data_8HB1 # _entry.id 8HB1 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.368 _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 8HB1 pdb_00008hb1 10.2210/pdb8hb1/pdb WWPDB D_1300033195 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8HB1 _pdbx_database_status.recvd_initial_deposition_date 2022-10-27 _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 'Peng, X.' 1 ? 'Lilley, D.M.J.' 2 ? 'Huang, L.' 3 ? # _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 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 51 _citation.language ? _citation.page_first 2904 _citation.page_last 2914 _citation.title 'Crystal structures of the NAD+-II riboswitch reveal two distinct ligand-binding pockets.' _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkad102 _citation.pdbx_database_id_PubMed 36840714 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Peng, X.' 1 ? primary 'Liao, W.' 2 0000-0001-9823-9949 primary 'Lin, X.' 3 ? primary 'Lilley, D.M.J.' 4 0000-0001-6882-2818 primary 'Huang, L.' 5 0000-0002-2121-365X # _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 8HB1 _cell.details ? _cell.formula_units_Z ? _cell.length_a 82.314 _cell.length_a_esd ? _cell.length_b 82.314 _cell.length_b_esd ? _cell.length_c 63.248 _cell.length_c_esd ? _cell.volume 371130.990 _cell.volume_esd ? _cell.Z_PDB 6 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8HB1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ;P 32 2" ; _symmetry.space_group_name_H-M 'P 32 2 1' _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 ;RNA (5'-R(*AP*GP*AP*GP*CP*GP*UP*UP*GP*CP*GP*UP*CP*CP*GP*AP*AP*AP*GP*UP*(CBV)P*GP*CP*C)-3') ; 7802.550 1 ? ? ? ? 2 polymer syn 'RNA (30-MER)' 9706.913 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 4 ? ? ? ? 4 non-polymer syn 'BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE' 335.227 2 ? ? ? ? 5 water nat water 18.015 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no yes 'AGAGCGUUGCGUCCGAAAGU(CBV)GCC' AGAGCGUUGCGUCCGAAAGUCGCC A ? 2 polyribonucleotide no no GCGACACGGCUCUUUAAAAACAAAAGGAGA GCGACACGGCUCUUUAAAAACAAAAGGAGA B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 A n 1 2 G n 1 3 A n 1 4 G n 1 5 C n 1 6 G n 1 7 U n 1 8 U n 1 9 G n 1 10 C n 1 11 G n 1 12 U n 1 13 C n 1 14 C n 1 15 G n 1 16 A n 1 17 A n 1 18 A n 1 19 G n 1 20 U n 1 21 CBV n 1 22 G n 1 23 C n 1 24 C n 2 1 G n 2 2 C n 2 3 G n 2 4 A n 2 5 C n 2 6 A n 2 7 C n 2 8 G n 2 9 G n 2 10 C n 2 11 U n 2 12 C n 2 13 U n 2 14 U n 2 15 U n 2 16 A n 2 17 A n 2 18 A n 2 19 A n 2 20 A n 2 21 C n 2 22 A n 2 23 A n 2 24 A n 2 25 A n 2 26 G n 2 27 G n 2 28 A n 2 29 G n 2 30 A 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 24 'Streptococcus parasanguinis' ? 1318 ? 2 1 sample 1 30 'Streptococcus parasanguinis' ? 1318 ? # 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 8HB1 8HB1 ? 1 ? 1 2 PDB 8HB1 8HB1 ? 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 8HB1 A 1 ? 24 ? 8HB1 1 ? 24 ? 1 24 2 2 8HB1 B 1 ? 30 ? 8HB1 26 ? 55 ? 26 55 # 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 CBV 'RNA linking' n ;5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) ; ? 'C9 H13 Br N3 O8 P' 402.093 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NMN non-polymer . 'BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE' 'NICOTINAMIDE MONONUCLEOTIDE' 'C11 H16 N2 O8 P 1' 335.227 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _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 8HB1 _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 3.69 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 66.70 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.0 _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 '2.0 M Ammonium Sulfate' _exptl_crystal_grow.pdbx_pH_range ? # _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 EIGER2 X 4M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2022-08-29 _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 