data_7TD7 # _entry.id 7TD7 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 7TD7 pdb_00007td7 10.2210/pdb7td7/pdb WWPDB D_1000262080 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7TD7 _pdbx_database_status.recvd_initial_deposition_date 2021-12-30 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Nuthanakanti, A.' 1 0000-0003-0105-3430 'Serganov, A.' 2 0000-0001-8328-9310 # _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 'Acs Chem.Biol.' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1554-8937 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 17 _citation.language ? _citation.page_first 438 _citation.page_last 448 _citation.title 'Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acschembio.1c00880 _citation.pdbx_database_id_PubMed 35060698 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zeller, M.J.' 1 ? primary 'Nuthanakanti, A.' 2 ? primary 'Li, K.' 3 ? primary 'Aube, J.' 4 ? primary 'Serganov, A.' 5 ? primary 'Weeks, K.M.' 6 ? # _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 7TD7 _cell.details ? _cell.formula_units_Z ? _cell.length_a 61.110 _cell.length_a_esd ? _cell.length_b 61.110 _cell.length_b_esd ? _cell.length_c 103.416 _cell.length_c_esd ? _cell.volume 334459.037 _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 ? # _symmetry.entry_id 7TD7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 153 _symmetry.space_group_name_Hall 'P 32 2 (x,y,z+1/6)' _symmetry.space_group_name_H-M 'P 32 1 2' _symmetry.pdbx_full_space_group_name_H-M ? # 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 'thiM riboswitch RNA (78-MER)' 26798.936 1 ? ? ? ? 2 non-polymer syn 'MANGANESE (II) ION' 54.938 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 4 non-polymer syn '3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM' 265.355 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;GCGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUC GCA ; _entity_poly.pdbx_seq_one_letter_code_can ;GCGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUC GCA ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # 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 G n 1 4 A n 1 5 C n 1 6 U n 1 7 C n 1 8 G n 1 9 G n 1 10 G n 1 11 G n 1 12 U n 1 13 G n 1 14 C n 1 15 C n 1 16 C n 1 17 U n 1 18 U n 1 19 C n 1 20 U n 1 21 G n 1 22 C n 1 23 G n 1 24 U n 1 25 G n 1 26 A n 1 27 A n 1 28 G n 1 29 G n 1 30 C n 1 31 U n 1 32 G n 1 33 A n 1 34 G n 1 35 A n 1 36 A n 1 37 A n 1 38 U n 1 39 A n 1 40 C n 1 41 C n 1 42 C n 1 43 G n 1 44 U n 1 45 A n 1 46 U n 1 47 C n 1 48 A n 1 49 C n 1 50 C n 1 51 U n 1 52 G n 1 53 A n 1 54 U n 1 55 C n 1 56 U n 1 57 G n 1 58 G n 1 59 A n 1 60 U n 1 61 A n 1 62 A n 1 63 U n 1 64 G n 1 65 C n 1 66 C n 1 67 A n 1 68 G n 1 69 C n 1 70 G n 1 71 U n 1 72 A n 1 73 G n 1 74 G n 1 75 G n 1 76 A n 1 77 A n 1 78 G n 1 79 U n 1 80 C n 1 81 G n 1 82 C n 1 83 A n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 83 _pdbx_entity_src_syn.organism_scientific 'Escherichia coli' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 562 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7TD7 _struct_ref.pdbx_db_accession 7TD7 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7TD7 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 83 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7TD7 _struct_ref_seq.db_align_beg 9 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 91 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 9 _struct_ref_seq.pdbx_auth_seq_align_end 91 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 VIB non-polymer . '3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM' 'THIAMIN; VITAMIN B1' 'C12 H17 N4 O S 1' 265.355 # _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 7TD7 _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 2.08 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 40.87 _exptl_crystal.description 'Rod-shaped crystals' _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, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;RNA (0.15 mM) was incubated in a buffer containing 5 mM Tris-HCl, pH 8.0, 3 mM MgCl2, 10 mM NaCl, 0.1 M KCl, and 0.5 mM spermine with 1.0 mM of thiamine. the reservoir solution was 50 mM Bis-Tris HCl, pH 6.5, 0.5 M NH4Cl, 10 mm MnCl2, and 30% (v/v) PEG2000 ; _exptl_crystal_grow.pdbx_pH_range 6.0-6.5 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2021-02-01 _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 0.9793 _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 'NSLS-II BEAMLINE 17-ID-2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9793 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 17-ID-2 _diffrn_source.pdbx_synchrotron_site NSLS-II # _reflns.B_iso_Wilson_estimate 89.44 _reflns.entry_id 