N 89 C C4 C N N 90 C N4 N N N 91 C C5 C N N 92 C C6 C N N 93 C HOP3 H N N 94 C HOP2 H N N 95 C "H5'" H N N 96 C "H5''" H N N 97 C "H4'" H N N 98 C "H3'" H N N 99 C "HO3'" H N N 100 C "H2'" H N N 101 C "HO2'" H N N 102 C "H1'" H N N 103 C H41 H N N 104 C H42 H N N 105 C H5 H N N 106 C H6 H N N 107 DA OP3 O N N 108 DA P P N N 109 DA OP1 O N N 110 DA OP2 O N N 111 DA "O5'" O N N 112 DA "C5'" C N N 113 DA "C4'" C N R 114 DA "O4'" O N N 115 DA "C3'" C N S 116 DA "O3'" O N N 117 DA "C2'" C N N 118 DA "C1'" C N R 119 DA N9 N Y N 120 DA C8 C Y N 121 DA N7 N Y N 122 DA C5 C Y N 123 DA C6 C Y N 124 DA N6 N N N 125 DA N1 N Y N 126 DA C2 C Y N 127 DA N3 N Y N 128 DA C4 C Y N 129 DA HOP3 H N N 130 DA HOP2 H N N 131 DA "H5'" H N N 132 DA "H5''" H N N 133 DA "H4'" H N N 134 DA "H3'" H N N 135 DA "HO3'" H N N 136 DA "H2'" H N N 137 DA "H2''" H N N 138 DA "H1'" H N N 139 DA H8 H N N 140 DA H61 H N N 141 DA H62 H N N 142 DA H2 H N N 143 DC OP3 O N N 144 DC P P N N 145 DC OP1 O N N 146 DC OP2 O N N 147 DC "O5'" O N N 148 DC "C5'" C N N 149 DC "C4'" C N R 150 DC "O4'" O N N 151 DC "C3'" C N S 152 DC "O3'" O N N 153 DC "C2'" C N N 154 DC "C1'" C N R 155 DC N1 N N N 156 DC C2 C N N 157 DC O2 O N N 158 DC N3 N N N 159 DC C4 C N N 160 DC N4 N N N 161 DC C5 C N N 162 DC C6 C N N 163 DC HOP3 H N N 164 DC HOP2 H N N 165 DC "H5'" H N N 166 DC "H5''" H N N 167 DC "H4'" H N N 168 DC "H3'" H N N 169 DC "HO3'" H N N 170 DC "H2'" H N N 171 DC "H2''" H N N 172 DC "H1'" H N N 173 DC H41 H N N 174 DC H42 H N N 175 DC H5 H N N 176 DC H6 H N N 177 DG OP3 O N N 178 DG P P N N 179 DG OP1 O N N 180 DG OP2 O N N 181 DG "O5'" O N N 182 DG "C5'" C N N 183 DG "C4'" C N R 184 DG "O4'" O N N 185 DG "C3'" C N S 186 DG "O3'" O N N 187 DG "C2'" C N N 188 DG "C1'" C N R 189 DG N9 N Y N 190 DG C8 C Y N 191 DG N7 N Y N 192 DG C5 C Y N 193 DG C6 C N N 194 DG O6 O N N 195 DG N1 N N N 196 DG C2 C N N 197 DG N2 N N N 198 DG N3 N N N 199 DG C4 C Y N 200 DG HOP3 H N N 201 DG HOP2 H N N 202 DG "H5'" H N N 203 DG "H5''" H N N 204 DG "H4'" H N N 205 DG "H3'" H N N 206 DG "HO3'" H N N 207 DG "H2'" H N N 208 DG "H2''" H N N 209 DG "H1'" H N N 210 DG H8 H N N 211 DG H1 H N N 212 DG H21 H N N 213 DG H22 H N N 214 DT OP3 O N N 215 DT P P N N 216 DT OP1 O N N 217 DT OP2 O N N 218 DT "O5'" O N N 219 DT "C5'" C N N 220 DT "C4'" C