0.91908 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'SSRF BEAMLINE BL02U1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.91908 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL02U1 _diffrn_source.pdbx_synchrotron_site SSRF # _reflns.B_iso_Wilson_estimate 43.50 _reflns.entry_id 8HB1 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.23 _reflns.d_resolution_low 47.31 _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 12413 _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 100.0 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 19.2 _reflns.pdbx_Rmerge_I_obs 0.073 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 22.4 _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 0.017 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_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.pdbx_CC_split_method ? # _reflns_shell.d_res_high 2.23 _reflns_shell.d_res_low 2.29 _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 900 _reflns_shell.percent_possible_all 100 _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 0.849 _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 ? _reflns_shell.pdbx_Rpim_I_all 0.224 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.973 _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 77.24 _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 8HB1 _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 2.23 _refine.ls_d_res_low 35.64 _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 11953 _refine.ls_number_reflns_R_free 592 _refine.ls_number_reflns_R_work 11361 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 96.46 _refine.ls_percent_reflns_R_free 4.95 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2274 _refine.ls_R_factor_R_free 0.2496 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2263 _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 1.33 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 40.0463 _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 0.4406 _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 2.23 _refine_hist.d_res_low 35.64 _refine_hist.number_atoms_solvent 1 _refine_hist.number_atoms_total 1206 _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 1157 _refine_hist.pdbx_number_atoms_ligand 48 _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' ? 0.0093 ? 1342 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.9315 ? 2088 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0781 ? 275 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0104 ? 58 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 15.4337 ? 651 ? 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' 2.23 2.45 . . 147 2489 86.77 . . . 0.5569 . 0.5465 . . . . . . . . . . . 'X-RAY DIFFRACTION' 2.45 2.81 . . 156 2891 99.38 . . . 0.3961 . 0.3791 . . . . . . . . . . . 'X-RAY DIFFRACTION' 2.81 3.54 . . 146 2936 99.77 . . . 0.2781 . 0.2430 . . . . . . . . . . . 'X-RAY DIFFRACTION' 3.54 35.64 . . 143 3045 99.66 . . . 0.1740 . 0.1590 . . . . . . . . . . . # _struct.entry_id 8HB1 _struct.title 'Crystal structure of NAD-II riboswitch (two strands) with NMN' _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 8HB1 _struct_keywords.text 'Aptamer, 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 3 ? F N N 4 ? G N N 4 ? H N N 3 ? I N N 5 ? # 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 U 20 "O3'" ? ? ? 1_555 A CBV 21 P ? ? A U 20 A CBV 21 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale2 covale one ? A CBV 21 "O3'" ? ? ? 1_555 A G 22 P ? ? A CBV 21 A G 22 1_555 ? ? ? ? ? ? ? 1.596 ? ? metalc1 metalc ? ? A G 9 OP2 ? ? ? 1_555 C MG . MG ? ? A G 9 A MG 101 1_555 ? ? ? ? ? ? ? 2.801 ? ? metalc2 metalc ? ? A C 10 "O2'" ? ? ? 1_555 D MG . MG ? ? A C 10 A MG 102 1_555 ? ? ? ? ? ? ? 2.928 ? ? metalc3 metalc ? ? A U 12 OP2 ? ? ? 1_555 D MG . MG ? ? A U 12 A MG 102 1_555 ? ? ? ? ? ? ? 