data_7BPF # _entry.id 7BPF # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 7BPF pdb_00007bpf 10.2210/pdb7bpf/pdb WWPDB D_1300016214 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2020-11-25 2 'Structure model' 1 1 2024-03-27 # _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 ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' atom_type 2 2 'Structure model' chem_comp_atom 3 2 'Structure model' chem_comp_bond 4 2 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_atom_type.pdbx_N_electrons' 2 2 'Structure model' '_atom_type.pdbx_scat_Z' 3 2 'Structure model' '_database_2.pdbx_DOI' 4 2 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7BPF _pdbx_database_status.recvd_initial_deposition_date 2020-03-22 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kamiya, Y.' 1 ? 'Satoh, T.' 2 ? 'Kodama, A.' 3 ? 'Suzuki, T.' 4 ? 'Uchiyama, S.' 5 ? 'Kato, K.' 6 ? 'Asanuma, H.' 7 ? # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Commun Chem' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2399-3669 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title ;Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA ; _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s42004-020-00400-2 _citation.pdbx_database_id_PubMed ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kamiya, Y.' 1 ? primary 'Satoh, T.' 2 ? primary 'Kodama, A.' 3 ? primary 'Suzuki, T.' 4 ? primary 'Murayama, K.' 5 ? primary 'Kashida, H.' 6 ? primary 'Uchiyama, S.' 7 ? primary 'Kato, K.' 8 ? primary 'Asanuma, H.' 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*CP*UP*GP*CP*(5BU)P*GP*C)-3') ; 2292.251 2 ? ? ? ? 2 polymer syn ;L-aTNA (3'-(*GP*CP*AP*GP*CP*AP*GP*C)-1') ; 2588.968 2 ? ? ? 'L-threoninol nucleic acid' 3 water nat water 18.015 21 ? ? ? ? # 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 yes 'GCUGC(5BU)G' GCUGCUG A,B ? 2 polydeoxyribonucleotide no yes '(F6X)(F73)(F6U)(F6X)(F73)(F6U)(F6X)(GT3)' XXXXXXXX C,D ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # 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 C n 1 3 U n 1 4 G n 1 5 C n 1 6 5BU n 1 7 G n 2 1 F6X n 2 2 F73 n 2 3 F6U n 2 4 F6X n 2 5 F73 n 2 6 F6U n 2 7 F6X n 2 8 GT3 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 7 'synthetic construct' ? 32630 ? 2 1 sample 1 8 'synthetic construct' ? 32630 ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 F6U 'DNA linking' . '[(2R,3R)-3-[2-(6-aminopurin-9-yl)ethanoylamino]-4-oxidanyl-butan-2-yl] dihydrogen phosphate' ? 'C11 H17 N6 O6 P' 360.263 F6X 'DNA linking' . '[(2R,3R)-3-[2-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)ethanoylamino]-4-oxidanyl-butan-2-yl] dihydrogen phosphate' ? 'C10 H17 N4 O7 P' 336.238 F73 'DNA linking' . '[(2R,3R)-3-[2-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)ethanoylamino]-4-oxidanyl-butan-2-yl] dihydrogen phosphate' ? 'C11 H17 N6 O7 P' 376.262 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GT3 non-polymer . '2-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-N-[(2R,3R)-1,3-bis(oxidanyl)butan-2-yl]ethanamide' ? 