N R 221 DT "O4'" O N N 222 DT "C3'" C N S 223 DT "O3'" O N N 224 DT "C2'" C N N 225 DT "C1'" C N R 226 DT N1 N N N 227 DT C2 C N N 228 DT O2 O N N 229 DT N3 N N N 230 DT C4 C N N 231 DT O4 O N N 232 DT C5 C N N 233 DT C7 C N N 234 DT C6 C N N 235 DT HOP3 H N N 236 DT HOP2 H N N 237 DT "H5'" H N N 238 DT "H5''" H N N 239 DT "H4'" H N N 240 DT "H3'" H N N 241 DT "HO3'" H N N 242 DT "H2'" H N N 243 DT "H2''" H N N 244 DT "H1'" H N N 245 DT H3 H N N 246 DT H71 H N N 247 DT H72 H N N 248 DT H73 H N N 249 DT H6 H N N 250 G OP3 O N N 251 G P P N N 252 G OP1 O N N 253 G OP2 O N N 254 G "O5'" O N N 255 G "C5'" C N N 256 G "C4'" C N R 257 G "O4'" O N N 258 G "C3'" C N S 259 G "O3'" O N N 260 G "C2'" C N R 261 G "O2'" O N N 262 G "C1'" C N R 263 G N9 N Y N 264 G C8 C Y N 265 G N7 N Y N 266 G C5 C Y N 267 G C6 C N N 268 G O6 O N N 269 G N1 N N N 270 G C2 C N N 271 G N2 N N N 272 G N3 N N N 273 G C4 C Y N 274 G HOP3 H N N 275 G HOP2 H N N 276 G "H5'" H N N 277 G "H5''" H N N 278 G "H4'" H N N 279 G "H3'" H N N 280 G "HO3'" H N N 281 G "H2'" H N N 282 G "HO2'" H N N 283 G "H1'" H N N 284 G H8 H N N 285 G H1 H N N 286 G H21 H N N 287 G H22 H N N 288 HOH O O N N 289 HOH H1 H N N 290 HOH H2 H N N 291 U OP3 O N N 292 U P P N N 293 U OP1 O N N 294 U OP2 O N N 295 U "O5'" O N N 296 U "C5'" C N N 297 U "C4'" C N R 298 U "O4'" O N N 299 U "C3'" C N S 300 U "O3'" O N N 301 U "C2'" C N R 302 U "O2'" O N N 303 U "C1'" C N R 304 U N1 N N N 305 U C2 C N N 306 U O2 O N N 307 U N3 N N N 308 U C4 C N N 309 U O4 O N N 310 U C5 C N N 311 U C6 C N N 312 U HOP3 H N N 313 U HOP2 H N N 314 U "H5'" H N N 315 U "H5''" H N N 316 U "H4'" H N N 317 U "H3'" H N N 318 U "HO3'" H N N 319 U "H2'" H N N 320 U "HO2'" H N N 321 U "H1'" H N N 322 U H3 H N N 323 U H5 H N N 324 U H6 H N N 325 # 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 A1ETT S1 C2 sing Y N 40 A1ETT S1 C5 sing Y N 41 A1ETT C2 C3 doub Y N 42 A1ETT C2 C6 sing N N 43 A1ETT C3 C4 sing Y N 44 A1ETT C4 C5 doub Y N 45 A1ETT C5 N15 sing N N 46 A1ETT C6 C7 sing N N 47 A1ETT C7 C8 doub Y N 48 A1ETT C7 S11 sing Y N 49 A1ETT C8 C9 sing Y N 50 A1ETT C9 C10 doub Y N 51 A1ETT C10 S11 sing Y N 52 A1ETT C10 N12 sing N N 53 A1ETT N12 C13 sing N N 54 A1ETT N12 C14 sing N N 55 A1ETT N15 C16 sing N N 56 A1ETT N15 C17 sing N N 57 A1ETT C3 H3 sing N N 58 