2.704 ? ? hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 2 B C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 2 B C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 2 B C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 11 N3 ? ? A A 3 B U 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 11 O4 ? ? A A 3 B U 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 4 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 4 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 4 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 B A 18 N1 ? ? A G 4 B A 43 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog10 hydrog ? ? A G 4 N3 ? ? ? 1_555 B A 18 N6 ? ? A G 4 B A 43 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 5 B G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 5 B G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 5 B G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 O2 ? ? ? 1_555 B A 20 N6 ? ? A C 5 B A 45 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog15 hydrog ? ? A G 6 N2 ? ? ? 1_555 A U 8 O4 ? ? A G 6 A U 8 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog16 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 6 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 6 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 6 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 22 N7 ? ? A U 7 B A 47 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog20 hydrog ? ? A U 7 O4 ? ? ? 1_555 B A 22 N6 ? ? A U 7 B A 47 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog21 hydrog ? ? A U 8 O4 ? ? ? 1_555 A G 15 N1 ? ? A U 8 A G 15 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog22 hydrog ? ? A U 8 N3 ? ? ? 1_555 B A 25 N1 ? ? A U 8 B A 50 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog23 hydrog ? ? A U 8 O2 ? ? ? 1_555 B A 25 N6 ? ? A U 8 B A 50 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog24 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 29 N1 ? ? A C 10 B G 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 29 O6 ? ? A C 10 B G 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 29 N2 ? ? A C 10 B G 54 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 12 N3 ? ? ? 1_555 B A 28 N1 ? ? A U 12 B A 53 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 12 O4 ? ? ? 1_555 B A 28 N6 ? ? A U 12 B A 53 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 27 N1 ? ? A C 13 B G 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 27 O6 ? ? A C 13 B G 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 27 N2 ? ? A C 13 B G 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 14 N3 ? ? ? 1_555 B G 26 N1 ? ? A C 14 B G 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 14 N4 ? ? ? 1_555 B G 26 O6 ? ? A C 14 B G 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 14 O2 ? ? ? 1_555 B G 26 N2 ? ? A C 14 B G 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 15 N2 ? ? ? 1_555 B A 6 N1 ? ? A G 15 B A 31 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog36 hydrog ? ? A G 15 N3 ? ? ? 1_555 B A 6 N6 ? ? A G 15 B A 31 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog37 hydrog ? ? A A 17 N1 ? ? ? 1_555 B G 26 N2 ? ? A A 17 B G 51 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog38 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A U 20 N3 ? ? ? 1_555 B A 4 N1 ? ? A U 20 B A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A U 20 O4 ? ? ? 1_555 B A 4 N6 ? ? A U 20 B A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A CBV 21 N3 ? ? ? 1_555 B G 3 N1 ? ? A CBV 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A CBV 21 N4 ? ? ? 1_555 B G 3 O6 ? ? A CBV 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A CBV 21 O2 ? ? ? 