'C11 H16 N6 O4' 296.283 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 G 1 1 1 G G A . n A 1 2 C 2 2 2 C C 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 5BU 6 6 6 5BU 5BU A . n A 1 7 G 7 7 7 G G A . n B 1 1 G 1 1 1 G G B . n B 1 2 C 2 2 2 C C B . n B 1 3 U 3 3 3 U U B . n B 1 4 G 4 4 4 G G B . n B 1 5 C 5 5 5 C C B . n B 1 6 5BU 6 6 6 5BU 5BU B . n B 1 7 G 7 7 7 G G B . n C 2 1 F6X 1 101 101 F6X F8X C . n C 2 2 F73 2 102 102 F73 F73 C . n C 2 3 F6U 3 103 103 F6U F6U C . n C 2 4 F6X 4 104 104 F6X F6X C . n C 2 5 F73 5 105 105 F73 F73 C . n C 2 6 F6U 6 106 106 F6U F6U C . n C 2 7 F6X 7 107 107 F6X F6X C . n C 2 8 GT3 8 108 108 GT3 GT3 C . n D 2 1 F6X 1 101 101 F6X F8X D . n D 2 2 F73 2 102 102 F73 F73 D . n D 2 3 F6U 3 103 103 F6U F6U D . n D 2 4 F6X 4 104 104 F6X F6X D . n D 2 5 F73 5 105 105 F73 F73 D . n D 2 6 F6U 6 106 106 F6U F6U D . n D 2 7 F6X 7 107 107 F6X F6X D . n D 2 8 GT3 8 108 108 GT3 GT3 D . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 3 HOH 1 101 7 HOH HOH A . E 3 HOH 2 102 4 HOH HOH A . E 3 HOH 3 103 1 HOH HOH A . E 3 HOH 4 104 11 HOH HOH A . E 3 HOH 5 105 10 HOH HOH A . F 3 HOH 1 101 20 HOH HOH B . F 3 HOH 2 102 2 HOH HOH B . F 3 HOH 3 103 19 HOH HOH B . G 3 HOH 1 201 21 HOH HOH C . G 3 HOH 2 202 15 HOH HOH C . G 3 HOH 3 203 9 HOH HOH C . G 3 HOH 4 204 14 HOH HOH C . G 3 HOH 5 205 12 HOH HOH C . G 3 HOH 6 206 17 HOH HOH C . G 3 HOH 7 207 16 HOH HOH C . G 3 HOH 8 208 8 HOH HOH C . H 3 HOH 1 201 6 HOH HOH D . H 3 HOH 2 202 3 HOH HOH D . H 3 HOH 3 203 18 HOH HOH D . H 3 HOH 4 204 5 HOH HOH D . H 3 HOH 5 205 13 HOH HOH D . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0266 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? Aimless ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? AutoSol ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 115.64 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 7BPF _cell.details ? _cell.formula_units_Z ? _cell.length_a 52.996 _cell.length_a_esd ? _cell.length_b 33.344 _cell.length_b_esd ? _cell.length_c 54.055 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _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 ? # _symmetry.entry_id 7BPF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 1 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 7BPF _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 2.21 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 44.22 _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_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 7.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '28% PEG 400, 0.1M HEPES (pH 7.5), 0.2M Calcium chloride' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 95 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2019-05-13 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.90000 _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 'SPRING-8 BEAMLINE BL44XU' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.90000 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL44XU _diffrn_source.pdbx_synchrotron_site SPring-8 # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 7BPF _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.750 _reflns.d_resolution_low 28.500 _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 8609 _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 98.7 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 4.300 _reflns.pdbx_Rmerge_I_obs 0.06 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 13.900 _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 0.079 _reflns.pdbx_Rpim_I_all 0.051 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.989 