A1ETT C4 H4 sing N N 59 A1ETT C6 H1 sing N N 60 A1ETT C6 H6 sing N N 61 A1ETT C8 H8 sing N N 62 A1ETT C9 H9 sing N N 63 A1ETT C13 H13A sing N N 64 A1ETT C13 H13C sing N N 65 A1ETT C13 H13B sing N N 66 A1ETT C14 H14A sing N N 67 A1ETT C14 H14B sing N N 68 A1ETT C14 H14C sing N N 69 A1ETT C16 H16C sing N N 70 A1ETT C16 H16A sing N N 71 A1ETT C16 H16B sing N N 72 A1ETT C17 H17C sing N N 73 A1ETT C17 H17B sing N N 74 A1ETT C17 H17A sing N N 75 C OP3 P sing N N 76 C OP3 HOP3 sing N N 77 C P OP1 doub N N 78 C P OP2 sing N N 79 C P "O5'" sing N N 80 C OP2 HOP2 sing N N 81 C "O5'" "C5'" sing N N 82 C "C5'" "C4'" sing N N 83 C "C5'" "H5'" sing N N 84 C "C5'" "H5''" sing N N 85 C "C4'" "O4'" sing N N 86 C "C4'" "C3'" sing N N 87 C "C4'" "H4'" sing N N 88 C "O4'" "C1'" sing N N 89 C "C3'" "O3'" sing N N 90 C "C3'" "C2'" sing N N 91 C "C3'" "H3'" sing N N 92 C "O3'" "HO3'" sing N N 93 C "C2'" "O2'" sing N N 94 C "C2'" "C1'" sing N N 95 C "C2'" "H2'" sing N N 96 C "O2'" "HO2'" sing N N 97 C "C1'" N1 sing N N 98 C "C1'" "H1'" sing N N 99 C N1 C2 sing N N 100 C N1 C6 sing N N 101 C C2 O2 doub N N 102 C C2 N3 sing N N 103 C N3 C4 doub N N 104 C C4 N4 sing N N 105 C C4 C5 sing N N 106 C N4 H41 sing N N 107 C N4 H42 sing N N 108 C C5 C6 doub N N 109 C C5 H5 sing N N 110 C C6 H6 sing N N 111 DA OP3 P sing N N 112 DA OP3 HOP3 sing N N 113 DA P OP1 doub N N 114 DA P OP2 sing N N 115 DA P "O5'" sing N N 116 DA OP2 HOP2 sing N N 117 DA "O5'" "C5'" sing N N 118 DA "C5'" "C4'" sing N N 119 DA "C5'" "H5'" sing N N 120 DA "C5'" "H5''" sing N N 121 DA "C4'" "O4'" sing N N 122 DA "C4'" "C3'" sing N N 123 DA "C4'" "H4'" sing N N 124 DA "O4'" "C1'" sing N N 125 DA "C3'" "O3'" sing N N 126 DA "C3'" "C2'" sing N N 127 DA "C3'" "H3'" sing N N 128 DA "O3'" "HO3'" sing N N 129 DA "C2'" "C1'" sing N N 130 DA "C2'" "H2'" sing N N 131 DA "C2'" "H2''" sing N N 132 DA "C1'" N9 sing N N 133 DA "C1'" "H1'" sing N N 134 DA N9 C8 sing Y N 135 DA N9 C4 sing Y N 136 DA C8 N7 doub Y N 137 DA C8 H8 sing N N 138 DA N7 C5 sing Y N 139 DA C5 C6 sing Y N 140 DA C5 C4 doub Y N 141 DA C6 N6 sing N N 142 DA C6 N1 doub Y N 143 DA N6 H61 sing N N 144 DA N6 H62 sing N N 145 DA N1 C2 sing Y N 146 DA C2 N3 doub Y N 147 DA C2 H2 sing N N 148 DA N3 C4 sing Y N 149 DC OP3 P sing N N 150 DC OP3 HOP3 sing N N 151 DC P OP1 doub