1_555 B G 3 N2 ? ? A CBV 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A G 22 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 22 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 22 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A C 23 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 23 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 23 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? B C 7 O2 ? ? ? 1_555 B A 22 N6 ? ? B C 32 B A 47 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog53 hydrog ? ? B G 8 N2 ? ? ? 1_555 B C 21 O2 ? ? B G 33 B C 46 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog54 hydrog ? ? B G 9 N2 ? ? ? 1_555 B A 20 N1 ? ? B G 34 B A 45 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog55 hydrog ? ? B C 10 O2 ? ? ? 1_555 B A 19 N6 ? ? B C 35 B A 44 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog56 hydrog ? ? B U 11 O2 ? ? ? 1_555 B A 17 N6 ? ? B U 36 B A 42 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog57 hydrog ? ? B C 12 O2 ? ? ? 1_555 B A 16 N6 ? ? B C 37 B A 41 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog58 hydrog ? ? B A 23 N6 ? ? ? 1_555 B G 26 O6 ? ? B A 48 B G 51 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # _atom_sites.entry_id 8HB1 _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] 0.012149 _atom_sites.fract_transf_matrix[1][2] 0.007014 _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] 0.014028 _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] 0.015811 _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 BR ? ? 25.79822 9.11301 ? ? 1.35700 25.34896 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? H ? ? 0.51345 0.48472 ? ? 24.73122 6.32584 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? 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. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 ? ? 15.80542 1.70748 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # 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 A 1 1 1 A A A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A 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 G 6 6 6 G G A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 G 9 9 9 G G A . n A 1 10 C 10 10 10 C C A . n A 1 11 G 11 11 11 G G A . n A 1 12 U 12 12 12 U U A . n A 1 13 C 13 13 13 C C A . n A 1 14 C 14 14 14 C C A . n A 1 15 G 15 15 15 G G A . n A 1 16 A 16 16 16 A A A . n A 1 17 A 17 17 17 A A A . n A 1 18 A 18 18 18 A A A . n A 1 19 G 19 19 19 G G A . n A 1 20 U 20 20 20 U U A . n A 1 21 CBV 21 21 21 CBV CBV A . n A 1 22 G 22 22 22 G G A . n A 1 23 C 23 23 23 C C A . n A 1 24 C 24 24 24 C C A . n B 2 1 G 1 26 26 G G B . n B 2 2 C 2 27 27 C C B . n B 2 3 G 3 28 28 G G B . n B 2 4 A 4 29 29 A A B . n B 2 5 C 5 30 30 C C B . n B 2 6 A 6 31 31 A A B . n B 2 7 C 7 32 32 C C B . n B 2 8 G 8 33 33 G G B . n B 2 9 G 9 34 34 G G B . n B 2 10 C 10 35 35 C C B . n B 2 11 U 11 36 36 U U B . n B 2 12 C 12 37 37 C C B . n B 2 13 U 13 38 38 U U B . n B 2 14 U 14 39 39 U U B . n B 2 15 U 15 40 40 U U B . n B 2 16 A 16 41 41 A A B . n B 2 17 A 17 42 42 A A B . n B 2 18 A 18 43 43 A A B . n B 2 19 A 19 44 44 A A B . n B 2 20 A 20 45 45 A A B . n B 2 21 C 21 46 46 C C B . n B 2 22 A 22 47 47 A A B . n B 2 23 A 23 48 48 A A B . n B 2 24 A 24 49 49 A A B . n B 2 25 A 25 50 50 A A B . n B 2 26 G 26 51 51 G G B . n B 2 27 G 27 52 52 G G B . n B 2 28 A 28 53 53 A A B . n B 2 29 G 29 54 54 G G B . n B 2 30 A 30 55 55 A A B . n # loop_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 2 huanglin36@mail.sysu.edu.cn Lin Huang ? 'principal investigator/group leader' 0000-0002-2121-365X 3 d.m.j.lilley@dundee.ac.uk David Lilley M.J 'principal investigator/group leader' 0000-0001-6882-2818 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 MG 1 101 1 MG MG A . D 3 MG 1 102 2 MG MG A . E 3 MG 1 103 3 MG MG A . F 4 NMN 1 101 101 NMN NMN B . G 4 NMN 1 102 102 NMN NMN B . H 3 MG 1 103 4 MG MG B . I 5 HOH 1 201 1 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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,F,G,H,I # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 4660 ? 