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.75 _reflns_shell.d_res_low 1.78 _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 2064 _reflns_shell.percent_possible_all 99.1 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.307 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all 0.397 _reflns_shell.pdbx_Rpim_I_all 0.250 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.944 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] 0.74 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 4.67 _refine.aniso_B[2][2] -3.81 _refine.aniso_B[2][3] 0.00 _refine.aniso_B[3][3] -0.97 _refine.B_iso_max ? _refine.B_iso_mean 46.734 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.948 _refine.correlation_coeff_Fo_to_Fc_free 0.939 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _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 7BPF _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 1.75 _refine.ls_d_res_low 20.00 _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 8218 _refine.ls_number_reflns_R_free 383 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.4 _refine.ls_percent_reflns_R_free 4.5 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.270 _refine.ls_R_factor_R_free 0.288 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.269 _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 MASK _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.267 _refine.pdbx_overall_ESU_R_Free 0.147 _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _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 ? _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 12.841 _refine.overall_SU_ML 0.173 _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 1 _refine_hist.details ? _refine_hist.d_res_high 1.75 _refine_hist.d_res_low 20.00 _refine_hist.number_atoms_solvent 21 _refine_hist.number_atoms_total 671 _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 294 _refine_hist.pdbx_number_atoms_ligand 356 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.007 0.017 706 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.006 0.021 356 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 1.655 2.089 994 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 14.460 3.024 810 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_1_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_2_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_3_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_4_deg ? ? 'X-RAY DIFFRACTION' ? 0.081 0.200 74 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.004 0.020 390 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.001 0.020 110 ? r_gen_planes_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcbond_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcangle_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcangle_other ? ? 'X-RAY DIFFRACTION' ? 3.335 4.789 706 ? r_scbond_it ? ? 'X-RAY DIFFRACTION' ? 3.293 4.804 651 ? r_scbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_scangle_it ? ? 'X-RAY DIFFRACTION' ? 4.081 7.242 911 ? r_scangle_other ? ? 'X-RAY DIFFRACTION' ? 4.938 47.034 1097 ? r_long_range_B_refined ? ? 'X-RAY DIFFRACTION' ? 4.937 47.035 1097 ? r_long_range_B_other ? ? 'X-RAY DIFFRACTION' ? 