7TD7 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.95 _reflns.d_resolution_low 30.0 _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 4766 _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 98.8 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 8.4 _reflns.pdbx_Rmerge_I_obs 0.111 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 47.6 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all 0.043 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.985 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # _reflns_shell.d_res_high 2.95 _reflns_shell.d_res_low 3.06 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.6 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 445 _reflns_shell.percent_possible_all 93.3 _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 0.555 _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 5.3 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all 0.237 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.933 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.pdbx_percent_possible_ellipsoidal ? _reflns_shell.pdbx_percent_possible_spherical ? _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns_shell.pdbx_percent_possible_spherical_anomalous ? _reflns_shell.pdbx_redundancy_anomalous ? _reflns_shell.pdbx_CC_half_anomalous ? _reflns_shell.pdbx_absDiff_over_sigma_anomalous ? _reflns_shell.pdbx_percent_possible_anomalous ? # _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 110.00 _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 7TD7 _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 2.95 _refine.ls_d_res_low 29.30 _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 4766 _refine.ls_number_reflns_R_free 857 _refine.ls_number_reflns_R_work 7875 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 96.37 _refine.ls_percent_reflns_R_free 9.81 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2353 _refine.ls_R_factor_R_free 0.2856 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2296 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.38 _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 2HOJ _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 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 41.5488 _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 0.3703 _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 2.95 _refine_hist.d_res_low 29.30 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1615 _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 1594 _refine_hist.pdbx_number_atoms_ligand 21 _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' ? 0.0051 ? 1800 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.0756 ? 2799 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0515 ? 369 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0074 ? 75 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 16.5773 ? 888 ? 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 _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.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.95 3.14 . . 124 1195 88.05 . . . 0.4200 . 0.3235 . . . . . . . . . . . 'X-RAY DIFFRACTION' 3.14 3.38 . . 152 1325 97.81 . . . 0.2829 . 0.2769 . . . . . . . . . . . 'X-RAY DIFFRACTION' 3.38 3.72 . . 144 1328 97.74 . . . 0.3421 . 0.2092 . . . . . . . . . . . 'X-RAY DIFFRACTION' 3.72 4.26 . . 146 1348 98.42 . . . 0.2492 . 0.2680 . . . . . . . . . . . 'X-RAY DIFFRACTION' 4.26 5.36 . . 147 1338 98.61 . . . 0.2504 . 0.2462 . . . . . . . . . . . 'X-RAY DIFFRACTION' 5.37 29.30 . . 144 1341 97.76 . . . 0.2926 . 0.1942 . . . . . . . . . . . # _struct.entry_id 7TD7 _struct.title 'Crystal structure of an E. coli thiM riboswitch bound to thiamine, manganese ions' _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 7TD7 _struct_keywords.text RNA _struct_keywords.pdbx_keywords RNA # 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 3 ? E N N 4 ? # 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 metalc1 metalc ? ? A A 27 OP2 ? ? ? 1_555 D MG . MG ? ? A A 35 A MG 103 1_555 ? ? ? ? ? ? ? 2.665 ? ? metalc2 metalc ? ? A A 33 N7 ? ? ? 1_555 B MN . MN ? ? A A 41 A MN 101 1_555 ? ? ? ? ? ? ? 