1 MORE -46 ? 1 'SSA (A^2)' 9240 ? # _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 # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id "O2'" _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id A _pdbx_struct_conn_angle.ptnr1_label_comp_id C _pdbx_struct_conn_angle.ptnr1_label_seq_id 10 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id A _pdbx_struct_conn_angle.ptnr1_auth_comp_id C _pdbx_struct_conn_angle.ptnr1_auth_seq_id 10 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id MG _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id D _pdbx_struct_conn_angle.ptnr2_label_comp_id MG _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id A _pdbx_struct_conn_angle.ptnr2_auth_comp_id MG _pdbx_struct_conn_angle.ptnr2_auth_seq_id 102 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id OP2 _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id A _pdbx_struct_conn_angle.ptnr3_label_comp_id U _pdbx_struct_conn_angle.ptnr3_label_seq_id 12 _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id A _pdbx_struct_conn_angle.ptnr3_auth_comp_id U _pdbx_struct_conn_angle.ptnr3_auth_seq_id 12 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 106.2 _pdbx_struct_conn_angle.value_esd ? # 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 2023-03-22 2 'Structure model' 1 1 2023-04-19 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category citation # 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' # 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 x-y,-y,-z+1/3 5 -x,-x+y,-z+2/3 6 y,x,-z # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[1][1]_esd _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][2]_esd _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[1][3]_esd _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[2][2]_esd _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.T[2][3]_esd _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[3][3]_esd _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[1][1]_esd _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][2]_esd _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[1][3]_esd _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[2][2]_esd _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.L[2][3]_esd _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[3][3]_esd _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][1]_esd _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][2]_esd _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[1][3]_esd _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][1]_esd _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][2]_esd _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][3]_esd _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][1]_esd _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][2]_esd _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[3][3]_esd 1 'X-RAY DIFFRACTION' ? refined -28.1585176018 14.7535961661 4.33186085388 0.614560400658 ? -0.113995016434 ? -0.0957887306289 ? 0.354872896439 ? 0.023119524027 ? 0.572001348052 ? 1.61989635159 ? 0.0797403919546 ? -1.6297938812 ? 5.3918681692 ? -4.31776265345 ? 1.69933082538 ? -0.17736179804 ? 0.205098279521 ? 0.304719113652 ? 0.252429245142 ? 0.189149121295 ? -0.158851322597 ? -0.243297310453 ? -0.00645407006353 ? 0.0250165671624 ? 2 'X-RAY DIFFRACTION' ? refined -23.1458555506 4.79593425885 -5.28499589579 1.10768613393 ? -0.36280670786 ? 0.27584339544 ? 0.898542737151 ? -0.356936130807 ? 0.943544574708 ? 4.38371559165 ? -0.991034441682 ? 2.81599261545 ? 8.66876997821 ? 4.25364019291 ? 4.65959488331 ? -0.510547051443 ? 1.75823879234 ? -1.25283979809 ? -1.69442162598 ? 0.216453609857 ? -0.965321019785 ? 0.399958614979 ? 0.830237350178 ? -0.0736312760168 ? 3 'X-RAY DIFFRACTION' ? refined -20.4570478884 4.81076069803 -24.0794174245 1.59821399816 ? -0.14865346049 ? 