1.244 3.000 1062 ? r_rigid_bond_restr ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_free ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.750 _refine_ls_shell.d_res_low 1.795 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 27 _refine_ls_shell.number_reflns_R_work 597 _refine_ls_shell.percent_reflns_obs 99.05 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.312 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.297 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_R_complete ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 7BPF _struct.title 'Structure of L-threoninol nucleic acid - RNA complex' _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 7BPF _struct_keywords.text 'Xeno nucleic acid, artificial nucleic acid, acyclic nucleic acid, L-threnoniol nucleic acid, RNA, RNA-NUCLEIC ACID complex' _struct_keywords.pdbx_keywords 'RNA/NUCLEIC ACID' # 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 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 3 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 7BPF 7BPF ? 1 ? 1 2 PDB 7BPF 7BPF ? 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 7BPF A 1 ? 7 ? 7BPF 1 ? 7 ? 1 7 2 1 7BPF B 1 ? 7 ? 7BPF 1 ? 7 ? 1 7 3 2 7BPF C 1 ? 8 ? 7BPF 101 ? 108 ? 101 108 4 2 7BPF D 1 ? 8 ? 7BPF 101 ? 108 ? 101 108 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C,E,G 2 1 B,D,F,H # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'mass spectrometry' _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A C 5 "O3'" ? ? ? 1_555 A 5BU 6 P ? ? A C 5 A 5BU 6 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale2 covale both ? A 5BU 6 "O3'" ? ? ? 1_555 A G 7 P ? ? A 5BU 6 A G 7 1_555 ? ? ? ? ? ? ? 1.591 ? ? covale3 covale both ? B C 5 "O3'" ? ? ? 1_555 B 5BU 6 P ? ? B C 5 B 5BU 6 1_555 ? ? ? ? ? ? ? 1.592 ? ? covale4 covale both ? B 5BU 6 "O3'" ? ? ? 1_555 B G 7 P ? ? B 5BU 6 B G 7 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale5 covale both ? C F6X 1 P ? ? ? 1_555 C F73 2 "O1'" ? ? C F6X 101 C F73 102 1_555 ? ? ? ? ? ? ? 1.508 ? ? covale6 covale both ? C F73 2 P ? ? ? 1_555 C F6U 3 "O1'" ? ? C F73 102 C F6U 103 1_555 ? ? ? ? ? ? ? 1.513 ? ? covale7 covale both ? C F6U 3 P ? ? ? 1_555 C F6X 4 "O1'" ? ? C F6U 103 C F6X 104 1_555 ? ? ? ? ? ? ? 1.519 ? ? covale8 covale both ? C F6X 4 P ? ? ? 1_555 C F73 5 "O1'" ? ? C F6X 104 C F73 105 1_555 ? ? ? ? ? ? ? 1.519 ? ? covale9 covale both ? C F73 5 P ? ? ? 1_555 C F6U 6 "O1'" ? ? C F73 105 C F6U 106 1_555 ? ? ? ? ? ? ? 1.520 ? ? covale10 covale both ? C F6U 6 P ? ? ? 1_555 C F6X 7 "O1'" ? ? C F6U 106 C F6X 107 1_555 ? ? ? ? ? ? ? 1.524 ? ? covale11 covale one ? C F6X 7 P ? ? ? 1_555 C GT3 8 "O1'" ? ? C F6X 107 C GT3 108 1_555 ? ? ? ? ? ? ? 1.526 ? ? covale12 covale both ? D F6X 1 P ? ? ? 1_555 D F73 2 "O1'" ? ? D F6X 101 D F73 102 1_555 ? ? ? ? ? ? ? 1.523 ? ? covale13 covale both ? D F73 2 P ? ? ? 1_555 D F6U 3 "O1'" ? ? D F73 102 D F6U 103 1_555 ? ? ? ? ? ? ? 1.521 ? ? covale14 covale both ? D F6U 3 P ? ? ? 1_555 D F6X 4 "O1'" ? ? D F6U 103 D F6X 104 1_555 ? ? ? ? ? ? ? 1.518 ? ? covale15 covale both ? D F6X 4 P ? ? ? 1_555 D F73 5 "O1'" ? ? D F6X 104 D F73 105 1_555 ? ? ? ? ? ? ? 1.517 ? ? covale16 covale both ? D F73 5 P ? ? ? 1_555 D F6U 6 "O1'" ? ? D F73 105 D F6U 106 1_555 ? ? ? ? ? ? ? 1.521 ? ? covale17 covale both ? D F6U 6 P ? ? ? 1_555 D F6X 7 "O1'" ? ? D F6U 106 D F6X 107 1_555 ? ? ? ? ? ? ? 