1.784 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 82 N3 ? ? A G 9 A C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 82 O2 ? ? A G 9 A C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 82 N4 ? ? A G 9 A C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 81 N1 ? ? A C 10 A G 89 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 81 O6 ? ? A C 10 A G 89 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 81 N2 ? ? A C 10 A G 89 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 80 N3 ? ? A G 11 A C 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 80 O2 ? ? A G 11 A C 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 80 N4 ? ? A G 11 A C 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 79 N3 ? ? A A 12 A U 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 A U 79 O4 ? ? A A 12 A U 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 78 N1 ? ? A C 13 A G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 78 O6 ? ? A C 13 A G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 78 N2 ? ? A C 13 A G 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 77 N1 ? ? A U 14 A A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 77 N6 ? ? A U 14 A A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 43 N1 ? ? A C 15 A G 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 43 O6 ? ? A C 15 A G 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 43 N2 ? ? A C 15 A G 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 42 N3 ? ? A G 16 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 42 O2 ? ? A G 16 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 42 N4 ? ? A G 16 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 8 N2 ? ? ? 1_555 A A 76 N3 ? ? A G 16 A A 84 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog24 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 41 N3 ? ? A G 17 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 41 O2 ? ? A G 17 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 41 N4 ? ? A G 17 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 9 N2 ? ? ? 1_555 A A 48 N3 ? ? A G 17 A A 56 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog28 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 40 N3 ? ? A G 18 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 40 O2 ? ? A G 18 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 40 N4 ? ? A G 18 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 11 N2 ? ? ? 1_555 A G 34 N3 ? ? A G 19 A G 42 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog32 hydrog ? ? A G 11 N3 ? ? ? 1_555 A G 34 N2 ? ? A G 19 A G 42 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog33 hydrog ? ? A G 11 N1 ? ? ? 1_555 A A 39 N1 ? ? A G 19 A A 47 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog34 hydrog ? ? A G 11 O6 ? ? ? 1_555 A A 39 N6 ? ? A G 19 A A 47 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog35 hydrog ? ? A U 12 N3 ? ? ? 1_555 A A 37 N1 ? ? A U 20 A A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A U 12 O4 ? ? ? 1_555 A A 37 N6 ? ? A U 20 A A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 13 N1 ? ? ? 1_555 A C 30 N3 ? ? A G 21 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 13 N2 ? ? ? 1_555 A C 30 O2 ? ? A G 21 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 13 O6 ? ? ? 1_555 A C 30 N4 ? ? A G 21 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 13 N2 ? ? ? 1_555 A U 63 O2 ? ? A G 21 A U 71 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog41 hydrog ? ? A C 14 N3 ? ? ? 1_555 A G 29 N1 ? ? A C 22 A G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 14 N4 ? ? ? 1_555 A G 29 O6 ? ? A C 22 A G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 14 O2 ? ? ? 1_555 A G 29 N2 ? ? A C 22 A G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 28 N1 ? ? A C 23 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 28 O6 ? ? A C 23 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 28 N2 ? ? A C 23 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 16 N3 ? ? ? 1_555 A A 27 N6 ? ? A C 24 A A 35 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog48 hydrog ? ? A G 29 N2 ? ? ? 1_555 A A 61 N1 ? ? A G 37 A A 69 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog49 hydrog ? ? A U 31 N3 ? ? ? 1_555 A A 35 N7 ? ? A U 39 A A 43 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog50 hydrog ? ? A U 31 O2 ? ? ? 1_555 A A 35 N6 ? ? A U 39 A A 43 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog51 hydrog ? ? A A 45 N7 ? ? ? 1_555 A A 76 N6 ? ? A A 53 A A 84 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog52 hydrog ? ? A A 48 N6 ? ? ? 1_555 A G 75 N3 ? ? A A 56 A G 83 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog53 hydrog ? ? A A 48 N7 ? ? ? 1_555 A G 75 N2 ? ? A A 56 A G 83 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog54 hydrog ? ? A C 49 N3 ? ? ? 1_555 A G 74 N1 ? ? A C 57 A G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A C 49 N4 ? ? ? 1_555 A G 74 O6 ? ? A C 57 A G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A C 49 O2 ? ? ? 1_555 A G 74 N2 ? ? A C 57 A G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A C 50 N3 ? ? ? 1_555 A G 73 N1 ? ? A C 58 A G 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A C 50 N4 ? ? ? 1_555 A G 73 O6 ? ? A C 58 A G 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A C 50 O2 ? ? ? 