N N 152 DC P OP2 sing N N 153 DC P "O5'" sing N N 154 DC OP2 HOP2 sing N N 155 DC "O5'" "C5'" sing N N 156 DC "C5'" "C4'" sing N N 157 DC "C5'" "H5'" sing N N 158 DC "C5'" "H5''" sing N N 159 DC "C4'" "O4'" sing N N 160 DC "C4'" "C3'" sing N N 161 DC "C4'" "H4'" sing N N 162 DC "O4'" "C1'" sing N N 163 DC "C3'" "O3'" sing N N 164 DC "C3'" "C2'" sing N N 165 DC "C3'" "H3'" sing N N 166 DC "O3'" "HO3'" sing N N 167 DC "C2'" "C1'" sing N N 168 DC "C2'" "H2'" sing N N 169 DC "C2'" "H2''" sing N N 170 DC "C1'" N1 sing N N 171 DC "C1'" "H1'" sing N N 172 DC N1 C2 sing N N 173 DC N1 C6 sing N N 174 DC C2 O2 doub N N 175 DC C2 N3 sing N N 176 DC N3 C4 doub N N 177 DC C4 N4 sing N N 178 DC C4 C5 sing N N 179 DC N4 H41 sing N N 180 DC N4 H42 sing N N 181 DC C5 C6 doub N N 182 DC C5 H5 sing N N 183 DC C6 H6 sing N N 184 DG OP3 P sing N N 185 DG OP3 HOP3 sing N N 186 DG P OP1 doub N N 187 DG P OP2 sing N N 188 DG P "O5'" sing N N 189 DG OP2 HOP2 sing N N 190 DG "O5'" "C5'" sing N N 191 DG "C5'" "C4'" sing N N 192 DG "C5'" "H5'" sing N N 193 DG "C5'" "H5''" sing N N 194 DG "C4'" "O4'" sing N N 195 DG "C4'" "C3'" sing N N 196 DG "C4'" "H4'" sing N N 197 DG "O4'" "C1'" sing N N 198 DG "C3'" "O3'" sing N N 199 DG "C3'" "C2'" sing N N 200 DG "C3'" "H3'" sing N N 201 DG "O3'" "HO3'" sing N N 202 DG "C2'" "C1'" sing N N 203 DG "C2'" "H2'" sing N N 204 DG "C2'" "H2''" sing N N 205 DG "C1'" N9 sing N N 206 DG "C1'" "H1'" sing N N 207 DG N9 C8 sing Y N 208 DG N9 C4 sing Y N 209 DG C8 N7 doub Y N 210 DG C8 H8 sing N N 211 DG N7 C5 sing Y N 212 DG C5 C6 sing N N 213 DG C5 C4 doub Y N 214 DG C6 O6 doub N N 215 DG C6 N1 sing N N 216 DG N1 C2 sing N N 217 DG N1 H1 sing N N 218 DG C2 N2 sing N N 219 DG C2 N3 doub N N 220 DG N2 H21 sing N N 221 DG N2 H22 sing N N 222 DG N3 C4 sing N N 223 DT OP3 P sing N N 224 DT OP3 HOP3 sing N N 225 DT P OP1 doub N N 226 DT P OP2 sing N N 227 DT P "O5'" sing N N 228 DT OP2 HOP2 sing N N 229 DT "O5'" "C5'" sing N N 230 DT "C5'" "C4'" sing N N 231 DT "C5'" "H5'" sing N N 232 DT "C5'" "H5''" sing N N 233 DT "C4'" "O4'" sing N N 234 DT "C4'" "C3'" sing N N 235 DT "C4'" "H4'" sing N N 236 DT "O4'" "C1'" sing N N 237 DT "C3'" "O3'" sing N N 238 DT "C3'" "C2'" sing N N 239 DT "C3'" "H3'" sing N N 240 DT "O3'" "HO3'" sing N N 241 DT "C2'" "C1'" sing N N 242 DT "C2'" "H2'" sing N N 243 DT "C2'" "H2''" sing N N 244 DT "C1'" N1 sing N N 245 DT "C1'" "H1'" sing N N 246 DT N1 C2 sing N N 247 DT N1 C6 sing N N 248 DT C2 O2 doub N N 249 DT C2 N3 sing N N 250 DT N3 C4 sing N N 251 DT N3 H3 sing N N 252 DT C4 O4 doub N N 253 DT C4 C5 sing N N 254 DT C5 C7 sing N N 255 DT C5 C6 doub N N 256 DT C7 H71 sing N N 257 DT C7 H72 sing N N 258 DT C7 H73 sing N N 259 DT C6 H6 sing N N 260 G OP3 P sing N N 261 G OP3 HOP3 sing N N 262 G P OP1 doub N N 263 G P OP2 sing N N 264 G P "O5'" sing N N 265 G OP2 HOP2 sing N N 266 G "O5'" "C5'" sing N N 267 G "C5'" "C4'" sing N N 268 G "C5'" "H5'" sing N N 269 G "C5'" "H5''" sing N N 270 G "C4'" "O4'" sing N N 271 G "C4'" "C3'" sing N N 272 G "C4'" "H4'" sing N N 273 G "O4'" "C1'" sing N N 274 G "C3'" "O3'" sing N N 275 G "C3'" "C2'" sing N N 276 G "C3'" "H3'" sing N N 277 G "O3'" "HO3'" sing N N 278 G "C2'" "O2'" sing N N 279 G "C2'" "C1'" sing N N 280 G "C2'" "H2'" sing N N 281 G "O2'" "HO2'" sing N N 282 G "C1'" N9 sing N N 283 G "C1'" "H1'" sing N N 284 G N9 C8 sing Y N 285 G N9 C4 sing Y N 286 G C8 N7 doub Y N 287 G C8 H8 sing N N 288 G N7 C5 sing Y N 289 G C5 C6 sing N N 290 G C5 C4 doub Y N 291 G C6 O6 doub N N 292 G C6 N1 sing N N 293 G N1 C2 sing N N 294 G N1 H1 sing N N 295 G C2 N2 sing N N 296 G C2 N3 doub N N 297 G N2 H21 sing N N 298 G N2 H22 sing N N 299 G N3 C4 sing N N 300 HOH O H1 sing N N 301 HOH O H2 sing N N 302 U OP3 P sing N N 303 U OP3 HOP3 sing N N 304 U P OP1 doub N N 305 U P OP2 sing N N 306 U P "O5'" sing N N 307 U OP2 HOP2 sing N N 308 U "O5'" "C5'" sing N N 309 U "C5'" "C4'" sing N N 310 U "C5'" "H5'" sing N N 311 U "C5'" "H5''" sing N N 312 U "C4'" "O4'" sing N N 313 U "C4'" "C3'" sing N N 314 U "C4'" "H4'" sing N N 315 U "O4'" "C1'" sing N N 316 U "C3'" "O3'" sing N N 317 U "C3'" "C2'" sing N N 318 U "C3'" "H3'" sing N N 319 U "O3'" "HO3'" sing N N 320 U "C2'" "O2'" sing N N 321 U "C2'" "C1'" sing N N 322 U "C2'" "H2'" sing N N 323 U "O2'" "HO2'" sing N N 324 U "C1'" N1 sing N N 325 U "C1'" "H1'" sing N N 326 U N1 C2 sing N N 327 U N1 C6 sing N N 328 U C2 O2 doub N N 329 U C2 N3 sing N N 330 U N3 C4 sing N N 331 U N3 H3 sing N N 332 U C4 O4 doub N N 333 U C4 C5 sing N N 334 U C5 C6 doub N N 335 U C5 H5 sing N N 336 U C6 H6 sing N N 337 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9VUO 'double helix' 9VUO '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 DC 1 1_555 B G 14 1_555 0.139 -0.142 0.174 -5.762 9.947 -9.540 1 A_DC1:G14_B A 1 ? B 14 ? 