0.388731769561 ? 1.26554642273 ? -0.193213238125 ? 0.899357343601 ? 5.0357575911 ? 1.02552541747 ? -3.76057000727 ? 6.58093771658 ? -0.474179939977 ? 4.15801269247 ? -0.524173836063 ? 1.59930827931 ? 0.130670158419 ? -1.51999920742 ? 0.850526775114 ? -1.82874694396 ? -0.215192025722 ? 0.458958134758 ? -0.260631912241 ? 4 'X-RAY DIFFRACTION' ? refined -17.6449758281 8.38900022563 -16.2630505171 1.42907354311 ? -0.155960182629 ? 0.281830313186 ? 1.24865544561 ? -0.407843405162 ? 1.1372297373 ? 6.81857663239 ? -1.30892616058 ? -1.04012589743 ? 3.60533386767 ? -0.726904413485 ? 4.47940416857 ? 1.3576511898 ? 1.10261734077 ? -0.388314187775 ? 2.09253613295 ? -0.833043832437 ? -0.340172208979 ? 1.07767453273 ? 0.627246744609 ? -0.212724002632 ? 5 'X-RAY DIFFRACTION' ? refined -23.5556851108 26.273005344 4.12547911831 0.800858834431 ? -0.16639483202 ? -0.181678637051 ? 0.445801590431 ? 0.0710325023081 ? 0.993947947601 ? 2.94860810124 ? 1.26187994908 ? -1.93595044443 ? 5.93930791942 ? -0.43068125969 ? 2.95907524857 ? 0.329134351673 ? -0.150441566829 ? 0.773132412263 ? 0.62672316937 ? -0.0116577602118 ? -0.617303122756 ? -0.474230157331 ? 0.421690023983 ? -0.290413320905 ? 6 'X-RAY DIFFRACTION' ? refined -37.9827017652 16.8091997523 2.90309907698 0.701043955404 ? -0.00783327476687 ? -0.132268414531 ? 0.463252644089 ? 0.130532894748 ? 0.674840510334 ? 4.50822297519 ? 1.79956870634 ? -2.81124841623 ? 8.47875338455 ? 4.07087691878 ? 5.14111778188 ? -0.185993213808 ? 0.70659589546 ? 1.09149096473 ? -0.489119239595 ? 0.280084310456 ? 0.568636287302 ? -1.06474425513 ? -0.616012464883 ? 0.188644652698 ? 7 'X-RAY DIFFRACTION' ? refined -33.6922972698 1.80347858761 -0.401409982734 0.876002034193 ? -0.271556556621 ? -0.0265954383633 ? 0.417966256896 ? -0.0319548550334 ? 0.453677747852 ? 3.57720133549 ? 0.350911717292 ? 0.578888689874 ? 9.73678432076 ? -0.999307802266 ? 0.265888266025 ? -0.0453244013264 ? 0.134124117953 ? -0.57963529461 ? -0.833158087711 ? 0.0504611476959 ? 0.169580888023 ? 1.47780036262 ? -0.625192430494 ? 0.0851608555765 ? # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_PDB_ins_code _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_PDB_ins_code _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 1 'X-RAY DIFFRACTION' 1 A ? A 1 ? A ? A 15 ? ? ;chain 'A' and (resid 1 through 15 ) ; 2 'X-RAY DIFFRACTION' 2 A ? A 16 ? A ? A 20 ? ? ;chain 'A' and (resid 16 through 20 ) ; 3 'X-RAY DIFFRACTION' 3 A ? A 22 ? A ? A 24 ? ? ;chain 'A' and (resid 22 through 24 ) ; 4 'X-RAY DIFFRACTION' 4 B ? B 26 ? B ? B 30 ? ? ;chain 'B' and (resid 26 through 30 ) ; 5 'X-RAY DIFFRACTION' 5 B ? B 31 ? B ? B 45 ? ? ;chain 'B' and (resid 31 through 45 ) ; 6 'X-RAY DIFFRACTION' 6 B ? B 46 ? B ? B 50 ? ? ;chain 'B' and (resid 46 through 50 ) ; 7 'X-RAY DIFFRACTION' 7 B ? B 51 ? B ? B 55 ? ? ;chain 'B' and (resid 51 through 55 ) ; # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? AutoSol ? ? ? . 4 # _pdbx_entry_details.entry_id 8HB1 _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 "HO3'" _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 CBV _pdbx_validate_close_contact.auth_seq_id_1 21 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 P _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 G _pdbx_validate_close_contact.auth_seq_id_2 22 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.39 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 C2 A A 1 ? ? N3 A A 1 ? ? C4 A A 1 ? ? 106.08 110.60 -4.52 0.50 N 2 1 C5 A A 1 ? ? C6 A A 1 ? ? N1 A A 1 ? ? 114.40 117.70 -3.30 0.50 N 3 1 "O5'" A G 6 ? ? P A G 6 ? ? OP1 A G 6 ? ? 98.04 105.70 -7.66 0.90 N 4 1 C6 A C 10 ? ? N1 A C 10 ? ? C2 A C 10 ? ? 123.27 120.30 2.97 0.40 N 5 1 N1 A G 11 ? ? C6 A G 11 ? ? O6 A G 11 ? ? 123.85 119.90 3.95 0.60 N 6 1 C6 A C 13 ? ? N1 A C 13 ? ? C2 A C 13 ? ? 122.73 120.30 2.43 0.40 N 7 1 C4 B G 34 ? ? C5 B G 34 ? ? N7 B G 34 ? ? 