1.517 ? ? covale18 covale one ? D F6X 7 P ? ? ? 1_555 D GT3 8 "O1'" ? ? D F6X 107 D GT3 108 1_555 ? ? ? ? ? ? ? 1.523 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 "O2'" _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 G _pdbx_validate_close_contact.auth_seq_id_1 7 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 "O2'" _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 G _pdbx_validate_close_contact.auth_seq_id_2 7 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.07 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id C _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 201 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id G _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_entry_details.entry_id 7BPF _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest N # 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 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 C OP3 O N N 35 C P P N N 36 C OP1 O N N 37 C OP2 O N N 38 C "O5'" O N N 39 C "C5'" C N N 40 C "C4'" C N R 41 C "O4'" O N N 42 C "C3'" C N S 43 C "O3'" O N N 44 C "C2'" C N R 45 C "O2'" O N N 46 C "C1'" C N R 47 C N1 N N N 48 C C2 C N N 49 C O2 O N N 50 C N3 N N N 51 C C4 C N N 52 C N4 N N N 53 C C5 C N N 54 C C6 C N N 55 C HOP3 H N N 56 C HOP2 H N N 57 C "H5'" H N N 58 C "H5''" H N N 59 C "H4'" H N N 60 C "H3'" H N N 61 C "HO3'" H N N 62 C "H2'" H N N 63 C "HO2'" H N N 64 C "H1'" H N N 65 C H41 H N N 66 C H42 H N N 67 C H5 H N N 68 C H6 H N N 69 F6U N1 N Y N 70 F6U C2 C Y N 71 F6U N3 N Y N 72 F6U C4 C Y N 73 F6U OP1 O N N 74 F6U P P N N 75 F6U OP2 O N N 76 F6U "O3'" O N N 77 F6U "C3'" C N R 78 F6U C3A C N N 79 F6U "C2'" C N R 80 F6U "C1'" C N N 81 F6U "O1'" O N N 82 F6U "N2'" N N N 83 F6U C2A C N N 84 F6U O2A O N N 85 F6U C2B C N N 86 F6U N9 N Y N 87 F6U C8 C Y N 88 F6U N7 N Y N 89 F6U C5 C Y N 90 F6U C6 C Y N 91 F6U N6 N N N 92 F6U H1 H N N 93 F6U HOP2 H N N 94 F6U H4 H N N 95 F6U H5 H N N 96 F6U H6 H N N 97 F6U H7 H N N 98 F6U H8 H N N 99 F6U H9 H N N 100 F6U H10 H N N 101 F6U H11 H N N 102 F6U H12 H N N 103 F6U H13 H N N 104 F6U H14 H N N 105 F6U H15 H N N 106 F6U H16 H N N 107 F6U H17 H N N 108 F6U OP3 O N N 109 F6U HOP3 H N N 110 F6X "C1'" C N N 111 F6X N1 N N N 112 F6X C6 C N N 113 F6X C5 C N N 114 F6X C4 C N N 115 F6X N3 N N N 116 F6X C2 C N N 117 F6X O2 O N N 118 F6X N4 N N N 119 F6X "C2'" C N R 120 F6X "C3'" C N R 121 F6X "O3'" O N N 122 F6X OP1 O N N 123 F6X P P N N 124 F6X OP2 O N N 125 F6X C3A C N N 126 F6X "O1'" O N N 127 F6X "N2'" N N N 128 F6X C2A C N N 129 F6X O2A O N N 130 F6X C2B C N N 131 F6X H1 H N N 132 F6X H2 H N N 133 F6X H3 H N N 134 F6X H4 H N N 135 F6X H5 H N N 136 F6X H6 H N N 137 F6X H7 H N N 138 F6X H8 H N N 139 F6X HOP2 H N N 140 F6X H11 H N N 141 F6X H12 H N N 142 F6X H13 H N N 143 F6X H14 H N N 144 F6X H15 H N N 145 F6X H16 H N N 146 F6X H17 H N N 147 F6X OP3 O N N 148 F6X HOP3 H N N 149 F73 O2A O N N 150 F73 "C3'" C N R 151 F73 "O3'" O N N 152 F73 "C2'" C N R 153 F73 "C1'" C N N 154 F73 N9 N Y N 155 F73 C8 C Y N 156 F73 N7 N Y N 157 F73 C5 C Y N 158 F73 C6 C N N 159 F73 O6 O N N 160 F73 N1 N N N 161 F73 C2 C N N 162 F73 N2 N N N 163 F73 N3 N N N 164 F73 C4 C Y N 165 F73 OP2 O N N 166 F73 P P N N 167 F73 OP1 O N N 168 F73 C3A C N N 169 F73 "O1'" O N N 170 F73 "N2'" N N N 171 F73 C2A C N N 172 F73 C2B C N N 173 F73 H1 H N N 174 F73 