19 1 1 A DG 2 1_555 B C 13 1_555 0.007 -0.153 -0.134 3.158 8.984 3.243 2 A_DG2:C13_B A 2 ? B 13 ? 19 1 1 A DT 3 1_555 B A 12 1_555 -0.178 -0.143 0.409 8.288 -10.282 3.212 3 A_DT3:A12_B A 3 ? B 12 ? 20 1 1 A DC 4 1_555 B G 11 1_555 0.383 -0.336 -0.167 6.151 -6.602 -0.522 4 A_DC4:G11_B A 4 ? B 11 ? 19 1 1 A DT 5 1_555 B A 10 1_555 0.034 -0.181 0.024 12.322 -12.536 3.074 5 A_DT5:A10_B A 5 ? B 10 ? 20 1 1 A DC 6 1_555 B G 9 1_555 0.420 -0.054 -0.100 12.341 -12.597 4.531 6 A_DC6:G9_B A 6 ? B 9 ? 19 1 1 A DC 7 1_555 B G 8 1_555 0.026 -0.087 -0.125 0.717 -10.450 6.528 7 A_DC7:G8_B A 7 ? B 8 ? 19 1 1 A DA 8 1_555 B U 7 1_555 0.324 -0.092 0.134 2.361 -3.153 7.628 8 A_DA8:U7_B A 8 ? B 7 ? 20 1 1 A DG 9 1_555 B C 6 1_555 -0.057 -0.174 -0.279 1.913 -4.906 2.978 9 A_DG9:C6_B A 9 ? B 6 ? 19 1 1 A DG 10 1_555 B C 5 1_555 0.055 -0.199 -0.244 -9.161 -7.736 1.021 10 A_DG10:C5_B A 10 ? B 5 ? 19 1 1 A DC 11 1_555 B G 4 1_555 -0.026 -0.234 -0.173 5.309 -10.123 4.226 11 A_DC11:G4_B A 11 ? B 4 ? 19 1 1 A DA 12 1_555 B U 3 1_555 0.575 -0.047 0.003 1.418 -9.985 6.748 12 A_DA12:U3_B A 12 ? B 3 ? 20 1 1 A DA 13 1_555 B U 2 1_555 0.357 -0.243 0.454 7.307 -22.310 3.526 13 A_DA13:U2_B A 13 ? B 2 ? 20 1 1 A DC 14 1_555 B G 1 1_555 -0.029 -0.002 0.144 11.916 -16.031 -1.302 14 A_DC14:G1_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 DC 1 1_555 B G 14 1_555 A DG 2 1_555 B C 13 1_555 0.847 -1.141 6.626 -0.226 2.365 4.551 -45.276 -12.571 5.311 27.451 2.628 5.133 1 AA_DC1DG2:C13G14_BB A 1 ? B 14 ? A 2 ? B 13 ? 1 A DG 2 1_555 B C 13 1_555 A DT 3 1_555 B A 12 1_555 -0.531 -0.815 3.294 -7.142 0.771 28.542 -1.774 -0.521 3.304 1.533 14.203 29.414 2 AA_DG2DT3:A12C13_BB A 2 ? B 13 ? A 3 ? B 12 ? 1 A DT 3 1_555 B A 12 1_555 A DC 4 1_555 B G 11 1_555 -0.303 -1.556 3.367 -0.808 4.387 35.647 -3.151 0.376 3.166 7.132 1.314 35.916 3 AA_DT3DC4:G11A12_BB A 3 ? B 12 ? A 4 ? B 11 ? 1 A DC 4 1_555 B G 11 1_555 A DT 5 1_555 B A 10 1_555 -1.070 -1.686 3.223 -3.984 7.760 23.261 -6.105 1.368 2.672 18.435 9.465 24.822 4 AA_DC4DT5:A10G11_BB A 4 ? B 11 ? A 5 ? B 10 ? 