1_555 A G 73 N2 ? ? A C 58 A G 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A U 51 N3 ? ? ? 1_555 A A 72 N1 ? ? A U 59 A A 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A U 51 O4 ? ? ? 1_555 A A 72 N6 ? ? A U 59 A A 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A G 52 O6 ? ? ? 1_555 A G 64 N1 ? ? A G 60 A G 72 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog63 hydrog ? ? A G 52 N1 ? ? ? 1_555 A G 70 O6 ? ? A G 60 A G 78 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog64 hydrog ? ? A G 52 N2 ? ? ? 1_555 A G 70 N7 ? ? A G 60 A G 78 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog65 hydrog ? ? A A 53 N1 ? ? ? 1_555 A G 64 N2 ? ? A A 61 A G 72 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog66 hydrog ? ? A C 55 N3 ? ? ? 1_555 A G 68 N1 ? ? A C 63 A G 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A C 55 N4 ? ? ? 1_555 A G 68 O6 ? ? A C 63 A G 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A C 55 O2 ? ? ? 1_555 A G 68 N2 ? ? A C 63 A G 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? A U 56 N3 ? ? ? 1_555 A A 67 N1 ? ? A U 64 A A 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? A U 56 O4 ? ? ? 1_555 A A 67 N6 ? ? A U 64 A A 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? A G 57 N1 ? ? ? 1_555 A C 66 N3 ? ? A G 65 A C 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? A G 57 N2 ? ? ? 1_555 A C 66 O2 ? ? A G 65 A C 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? A G 57 O6 ? ? ? 1_555 A C 66 N4 ? ? A G 65 A C 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? A G 58 N1 ? ? ? 1_555 A C 65 N3 ? ? A G 66 A C 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? A G 58 N2 ? ? ? 1_555 A C 65 O2 ? ? A G 66 A C 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? A G 58 O6 ? ? ? 1_555 A C 65 N4 ? ? A G 66 A C 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # _atom_sites.entry_id 7TD7 _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] 0.016364 _atom_sites.fract_transf_matrix[1][2] 0.009448 _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] 0.018895 _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] 0.009670 _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. ; ? MG ? ? 9.41153 2.53737 ? ? 2.59044 63.03566 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? MN ? ? 20.23591 4.67902 ? ? 2.76514 44.01191 ? ? 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 ? ? 6.96715 ? ? ? 11.43723 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 7.96527 ? ? ? 9.05267 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 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_ _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 9 9 G G A . n A 1 2 C 2 10 10 C C A . n A 1 3 G 3 11 11 G G A . n A 1 4 A 4 12 12 A A A . n A 1 5 C 5 13 13 C C A . n A 1 6 U 6 14 14 U U A . n A 1 7 C 7 15 15 C C A . n A 1 8 G 8 16 16 G G A . n A 1 9 G 9 17 17 G G A . n A 1 10 G 10 18 18 G G A . n A 1 11 G 11 19 19 G G A . n A 1 12 U 12 20 20 U U A . n A 1 13 G 13 21 21 G G A . n A 1 14 C 14 22 22 C C A . n A 1 15 C 15 23 23 C C A . n A 1 16 C 16 24 24 C C A . n A 1 17 U 17 25 ? ? ? A . n A 1 18 U 18 26 ? ? ? A . n A 1 19 C 19 27 ? ? ? A . n A 1 20 U 20 28 ? ? ? A . n A 1 21 G 21 29 ? ? ? A . n A 1 22 C 22 30 30 C C A . n A 1 23 G 23 31 31 G G A . n A 1 24 U 24 32 32 U U A . n A 1 25 G 25 33 33 G G A . n A 1 26 A 26 34 34 A A A . n A 1 27 A 27 35 35 A A A . n A 1 28 G 28 36 36 G G A . n A 1 29 G 29 37 37 G G A . n A 1 30 C 30 38 38 C C A . n A 1 31 U 31 39 39 U U A . n A 1 32 G 32 40 40 G G A . n A 1 33 A 33 41 41 A A A . n A 1 34 G 34 42 42 G G A . n A 1 35 A 35 43 43 A A A . n A 1 36 A 36 44 44 A A A . n A 1 37 A 37 45 45 A A A . n A 1 38 U 38 46 46 U U A . n A 1 39 A 39 47 47 A A A . n A 1 40 C 40 48 48 C C A . n A 1 41 C 41 49 49 C C A . n A 1 42 C 42 50 50 C C A . n A 1 43 G 43 51 51 G G A . n A 1 44 U 44 52 52 U U A . n A 1 45 A 45 53 53 A A A . n A 1 46 U 46 54 54 U U A . n A 1 47 C 47 55 55 C C A . n A 1 48 A 48 56 56 A A A . n A 1 49 C 49 57 57 C C A . n A 1 50 C 50 58 58 C C A . n A 1 51 U 51 59 59 U U A . n A 1 52 G 52 60 60 G G A . n A 1 53 A 53 61 61 A A A . n A 1 54 U 54 62 62 U U A . n A 1 55 C 55 63 63 C C A . n A 1 56 U 56 64 64 U U A . n A 1 57 G 57 65 65 G G A . n A 1 58 G 58 66 66 G G A . n A 1 59 A 59 67 67 A A A . n A 1 60 U 60 68 68 U U A . n A 1 61 A 61 69 69 A A A . n A 1 62 A 62 70 70 A A A . n A 1 63 U 63 71 71 U U A . n A 1 64 G 64 72 72 G G A . n A 1 65 C 65 73 73 C C A . n A 1 66 C 66 74 74 C C A . n A 1 67 A 67 75 75 A A A . n A 1 68 G 68 76 76 G G A . n A 1 69 C 69 77 77 C C A . n A 1 70 G 70 78 78 G G A . n A 1 71 U 71 79 79 U U A . n A 1 72 A 72 80 80 A A A . n A 1 73 G 73 81 81 G G A . n A 1 74 G 74 82 82 G G A . n A 1 75 G 75 83 83 G G A . n A 1 76 A 76 84 84 A A A . n A 1 77 A 77 85 85 A A A . n A 1 78 G 78 86 86 G G A . n A 1 79 U 79 87 87 U U A . n A 1 80 C 80 88 88 C C A . n A 1 81 G 81 89 89 G G A . n A 1 82 C 82 90 90 C C A . n A 1 83 A 83 91 91 A A A . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email Alexander.Serganov@nyulangone.org _pdbx_contact_author.name_first Alexander _pdbx_contact_author.name_last Serganov _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0001-8328-9310 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 MN 1 101 1 MN MN A . C 3 MG 1 102 1 MG MG A . D 3 MG 1 103 2 MG MG A . E 4 VIB 1 104 1 VIB VIB A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _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_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_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2022-02-16 2 'Structure model' 1 1 2022-03-02 3 'Structure model' 1 2 2023-10-18 # _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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Refinement description' # 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' citation 2 2 'Structure model' citation_author 3 3 'Structure model' chem_comp_atom 4 3 'Structure model' chem_comp_bond 5 3 'Structure model' diffrn_radiation 6 3 'Structure model' pdbx_initial_refinement_model # 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' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation_author.identifier_ORCID' 5 3 'Structure model' '_diffrn_radiation.pdbx_diffrn_protocol' 6 3 'Structure model' '_diffrn_radiation.pdbx_monochromatic_or_laue_m_l' # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y,x-y,z+2/3 3 -x+y,-x,z+1/3 4 -y,-x,-z+1/3 5 -x+y,y,-z+2/3 6 x,x-y,-z # _pdbx_refine_tls.id 1 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 10.6305134248 _pdbx_refine_tls.origin_y 19.5574279931 _pdbx_refine_tls.origin_z -5.61707477954 _pdbx_refine_tls.T[1][1] 0.541219629849 _pdbx_refine_tls.T[1][1]_esd ? _pdbx_refine_tls.T[1][2] 0.106742539844 _pdbx_refine_tls.T[1][2]_esd ? _pdbx_refine_tls.T[1][3] -0.0185633808709 _pdbx_refine_tls.T[1][3]_esd ? _pdbx_refine_tls.T[2][2] 1.01212353254 _pdbx_refine_tls.T[2][2]_esd ? _pdbx_refine_tls.T[2][3] -0.00401698921629 _pdbx_refine_tls.T[2][3]_esd ? _pdbx_refine_tls.T[3][3] 0.636771232433 _pdbx_refine_tls.T[3][3]_esd ? _pdbx_refine_tls.L[1][1] 2.96648363931 _pdbx_refine_tls.L[1][1]_esd ? _pdbx_refine_tls.L[1][2] -0.232260240671 _pdbx_refine_tls.L[1][2]_esd ? _pdbx_refine_tls.L[1][3] 0.312430883359 _pdbx_refine_tls.L[1][3]_esd ? _pdbx_refine_tls.L[2][2] 1.36921220898 _pdbx_refine_tls.L[2][2]_esd ? _pdbx_refine_tls.L[2][3] -0.474667000177 _pdbx_refine_tls.L[2][3]_esd ? _pdbx_refine_tls.L[3][3] 1.88117881239 _pdbx_refine_tls.L[3][3]_esd ? _pdbx_refine_tls.S[1][1] -0.199651439037 _pdbx_refine_tls.S[1][1]_esd ? _pdbx_refine_tls.S[1][2] -1.03422595504 _pdbx_refine_tls.S[1][2]_esd ? _pdbx_refine_tls.S[1][3] -0.238701582226 _pdbx_refine_tls.S[1][3]_esd ? _pdbx_refine_tls.S[2][1] 0.330842753436 _pdbx_refine_tls.S[2][1]_esd ? _pdbx_refine_tls.S[2][2] 0.261783459901 _pdbx_refine_tls.S[2][2]_esd ? _pdbx_refine_tls.S[2][3] 0.000488857121416 _pdbx_refine_tls.S[2][3]_esd ? _pdbx_refine_tls.S[3][1] -0.15103974695 _pdbx_refine_tls.S[3][1]_esd ? _pdbx_refine_tls.S[3][2] 0.0745204598246 _pdbx_refine_tls.S[3][2]_esd ? _pdbx_refine_tls.S[3][3] 0.000769678122241 _pdbx_refine_tls.S[3][3]_esd ? # _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id ? _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 9 _pdbx_refine_tls_group.beg_PDB_ins_code ? _pdbx_refine_tls_group.end_label_asym_id E _pdbx_refine_tls_group.end_label_seq_id ? _pdbx_refine_tls_group.end_auth_asym_id D _pdbx_refine_tls_group.end_auth_seq_id 1 _pdbx_refine_tls_group.end_PDB_ins_code ? _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.selection_details all # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.14_3260 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? 1.14_3260 4 # _pdbx_entry_details.entry_id 7TD7 _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_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 N6 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 A _pdbx_validate_close_contact.auth_seq_id_1 61 _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 A _pdbx_validate_close_contact.auth_comp_id_2 C _pdbx_validate_close_contact.auth_seq_id_2 77 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.15 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A C 30 ? P ? A C 22 P 2 1 Y 1 A C 30 ? OP1 ? A C 22 OP1 3 1 Y 1 A C 30 ? OP2 ? A C 22 OP2 4 1 Y 1 A C 30 ? "O5'" ? A C 22 "O5'" 5 1 Y 1 A U 46 ? P ? A U 38 P 6 1 Y 1 A U 46 ? OP1 ? A U 38 OP1 7 1 Y 1 A U 46 ? OP2 ? A U 38 OP2 8 1 Y 1 A U 46 ? "O5'" ? A U 38 "O5'" 9 1 Y 1 A U 46 ? "C5'" ? A U 38 "C5'" 10 1 Y 1 A U 46 ? "C4'" ? A U 38 "C4'" 11 1 Y 1 A U 46 ? "O4'" ? A U 38 "O4'" 12 1 Y 1 A U 46 ? "C2'" ? A U 38 "C2'" 13 1 Y 1 A U 46 ? "O2'" ? A U 38 "O2'" 14 1 Y 1 A U 46 ? "C1'" ? A U 38 "C1'" 15 1 Y 1 A U 46 ? N1 ? A U 38 N1 16 1 Y 1 A U 46 ? C2 ? A U 38 C2 17 1 Y 1 A U 46 ? O2 ? A U 38 O2 18 1 Y 1 A U 46 ? N3 ? A U 38 N3 19 1 Y 1 A U 46 ? C4 ? A U 38 C4 20 1 Y 1 A U 46 ? O4 ? A U 38 O4 21 1 Y 1 A U 46 ? C5 ? A U 38 C5 22 1 Y 1 A U 46 ? C6 ? A U 38 C6 23 1 Y 1 A U 54 ? "C5'" ? A U 46 "C5'" 24 1 Y 1 A U 54 ? "C4'" ? A U 46 "C4'" 25 1 Y 1 A U 54 ? "O4'" ? A U 46 "O4'" 26 1 Y 1 A U 54 ? "C3'" ? A U 46 "C3'" 27 1 Y 1 A U 54 ? "O3'" ? A U 46 "O3'" 28 1 Y 1 A U 54 ? "C2'" ? A U 46 "C2'" 29 1 Y 1 A U 54 ? "O2'" ? A U 46 "O2'" 30 1 Y 1 A U 54 ? "C1'" ? A U 46 "C1'" 31 1 Y 1 A U 54 ? N1 ? A U 46 N1 32 1 Y 1 A U 54 ? C2 ? A U 46 C2 33 1 Y 1 A U 54 ? O2 ? A U 46 O2 34 1 Y 1 A U 54 ? N3 ? A U 46 N3 35 1 Y 1 A U 54 ? C4 ? A U 46 C4 36 1 Y 1 A U 54 ? O4 ? A U 46 O4 37 1 Y 1 A U 54 ? C5 ? A U 46 C5 38 1 Y 1 A U 54 ? C6 ? A U 46 C6 39 1 Y 1 A C 55 ? P ? A C 47 P 40 1 Y 1 A C 55 ? OP1 ? A C 47 OP1 41 1 Y 1 A C 55 ? OP2 ? A C 47 OP2 42 1 Y 1 A C 55 ? "O5'" ? A C 47 "O5'" 43 1 Y 1 A C 55 ? "C5'" ? A C 47 "C5'" 44 1 Y 1 A C 55 ? "C4'" ? A C 47 "C4'" 45 1 Y 1 A C 55 ? "O4'" ? A C 47 "O4'" 46 1 Y 1 A C 55 ? "C2'" ? A C 47 "C2'" 47 1 Y 1 A C 55 ? "O2'" ? A C 47 "O2'" 48 1 Y 1 A C 55 ? "C1'" ? A C 47 "C1'" 49 1 Y 1 A C 55 ? N1 ? A C 47 N1 50 1 Y 1 A C 55 ? C2 ? A C 47 C2 51 1 Y 1 A C 55 ? O2 ? A C 47 O2 52 1 Y 1 A C 55 ? N3 ? A C 47 N3 53 1 Y 1 A C 55 ? C4 ? A C 47 C4 54 1 Y 1 A C 55 ? N4 ? A C 47 N4 55 1 Y 1 A C 55 ? C5 ? A C 47 C5 56 1 Y 1 A C 55 ? C6 ? A C 47 C6 57 1 Y 1 A U 62 ? N1 ? A U 54 N1 58 1 Y 1 A U 62 ? C2 ? A U 54 C2 59 1 Y 1 A U 62 ? O2 ? A U 54 O2 60 1 Y 1 A U 62 ? N3 ? A U 54 N3 61 1 Y 1 A U 62 ? C4 ? A U 54 C4 62 1 Y 1 A U 62 ? O4 ? A U 54 O4 63 1 Y 1 A U 62 ? C5 ? A U 54 C5 64 1 Y 1 A U 62 ? C6 ? A U 54 C6 65 1 Y 1 A U 79 ? "O4'" ? A U 71 "O4'" 66 1 Y 1 A U 79 ? "C2'" ? A U 71 "C2'" 67 1 Y 1 A U 79 ? "O2'" ? A U 71 "O2'" 68 1 Y 1 A U 79 ? "C1'" ? A U 71 "C1'" 69 1 Y 1 A U 79 ? N1 ? A U 71 N1 70 1 Y 1 A U 79 ? C2 ? A U 71 C2 71 1 Y 1 A U 79 ? O2 ? A U 71 O2 72 1 Y 1 A U 79 ? N3 ? A U 71 N3 73 1 Y 1 A U 79 ? C4 ? A U 71 C4 74 1 Y 1 A U 79 ? O4 ? A U 71 O4 75 1 Y 1 A U 79 ? C5 ? A U 71 C5 76 1 Y 1 A U 79 ? C6 ? A U 71 C6 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A U 25 ? A U 17 2 1 Y 1 A U 26 ? A U 18 3 1 Y 1 A C 27 ? A C 19 4 1 Y 1 A U 28 ? A U 20 5 1 Y 1 A G 29 ? A G 21 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 MG MG MG N N 111 MN MN MN N N 112 U OP3 O N N 113 U P P N N 114 U OP1 O N N 115 U OP2 O N N 116 U "O5'" O N N 117 U "C5'" C N N 118 U "C4'" C N R 119 U "O4'" O N N 120 U "C3'" C N S 121 U "O3'" O N N 122 U "C2'" C N R 123 U "O2'" O N N 124 U "C1'" C N R 125 U N1 N N N 126 U C2 C N N 127 U O2 O N N 128 U N3 N N N 129 U C4 C N N 130 U O4 O N N 131 U C5 C N N 132 U C6 C N N 133 U HOP3 H N N 134 U HOP2 H N N 135 U "H5'" H N N 136 U "H5''" H N N 137 U "H4'" H N N 138 U "H3'" H N N 139 U "HO3'" H N N 140 U "H2'" H N N 141 U "HO2'" H N N 142 U "H1'" H N N 143 U H3 H N N 144 U H5 H N N 145 U H6 H N N 146 VIB CM2 C N N 147 VIB N4A N N N 148 VIB CM4 C N N 149 VIB O1 O N N 150 VIB C7 C N N 151 VIB C6 C N N 152 VIB C2 C Y N 153 VIB S1 S Y N 154 VIB C5 C Y N 155 VIB C4 C Y N 156 VIB N3 N Y N 157 VIB C7A C N N 158 VIB C4A C Y N 159 VIB N3A N Y N 160 VIB C2A C Y N 161 VIB N1A N Y N 162 VIB C6A C Y N 163 VIB C5A C Y N 164 VIB HM21 H N N 165 VIB HM22 H N N 166 VIB HM23 H N N 167 VIB H4A1 H N N 168 VIB H4A2 H N N 169 VIB HM41 H N N 170 VIB HM42 H N N 171 VIB HM43 H N N 172 VIB HO1 H N N 173 VIB HC71 H N N 174 VIB HC72 H N N 175 VIB HC61 H N N 176 VIB HC62 H N N 177 VIB HC2 H N N 178 VIB H7A1 H N N 179 VIB H7A2 H N N 180 VIB H6AC H N N 181 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 U OP3 P sing N N 116 U OP3 HOP3 sing N N 117 U P OP1 doub N N 118 U P OP2 sing N N 119 U P "O5'" sing N N 120 U OP2 HOP2 sing N N 121 U "O5'" "C5'" sing N N 122 U "C5'" "C4'" sing N N 123 U "C5'" "H5'" sing N N 124 U "C5'" "H5''" sing N N 125 U "C4'" "O4'" sing N N 126 U "C4'" "C3'" sing N N 127 U "C4'" "H4'" sing N N 128 U "O4'" "C1'" sing N N 129 U "C3'" "O3'" sing N N 130 U "C3'" "C2'" sing N N 131 U "C3'" "H3'" sing N N 132 U "O3'" "HO3'" sing N N 133 U "C2'" "O2'" sing N N 134 U "C2'" "C1'" sing N N 135 U "C2'" "H2'" sing N N 136 U "O2'" "HO2'" sing N N 137 U "C1'" N1 sing N N 138 U "C1'" "H1'" sing N N 139 U N1 C2 sing N N 140 U N1 C6 sing N N 141 U C2 O2 doub N N 142 U C2 N3 sing N N 143 U N3 C4 sing N N 144 U N3 H3 sing N N 145 U C4 O4 doub N N 146 U C4 