H2 H N N 175 F73 H3 H N N 176 F73 H4 H N N 177 F73 H5 H N N 178 F73 H6 H N N 179 F73 H7 H N N 180 F73 H8 H N N 181 F73 HOP2 H N N 182 F73 H11 H N N 183 F73 H12 H N N 184 F73 H13 H N N 185 F73 H14 H N N 186 F73 H15 H N N 187 F73 H16 H N N 188 F73 H17 H N N 189 F73 OP3 O N N 190 F73 HOP3 H N N 191 G OP3 O N N 192 G P P N N 193 G OP1 O N N 194 G OP2 O N N 195 G "O5'" O N N 196 G "C5'" C N N 197 G "C4'" C N R 198 G "O4'" O N N 199 G "C3'" C N S 200 G "O3'" O N N 201 G "C2'" C N R 202 G "O2'" O N N 203 G "C1'" C N R 204 G N9 N Y N 205 G C8 C Y N 206 G N7 N Y N 207 G C5 C Y N 208 G C6 C N N 209 G O6 O N N 210 G N1 N N N 211 G C2 C N N 212 G N2 N N N 213 G N3 N N N 214 G C4 C Y N 215 G HOP3 H N N 216 G HOP2 H N N 217 G "H5'" H N N 218 G "H5''" H N N 219 G "H4'" H N N 220 G "H3'" H N N 221 G "HO3'" H N N 222 G "H2'" H N N 223 G "HO2'" H N N 224 G "H1'" H N N 225 G H8 H N N 226 G H1 H N N 227 G H21 H N N 228 G H22 H N N 229 GT3 O6 O N N 230 GT3 C6 C N N 231 GT3 N1 N N N 232 GT3 C2 C N N 233 GT3 N2 N N N 234 GT3 N3 N N N 235 GT3 C4 C Y N 236 GT3 C5 C Y N 237 GT3 N7 N Y N 238 GT3 C8 C Y N 239 GT3 N9 N Y N 240 GT3 C2B C N N 241 GT3 C2A C N N 242 GT3 O2A O N N 243 GT3 "N2'" N N N 244 GT3 "C2'" C N R 245 GT3 "C3'" C N R 246 GT3 C3A C N N 247 GT3 "O3'" O N N 248 GT3 "C1'" C N N 249 GT3 "O1'" O N N 250 GT3 H1 H N N 251 GT3 H2 H N N 252 GT3 H3 H N N 253 GT3 H4 H N N 254 GT3 H5 H N N 255 GT3 H6 H N N 256 GT3 H7 H N N 257 GT3 H8 H N N 258 GT3 H9 H N N 259 GT3 H10 H N N 260 GT3 H11 H N N 261 GT3 H12 H N N 262 GT3 H13 H N N 263 GT3 H14 H N N 264 GT3 H15 H N N 265 GT3 H16 H N N 266 HOH O O N N 267 HOH H1 H N N 268 HOH H2 H N N 269 U OP3 O N N 270 U P P N N 271 U OP1 O N N 272 U OP2 O N N 273 U "O5'" O N N 274 U "C5'" C N N 275 U "C4'" C N R 276 U "O4'" O N N 277 U "C3'" C N S 278 U "O3'" O N N 279 U "C2'" C N R 280 U "O2'" O N N 281 U "C1'" C N R 282 U N1 N N N 283 U C2 C N N 284 U O2 O N N 285 U N3 N N N 286 U C4 C N N 287 U O4 O N N 288 U C5 C N N 289 U C6 C N N 290 U HOP3 H N N 291 U HOP2 H N N 292 U "H5'" H N N 293 U "H5''" H N N 294 U "H4'" H N N 295 U "H3'" H N N 296 U "HO3'" H N N 297 U "H2'" H N N 298 U "HO2'" H N N 299 U "H1'" H N N 300 U H3 H N N 301 U H5 H N N 302 U H6 H N N 303 # 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 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 C OP3 P sing N N 36 C OP3 HOP3 sing N N 37 C P OP1 doub N N 38 C P OP2 sing N N 39 C P "O5'" sing N N 40 C OP2 HOP2 sing N N 41 C "O5'" "C5'" sing N N 42 C "C5'" "C4'" sing N N 43 C "C5'" "H5'" sing N N 44 C "C5'" "H5''" sing N N 45 C "C4'" "O4'" sing N N 46 C "C4'" "C3'" sing N N 47 C "C4'" "H4'" sing N N 48 C "O4'" "C1'" sing N N 49 C "C3'" "O3'" sing N N 50 C "C3'" "C2'" sing N N 51 C "C3'" "H3'" sing N N 52 C "O3'" "HO3'" sing N N 53 C "C2'" "O2'" sing N N 54 C "C2'" "C1'" sing N N 55 C "C2'" "H2'" sing N N 56 C "O2'" "HO2'" sing N N 57 C "C1'" N1 sing N N 58 C "C1'" "H1'" sing N N 59 C N1 C2 sing N N 60 C N1 C6 sing N N 61 C C2 O2 doub N N 62 C C2 N3 sing N N 63 C N3 C4 doub N N 64 C C4 N4 sing N N 65 C C4 C5 sing N N 66 C N4 H41 sing N N 67 C N4 H42 sing N N 68 C C5 C6 doub N N 69 C C5 H5 sing N N 70 C C6 H6 sing N N 71 F6U OP2 P sing N N 72 F6U P OP1 doub N N 73 F6U P "O3'" sing N N 74 F6U "O3'" "C3'" sing N N 75 F6U "C3'" C3A sing N N 76 F6U "C3'" "C2'" sing N N 77 F6U "C1'" "O1'" sing