1 A DT 5 1_555 B A 10 1_555 A DC 6 1_555 B G 9 1_555 0.056 -1.398 3.195 -1.447 8.542 34.939 -3.393 -0.282 2.783 13.963 2.364 35.965 5 AA_DT5DC6:G9A10_BB A 5 ? B 10 ? A 6 ? B 9 ? 1 A DC 6 1_555 B G 9 1_555 A DC 7 1_555 B G 8 1_555 -0.105 -1.755 3.571 0.369 8.555 29.115 -5.108 0.276 2.946 16.571 -0.714 30.322 6 AA_DC6DC7:G8G9_BB A 6 ? B 9 ? A 7 ? B 8 ? 1 A DC 7 1_555 B G 8 1_555 A DA 8 1_555 B U 7 1_555 0.038 -1.524 3.013 -1.788 11.252 32.492 -4.067 -0.300 2.365 19.381 3.080 34.381 7 AA_DC7DA8:U7G8_BB A 7 ? B 8 ? A 8 ? B 7 ? 1 A DA 8 1_555 B U 7 1_555 A DG 9 1_555 B C 6 1_555 -0.170 -1.806 3.132 3.379 11.513 26.904 -5.645 0.947 2.158 23.328 -6.847 29.414 8 AA_DA8DG9:C6U7_BB A 8 ? B 7 ? A 9 ? B 6 ? 1 A DG 9 1_555 B C 6 1_555 A DG 10 1_555 B C 5 1_555 0.752 -2.111 3.498 2.053 12.147 30.882 -5.652 -0.986 2.552 21.757 -3.677 33.193 9 AA_DG9DG10:C5C6_BB A 9 ? B 6 ? A 10 ? B 5 ? 1 A DG 10 1_555 B C 5 1_555 A DC 11 1_555 B G 4 1_555 -0.937 -2.169 2.913 -2.213 0.184 26.052 -4.840 1.530 2.966 0.408 4.899 26.145 10 AA_DG10DC11:G4C5_BB A 10 ? B 5 ? A 11 ? B 4 ? 1 A DC 11 1_555 B G 4 1_555 A DA 12 1_555 B U 3 1_555 -0.045 -1.194 3.380 -1.320 10.419 33.524 -3.513 -0.119 2.891 17.536 2.221 35.086 11 AA_DC11DA12:U3G4_BB A 11 ? B 4 ? A 12 ? B 3 ? 1 A DA 12 1_555 B U 3 1_555 A DA 13 1_555 B U 2 1_555 -0.290 -0.902 3.098 -0.807 5.143 32.377 -2.419 0.385 2.930 9.149 1.435 32.782 12 AA_DA12DA13:U2U3_BB A 12 ? B 3 ? A 13 ? B 2 ? 1 A DA 13 1_555 B U 2 1_555 A DC 14 1_555 B G 1 1_555 0.472 -1.236 3.046 3.258 3.347 32.898 -2.678 -0.324 2.941 5.874 -5.716 33.219 13 AA_DA13DC14:G1U2_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 31 2 1' _space_group.name_Hall ;P 31 2" ; _space_group.IT_number 152 _space_group.crystal_system trigonal _space_group.id 1 # _atom_sites.entry_id 9VUO _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] 0.021445 _atom_sites.fract_transf_matrix[1][2] 0.012382 _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] 0.024763 _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] 0.010611 _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. ; ? H ? ? 0.51345 0.48472 ? ? 24.73122 6.32584 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 ? ? 15.80542 1.70748 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? S ? ? 9.55732 6.39887 ? ? 1.23737 29.19336 ? ? 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_ #