C5 sing N N 147 U C5 C6 doub N N 148 U C5 H5 sing N N 149 U C6 H6 sing N N 150 VIB CM2 C2A sing N N 151 VIB CM2 HM21 sing N N 152 VIB CM2 HM22 sing N N 153 VIB CM2 HM23 sing N N 154 VIB N4A C4A sing N N 155 VIB N4A H4A1 sing N N 156 VIB N4A H4A2 sing N N 157 VIB CM4 C4 sing N N 158 VIB CM4 HM41 sing N N 159 VIB CM4 HM42 sing N N 160 VIB CM4 HM43 sing N N 161 VIB O1 C7 sing N N 162 VIB O1 HO1 sing N N 163 VIB C7 C6 sing N N 164 VIB C7 HC71 sing N N 165 VIB C7 HC72 sing N N 166 VIB C6 C5 sing N N 167 VIB C6 HC61 sing N N 168 VIB C6 HC62 sing N N 169 VIB C2 S1 sing Y N 170 VIB C2 N3 doub Y N 171 VIB C2 HC2 sing N N 172 VIB S1 C5 sing Y N 173 VIB C5 C4 doub Y N 174 VIB C4 N3 sing Y N 175 VIB N3 C7A sing N N 176 VIB C7A C5A sing N N 177 VIB C7A H7A1 sing N N 178 VIB C7A H7A2 sing N N 179 VIB C4A N3A sing Y N 180 VIB C4A C5A doub Y N 181 VIB N3A C2A doub Y N 182 VIB C2A N1A sing Y N 183 VIB N1A C6A doub Y N 184 VIB C6A C5A sing Y N 185 VIB C6A H6AC sing N N 186 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7TD7 'double helix' 7TD7 'a-form double helix' 7TD7 'hairpin loop' 7TD7 'bulge loop' 7TD7 'mismatched base pair' 7TD7 'internal loop' 7TD7 'three-way junction' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 82 1_555 -0.121 -0.225 0.690 7.130 -4.520 1.363 1 A_G9:C90_A A 9 ? A 90 ? 19 1 1 A C 2 1_555 A G 81 1_555 0.040 -0.212 0.622 -0.106 -10.008 1.118 2 A_C10:G89_A A 10 ? A 89 ? 19 1 1 A G 3 1_555 A C 80 1_555 -0.243 -0.210 0.492 -0.092 -14.218 -0.419 3 A_G11:C88_A A 11 ? A 88 ? 19 1 1 A A 4 1_555 A U 79 1_555 -0.086 -0.210 0.388 -3.295 -10.190 -1.795 4 A_A12:U87_A A 12 ? A 87 ? 20 1 1 A C 5 1_555 A G 78 1_555 0.217 -0.181 0.260 -2.520 -9.263 -0.405 5 A_C13:G86_A A 13 ? A 86 ? 19 1 1 A U 6 1_555 A A 77 1_555 -0.251 -0.190 0.160 -6.996 -10.245 1.642 6 A_U14:A85_A A 14 ? A 85 ? 20 1 1 A C 7 1_555 A G 43 1_555 0.134 -0.174 0.532 0.942 -12.422 0.028 7 A_C15:G51_A A 15 ? A 51 ? 19 1 1 A G 8 1_555 A C 42 1_555 -0.076 -0.186 0.340 2.090 -14.639 1.572 8 A_G16:C50_A A 16 ? A 50 ? 19 1 1 A G 9 1_555 A C 41 1_555 -0.330 -0.242 0.376 -11.596 -11.581 -0.739 9 A_G17:C49_A A 17 ? A 49 ? 19 1 1 A G 10 1_555 A C 40 1_555 -0.140 -0.209 0.433 -3.800 -13.394 1.241 10 A_G18:C48_A A 18 ? A 48 ? 19 1 1 A G 11 1_555 A A 39 1_555 0.445 1.580 0.188 1.635 -2.604 -21.143 11 A_G19:A47_A A 19 ? A 47 ? 8 1 1 A U 12 1_555 A A 37 1_555 0.018 -0.248 0.609 7.795 11.939 18.874 12 A_U20:A45_A A 20 ? A 45 ? 20 1 1 A A 27 1_555 A C 16 1_555 -3.545 -1.208 -0.054 -10.723 -4.083 -15.557 13 A_A35:C24_A A 35 ? A 24 ? ? 1 1 A G 28 1_555 A C 15 1_555 -0.154 -0.069 -0.125 -0.279 -2.463 3.462 14 A_G36:C23_A A 36 ? A 23 ? 19 1 1 A G 29 1_555 A C 14 1_555 -0.244 -0.146 0.265 -3.142 0.363 1.814 15 A_G37:C22_A A 37 ? A 22 ? 19 1 1 A C 30 1_555 A G 13 1_555 0.237 -0.207 0.443 -14.170 7.031 -5.314 16 A_C38:G21_A A 38 ? A 21 ? 19 1 1 A U 31 1_555 A A 35 1_555 4.020 -1.749 0.671 9.419 6.521 -102.795 17 A_U39:A43_A A 39 ? A 43 ? 24 4 1 A A 45 1_555 A A 76 1_555 6.973 -5.179 0.469 -27.505 11.106 164.465 18 A_A53:A84_A A 53 ? A 84 ? ? ? 1 A A 48 1_555 A G 75 1_555 -6.799 -4.471 0.248 10.451 -15.288 -13.541 19 A_A56:G83_A A 56 ? A 83 ? 11 10 1 A C 49 1_555 A G 74 1_555 0.263 -0.166 0.253 5.159 -8.803 1.105 20 A_C57:G82_A A 57 ? A 82 ? 19 1 1 A C 50 1_555 A G 73 1_555 0.176 -0.138 -0.167 -0.720 -3.935 0.359 21 A_C58:G81_A A 58 ? A 81 ? 19 1 1 A U 51 1_555 A A 72 1_555 0.050 -0.217 0.846 -0.099 -0.371 -0.231 22 A_U59:A80_A A 59 ? A 80 ? 20 1 1 A G 52 1_555 A G 70 1_555 2.259 3.403 0.335 -22.252 6.934 -78.174 23 A_G60:G78_A A 60 ? A 78 ? 6 3 1 A A 53 1_555 A G 64 1_555 1.788 -5.005 -2.134 -14.921 57.900 -125.867 24 A_A61:G72_A A 61 ? A 72 ? ? ? 1 A C 55 1_555 A G 68 1_555 0.260 -0.143 -0.001 -0.829 1.091 3.217 25 A_C63:G76_A A 63 ? A 76 ? 19 1 1 A U 56 1_555 A A 67 1_555 -0.120 -0.116 0.337 1.844 1.471 -0.543 26 A_U64:A75_A A 64 ? A 75 ? 20 1 1 A G 57 1_555 A C 66 1_555 -0.196 -0.175 -0.102 -6.206 -1.432 -1.170 27 A_G65:C74_A A 65 ? A 74 ? 19 1 1 A G 58 1_555 A C 65 1_555 -0.147 -0.023 -0.526 -2.461 3.243 5.299 28 A_G66:C73_A A 66 ? A 73 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 82 1_555 A C 2 1_555 A G 81 1_555 -0.007 -1.312 3.334 -0.227 5.484 37.302 -2.736 -0.019 3.117 8.517 0.352 37.689 1 AA_G9C10:G89C90_AA A 9 ? A 90 ? A 10 ? A 89 ? 1 A C 2 1_555 A G 81 1_555 A G 3 1_555 A C 80 1_555 -0.430 -1.793 2.813 -3.490 9.865 31.068 -4.518 0.290 2.190 17.796 6.295 32.742 2 AA_C10G11:C88G89_AA A 10 ? A 89 ? A 11 ? A 88 ? 1 A G 3 1_555 A C 80 1_555 A A 4 1_555 A U 79 1_555 -0.553 -1.428 3.400 -2.312 -1.946 33.342 -2.140 0.556 3.505 -3.383 4.020 33.474 3 AA_G11A12:U87C88_AA A 11 ? A 88 ? A 12 ? A 87 ? 1 A A 4 1_555 A U 79 1_555 A C 5 1_555 A G 78 1_555 -0.155 -1.504 3.165 0.648 3.197 33.076 -3.136 0.374 3.007 5.599 -1.134 33.232 4 AA_A12C13:G86U87_AA A 12 ? A 87 ? A 13 ? A 86 ? 