N N 78 F6U "C1'" "C2'" sing N N 79 F6U "N2'" "C2'" sing N N 80 F6U "N2'" C2A sing N N 81 F6U C2B C2A sing N N 82 F6U C2B N9 sing N N 83 F6U C2A O2A doub N N 84 F6U N9 C8 sing Y N 85 F6U N9 C4 sing Y N 86 F6U C8 N7 doub Y N 87 F6U C4 N3 sing Y N 88 F6U C4 C5 doub Y N 89 F6U N7 C5 sing Y N 90 F6U N3 C2 doub Y N 91 F6U C5 C6 sing Y N 92 F6U C2 N1 sing Y N 93 F6U C6 N1 doub Y N 94 F6U C6 N6 sing N N 95 F6U C2 H1 sing N N 96 F6U OP2 HOP2 sing N N 97 F6U "C3'" H4 sing N N 98 F6U C3A H5 sing N N 99 F6U C3A H6 sing N N 100 F6U C3A H7 sing N N 101 F6U "C2'" H8 sing N N 102 F6U "C1'" H9 sing N N 103 F6U "C1'" H10 sing N N 104 F6U "O1'" H11 sing N N 105 F6U "N2'" H12 sing N N 106 F6U C2B H13 sing N N 107 F6U C2B H14 sing N N 108 F6U C8 H15 sing N N 109 F6U N6 H16 sing N N 110 F6U N6 H17 sing N N 111 F6U P OP3 sing N N 112 F6U OP3 HOP3 sing N N 113 F6X OP2 P sing N N 114 F6X OP1 P doub N N 115 F6X P "O3'" sing N N 116 F6X C3A "C3'" sing N N 117 F6X "O3'" "C3'" sing N N 118 F6X C5 C6 doub N N 119 F6X C5 C4 sing N N 120 F6X C6 N1 sing N N 121 F6X "C3'" "C2'" sing N N 122 F6X C2B N1 sing N N 123 F6X C2B C2A sing N N 124 F6X "N2'" "C2'" sing N N 125 F6X "N2'" C2A sing N N 126 F6X N1 C2 sing N N 127 F6X C4 N4 sing N N 128 F6X C4 N3 doub N N 129 F6X "C2'" "C1'" sing N N 130 F6X C2A O2A doub N N 131 F6X C2 N3 sing N N 132 F6X C2 O2 doub N N 133 F6X "C1'" "O1'" sing N N 134 F6X "C1'" H1 sing N N 135 F6X "C1'" H2 sing N N 136 F6X C6 H3 sing N N 137 F6X C5 H4 sing N N 138 F6X N4 H5 sing N N 139 F6X N4 H6 sing N N 140 F6X "C2'" H7 sing N N 141 F6X "C3'" H8 sing N N 142 F6X OP2 HOP2 sing N N 143 F6X C3A H11 sing N N 144 F6X C3A H12 sing N N 145 F6X C3A H13 sing N N 146 F6X "O1'" H14 sing N N 147 F6X "N2'" H15 sing N N 148 F6X C2B H16 sing N N 149 F6X C2B H17 sing N N 150 F6X P OP3 sing N N 151 F6X OP3 HOP3 sing N N 152 F73 OP2 P sing N N 153 F73 P OP1 doub N N 154 F73 P "O3'" sing N N 155 F73 "O3'" "C3'" sing N N 156 F73 C3A "C3'" sing N N 157 F73 "C3'" "C2'" sing N N 158 F73 "N2'" "C2'" sing N N 159 F73 "N2'" C2A sing N N 160 F73 "C2'" "C1'" sing N N 161 F73 C2B C2A sing N N 162 F73 C2B N9 sing N N 163 F73 "C1'" "O1'" sing N N 164 F73 C8 N9 sing Y N 165 F73 C8 N7 doub Y N 166 F73 C2A O2A doub N N 167 F73 N9 C4 sing Y N 168 F73 N7 C5 sing Y N 169 F73 C4 C5 doub Y N 170 F73 C4 N3 sing N N 171 F73 C5 C6 sing N N 172 F73 N3 C2 doub N N 173 F73 C6 O6 doub N N 174 F73 C6 N1 sing N N 175 F73 C2 N1 sing N N 176 F73 C2 N2 sing N N 177 F73 "C3'" H1 sing N N 178 F73 "C2'" H2 sing N N 179 F73 "C1'" H3 sing N N 180 F73 "C1'" H4 sing N N 181 F73 C8 H5 sing N N 182 F73 N1 H6 sing N N 183 F73 N2 H7 sing N N 184 F73 N2 H8 sing N N 185 F73 OP2 HOP2 sing N N 186 F73 C3A H11 sing N N 187 F73 C3A H12 sing N N 188 F73 C3A H13 sing N N 189 F73 "O1'" H14 sing N N 190 F73 "N2'" H15 sing N N 191 F73 C2B H16 sing N N 192 F73 C2B H17 sing N N 193 F73 P OP3 sing N N 194 F73 OP3 HOP3 sing N N 195 G OP3 P sing N N 196 G OP3 HOP3 sing N N 197 G P OP1 doub N N 198 G P OP2 sing N N 199 G P "O5'" sing N N 200 G OP2 HOP2 sing N N 201 G "O5'" "C5'" sing N N 202 G "C5'" "C4'" sing N N 203 G "C5'" "H5'" sing N N 204 G "C5'" "H5''" sing N N 205 G "C4'" "O4'" sing N N 206 G "C4'" "C3'" sing N N 207 G "C4'" "H4'" sing N N 208 G "O4'" "C1'" sing N N 209 G "C3'" "O3'" sing N N 210 G "C3'" "C2'" sing N N 211 G "C3'" "H3'" sing N N 