1 A C 5 1_555 A G 78 1_555 A U 6 1_555 A A 77 1_555 0.407 -1.074 3.107 4.492 2.063 32.865 -2.206 0.001 3.063 3.622 -7.884 33.224 5 AA_C13U14:A85G86_AA A 13 ? A 86 ? A 14 ? A 85 ? 1 A U 6 1_555 A A 77 1_555 A C 7 1_555 A G 43 1_555 1.183 -0.942 2.959 -1.733 4.778 43.645 -1.659 -1.726 2.800 6.400 2.321 43.926 6 AA_U14C15:G51A85_AA A 14 ? A 85 ? A 15 ? A 51 ? 1 A C 7 1_555 A G 43 1_555 A G 8 1_555 A C 42 1_555 0.836 -2.071 3.024 1.356 6.478 27.936 -5.434 -1.425 2.526 13.185 -2.760 28.694 7 AA_C15G16:C50G51_AA A 15 ? A 51 ? A 16 ? A 50 ? 1 A G 8 1_555 A C 42 1_555 A G 9 1_555 A C 41 1_555 -0.659 -1.801 3.380 -1.036 3.335 35.872 -3.389 0.916 3.222 5.398 1.677 36.036 8 AA_G16G17:C49C50_AA A 16 ? A 50 ? A 17 ? A 49 ? 1 A G 9 1_555 A C 41 1_555 A G 10 1_555 A C 40 1_555 0.286 -1.457 3.084 2.567 5.020 33.072 -3.278 -0.110 2.852 8.740 -4.469 33.536 9 AA_G17G18:C48C49_AA A 17 ? A 49 ? A 18 ? A 48 ? 1 A G 10 1_555 A C 40 1_555 A G 11 1_555 A A 39 1_555 -1.309 -0.618 3.107 3.776 3.702 37.782 -1.378 2.443 2.896 5.684 -5.797 38.136 10 AA_G18G19:A47C48_AA A 18 ? A 48 ? A 19 ? A 47 ? 1 A G 11 1_555 A A 39 1_555 A U 12 1_555 A A 37 1_555 0.142 0.283 3.309 -1.628 13.092 -0.333 -14.408 -1.019 -0.180 -87.882 -10.929 -13.197 11 AA_G19U20:A45A47_AA A 19 ? A 47 ? A 20 ? A 45 ? 1 A A 27 1_555 A C 16 1_555 A G 28 1_555 A C 15 1_555 1.807 -0.126 3.424 -4.725 4.476 48.021 -0.507 -2.576 3.220 5.470 5.775 48.434 12 AA_A35G36:C23C24_AA A 35 ? A 24 ? A 36 ? A 23 ? 1 A G 28 1_555 A C 15 1_555 A G 29 1_555 A C 14 1_555 -0.619 -2.235 3.096 -8.461 13.669 31.083 -5.460 -0.042 2.059 23.631 14.628 34.903 13 AA_G36G37:C22C23_AA A 36 ? A 23 ? A 37 ? A 22 ? 1 A G 29 1_555 A C 14 1_555 A C 30 1_555 A G 13 1_555 -1.044 -1.810 3.497 -0.286 11.128 39.150 -3.840 1.471 2.905 16.212 0.417 40.642 14 AA_G37C38:G21C22_AA A 37 ? A 22 ? A 38 ? A 21 ? 1 A C 30 1_555 A G 13 1_555 A U 31 1_555 A A 35 1_555 -3.353 -1.244 2.750 6.614 2.780 71.264 -1.139 3.045 2.429 2.380 -5.663 71.577 15 AA_C38U39:A43G21_AA A 38 ? A 21 ? A 39 ? A 43 ? 1 A A 45 1_555 A A 76 1_555 A A 48 1_555 A G 75 1_555 -2.563 -2.132 0.225 150.883 -78.844 -35.296 1.327 -0.793 1.292 40.995 78.452 -170.702 16 AA_A53A56:G83A84_AA A 53 ? A 84 ? A 56 ? A 83 ? 1 A A 48 1_555 A G 75 1_555 A C 49 1_555 A G 74 1_555 1.057 -0.952 3.498 -3.396 6.218 67.407 -1.103 -1.084 3.359 5.587 3.051 67.734 17 AA_A56C57:G82G83_AA A 56 ? A 83 ? A 57 ? A 82 ? 1 A C 49 1_555 A G 74 1_555 A C 50 1_555 A G 73 1_555 -0.774 -1.763 3.334 1.516 7.314 30.252 -4.614 1.718 2.800 13.753 -2.851 31.139 18 AA_C57C58:G81G82_AA A 57 ? A 82 ? A 58 ? A 81 ? 1 A C 50 1_555 A G 73 1_555 A U 51 1_555 A A 72 1_555 0.471 -1.521 3.249 -6.675 5.544 39.855 -2.768 -1.379 2.908 8.018 9.653 40.751 19 AA_C58U59:A80G81_AA A 58 ? A 81 ? A 59 ? A 80 ? 1 A U 51 1_555 A A 72 1_555 A G 52 1_555 A G 70 1_555 3.147 -1.988 3.128 22.165 4.786 95.390 -1.406 -1.709 3.547 3.202 -14.827 97.409 20 AA_U59G60:G78A80_AA A 59 ? A 80 ? A 60 ? A 78 ? 1 A G 52 1_555 A G 70 1_555 A A 53 1_555 A G 64 1_555 -0.276 3.267 -1.987 119.042 93.884 -135.073 -1.371 -0.481 -2.516 -47.585 60.336 -169.247 21 AA_G60A61:G72G78_AA A 60 ? A 78 ? A 61 ? A 72 ? 1 A A 53 1_555 A G 64 1_555 A C 55 1_555 A G 68 1_555 -5.039 -0.960 -0.650 -64.253 -133.629 20.449 0.366 2.200 2.877 -78.508 37.749 148.791 22 AA_A61C63:G76G72_AA A 61 ? A 72 ? A 63 ? A 76 ? 1 A C 55 1_555 A G 68 1_555 A U 56 1_555 A A 67 1_555 -0.755 -2.463 2.946 -5.910 16.479 31.686 -5.718 0.593 1.621 27.696 9.934 36.092 23 AA_C63U64:A75G76_AA A 63 ? A 76 ? A 64 ? A 75 ? 1 A U 56 1_555 A A 67 1_555 A G 57 1_555 A C 66 1_555 -0.122 -1.683 3.878 4.232 -0.100 32.193 -2.989 1.098 3.836 -0.180 -7.590 32.463 24 AA_U64G65:C74A75_AA A 64 ? A 75 ? A 65 ? A 74 ? 1 A G 57 1_555 A C 66 1_555 A G 58 1_555 A C 65 1_555 1.058 -2.198 3.153 4.149 10.478 33.870 -4.940 -1.194 2.493 17.397 -6.888 35.644 25 AA_G65G66:C73C74_AA A 65 ? A 74 ? A 66 ? A 73 ? # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number 'R01 GM112940' _pdbx_audit_support.ordinal 1 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id VIB _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id VIB _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_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MANGANESE (II) ION' MN 3 'MAGNESIUM ION' MG 4 '3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM' VIB # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 2HOJ _pdbx_initial_refinement_model.details ? # _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 ? # _space_group.name_H-M_alt 'P 32 1 2' _space_group.name_Hall 'P 32 2 (x,y,z+1/6)' _space_group.IT_number 153 _space_group.crystal_system trigonal _space_group.id 1 #