212 G "O3'" "HO3'" sing N N 213 G "C2'" "O2'" sing N N 214 G "C2'" "C1'" sing N N 215 G "C2'" "H2'" sing N N 216 G "O2'" "HO2'" sing N N 217 G "C1'" N9 sing N N 218 G "C1'" "H1'" sing N N 219 G N9 C8 sing Y N 220 G N9 C4 sing Y N 221 G C8 N7 doub Y N 222 G C8 H8 sing N N 223 G N7 C5 sing Y N 224 G C5 C6 sing N N 225 G C5 C4 doub Y N 226 G C6 O6 doub N N 227 G C6 N1 sing N N 228 G N1 C2 sing N N 229 G N1 H1 sing N N 230 G C2 N2 sing N N 231 G C2 N3 doub N N 232 G N2 H21 sing N N 233 G N2 H22 sing N N 234 G N3 C4 sing N N 235 GT3 N2 C2 sing N N 236 GT3 "O1'" "C1'" sing N N 237 GT3 "C1'" "C2'" sing N N 238 GT3 C2 N3 doub N N 239 GT3 C2 N1 sing N N 240 GT3 N3 C4 sing N N 241 GT3 N1 C6 sing N N 242 GT3 "N2'" "C2'" sing N N 243 GT3 "N2'" C2A sing N N 244 GT3 "C2'" "C3'" sing N N 245 GT3 C4 N9 sing Y N 246 GT3 C4 C5 doub Y N 247 GT3 C2B C2A sing N N 248 GT3 C2B N9 sing N N 249 GT3 C2A O2A doub N N 250 GT3 C6 C5 sing N N 251 GT3 C6 O6 doub N N 252 GT3 N9 C8 sing Y N 253 GT3 C5 N7 sing Y N 254 GT3 "C3'" "O3'" sing N N 255 GT3 "C3'" C3A sing N N 256 GT3 C8 N7 doub Y N 257 GT3 N1 H1 sing N N 258 GT3 N2 H2 sing N N 259 GT3 N2 H3 sing N N 260 GT3 C8 H4 sing N N 261 GT3 C2B H5 sing N N 262 GT3 C2B H6 sing N N 263 GT3 "N2'" H7 sing N N 264 GT3 "C2'" H8 sing N N 265 GT3 "C3'" H9 sing N N 266 GT3 C3A H10 sing N N 267 GT3 C3A H11 sing N N 268 GT3 C3A H12 sing N N 269 GT3 "O3'" H13 sing N N 270 GT3 "C1'" H14 sing N N 271 GT3 "C1'" H15 sing N N 272 GT3 "O1'" H16 sing N N 273 HOH O H1 sing N N 274 HOH O H2 sing N N 275 U OP3 P sing N N 276 U OP3 HOP3 sing N N 277 U P OP1 doub N N 278 U P OP2 sing N N 279 U P "O5'" sing N N 280 U OP2 HOP2 sing N N 281 U "O5'" "C5'" sing N N 282 U "C5'" "C4'" sing N N 283 U "C5'" "H5'" sing N N 284 U "C5'" "H5''" sing N N 285 U "C4'" "O4'" sing N N 286 U "C4'" "C3'" sing N N 287 U "C4'" "H4'" sing N N 288 U "O4'" "C1'" sing N N 289 U "C3'" "O3'" sing N N 290 U "C3'" "C2'" sing N N 291 U "C3'" "H3'" sing N N 292 U "O3'" "HO3'" sing N N 293 U "C2'" "O2'" sing N N 294 U "C2'" "C1'" sing N N 295 U "C2'" "H2'" sing N N 296 U "O2'" "HO2'" sing N N 297 U "C1'" N1 sing N N 298 U "C1'" "H1'" sing N N 299 U N1 C2 sing N N 300 U N1 C6 sing N N 301 U C2 O2 doub N N 302 U C2 N3 sing N N 303 U N3 C4 sing N N 304 U N3 H3 sing N N 305 U C4 O4 doub N N 306 U C4 C5 sing N N 307 U C5 C6 doub N N 308 U C5 H5 sing N N 309 U C6 H6 sing N N 310 # _pdbx_audit_support.funding_organization 'Japan Agency for Medical Research and Development (AMED)' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 7BPF _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.018869 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.009059 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.029990 _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] 0.020521 _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.pdbx_scat_Z _atom_type.pdbx_N_electrons _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c BR 35 35 17.182 2.172 5.237 16.580 5.639 0.261 3.986 41.433 -0.162 C 6 6 2.310 20.844 1.020 10.208 1.589 0.569 0.865 51.651 0.216 H 1 1 0.493 10.511 0.323 26.126 0.140 3.142 0.041 57.800 0.003 N 7 7 12.222 0.006 3.135 9.893 2.014 28.997 1.167 0.583 -11.538 O 8 8 3.049 13.277 2.287 5.701 1.546 0.324 0.867 32.909 0.251 P 15 15 6.435 1.907 4.179 27.157 1.780 0.526 1.491 68.164 1.247 # loop_