114.35 110.80 3.55 0.40 N 8 1 N9 B G 34 ? ? C4 B G 34 ? ? C5 B G 34 ? ? 102.98 105.40 -2.42 0.40 N 9 1 C6 B C 35 ? ? N1 B C 35 ? ? C2 B C 35 ? ? 122.88 120.30 2.58 0.40 N 10 1 N3 B C 35 ? ? C4 B C 35 ? ? C5 B C 35 ? ? 124.74 121.90 2.84 0.40 N 11 1 C8 B A 41 ? ? N9 B A 41 ? ? C4 B A 41 ? ? 108.54 105.80 2.74 0.40 N 12 1 C6 B C 46 ? ? N1 B C 46 ? ? C2 B C 46 ? ? 123.37 120.30 3.07 0.40 N 13 1 C4 B G 51 ? ? C5 B G 51 ? ? N7 B G 51 ? ? 113.59 110.80 2.79 0.40 N 14 1 "O5'" B G 52 ? ? P B G 52 ? ? OP2 B G 52 ? ? 100.04 105.70 -5.66 0.90 N 15 1 C8 B G 54 ? ? N9 B G 54 ? ? C4 B G 54 ? ? 109.23 106.40 2.83 0.40 N 16 1 N9 B G 54 ? ? C4 B G 54 ? ? C5 B G 54 ? ? 102.18 105.40 -3.22 0.40 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8HB1 'double helix' 8HB1 'a-form double helix' 8HB1 'mismatched base pair' # 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 2 1_555 B C 12 1_555 -0.300 -0.195 -0.075 -0.492 -8.418 0.892 1 A_G2:C37_B A 2 ? B 37 ? 19 1 1 A A 3 1_555 B U 11 1_555 -0.009 -0.107 -0.003 -2.554 -9.953 4.367 2 A_A3:U36_B A 3 ? B 36 ? 20 1 1 A G 4 1_555 B C 10 1_555 -0.136 -0.110 -0.037 -6.178 -9.108 -0.177 3 A_G4:C35_B A 4 ? B 35 ? 19 1 1 A C 5 1_555 B G 9 1_555 0.247 -0.147 0.118 -2.830 -5.092 -0.633 4 A_C5:G34_B A 5 ? B 34 ? 19 1 1 B C 21 1_555 B G 8 1_555 3.090 1.051 0.161 4.052 -15.458 47.542 5 B_C46:G33_B B 46 ? B 33 ? ? 5 1 A U 7 1_555 B A 22 1_555 -0.543 3.529 -0.337 4.141 0.838 -67.824 6 A_U7:A47_B A 7 ? B 47 ? 23 3 1 A U 8 1_555 B A 25 1_555 -0.202 -1.334 -0.299 0.582 -5.287 -164.927 7 A_U8:A50_B A 8 ? B 50 ? 21 2 1 B A 6 1_555 A G 15 1_555 -3.497 3.642 -0.021 13.073 0.222 72.660 8 B_A31:G15_A B 31 ? A 15 ? 10 6 1 B G 26 1_555 A C 14 1_555 -0.076 -0.119 0.197 4.701 -4.808 0.173 9 B_G51:C14_A B 51 ? A 14 ? 19 1 1 B G 27 1_555 A C 13 1_555 -0.147 -0.266 -0.167 -2.410 -5.184 0.327 10 B_G52:C13_A B 52 ? A 13 ? 19 1 1 B A 28 1_555 A U 12 1_555 -0.020 -0.087 -0.112 5.733 5.372 8.201 11 B_A53:U12_A B 53 ? A 12 ? 20 1 1 B G 29 1_555 A C 10 1_555 -0.297 -0.149 -0.114 5.308 1.634 -1.902 12 B_G54:C10_A B 54 ? A 10 ? 19 1 1 A G 19 1_555 B C 5 1_555 -0.178 -0.206 -0.965 -13.066 1.226 -1.219 13 A_G19:C30_B A 19 ? B 30 ? 19 1 1 A U 20 1_555 B A 4 1_555 -0.027 0.127 -0.273 3.620 -0.242 -7.672 14 A_U20:A29_B A 20 ? B 29 ? 20 1 1 A CBV 21 1_555 B G 3 1_555 -0.692 0.295 -0.148 2.628 -4.697 3.987 15 A_CBV21:G28_B A 21 ? B 28 ? 19 1 1 A G 22 1_555 B C 2 1_555 -0.130 -0.139 -0.760 -14.622 0.585 -1.899 16 A_G22:C27_B A 22 ? B 27 ? 19 1 1 A C 23 1_555 B G 1 1_555 0.204 -0.189 -0.420 8.507 -0.087 -2.056 17 A_C23:G26_B A 23 ? B 26 ? 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 2 1_555 B C 12 1_555 A A 3 1_555 B U 11 1_555 0.018 -1.146 3.416 0.609 2.551 33.040 -2.452 0.074 3.321 4.476 -1.069 33.141 1 AA_G2A3:U36C37_BB A 2 ? B 37 ? A 3 ? B 36 ? 1 A A 3 1_555 B U 11 1_555 A G 4 1_555 B C 10 1_555 -0.469 -1.390 3.354 0.015 5.267 30.631 -3.596 0.878 3.078 9.879 -0.027 31.070 2 AA_A3G4:C35U36_BB A 3 ? B 36 ? A 4 ? B 35 ? 1 A G 4 1_555 B C 10 1_555 A C 5 1_555 B G 9 1_555 0.794 -1.819 3.208 1.729 3.407 32.402 -3.806 -1.125 3.043 6.078 -3.084 32.620 3 AA_G4C5:G34C35_BB A 4 ? B 35 ? A 5 ? B 34 ? 1 A C 5 1_555 B G 9 1_555 B C 21 1_555 B G 8 1_555 -2.879 1.104 3.462 6.505 1.437 76.996 0.842 2.498 3.266 1.152 -5.216 77.239 4 AB_C5C46:G33G34_BB A 5 ? B 34 ? B 46 ? B 33 ? 1 B C 21 1_555 B G 8 1_555 A U 7 1_555 B A 22 1_555 -1.446 -3.230 3.446 -0.301 0.652 -23.062 7.832 -3.728 3.516 -1.630 -0.754 -23.073 5 BA_C46U7:A47G33_BB B 46 ? B 33 ? A 7 ? B 47 ? 1 A U 7 1_555 B A 22 1_555 A U 8 1_555 B A 25 1_555 -0.419 0.064 3.221 3.039 -0.190 85.745 0.051 0.375 3.208 -0.140 -2.233 85.788 6 AA_U7U8:A50A47_BB A 7 ? B 47 ? A 8 ? B 50 ? 1 A U 8 1_555 B A 25 1_555 B A 6 1_555 A G 15 1_555 4.976 -0.350 1.552 173.105 -35.131 -93.832 0.148 2.355 -2.244 17.656 86.997 -177.701 7 AB_U8A31:G15A50_AB A 8 ? B 50 ? B 31 ? A 15 ? 1 B A 6 1_555 A G 15 1_555 B G 26 1_555 A C 14 1_555 -2.281 -2.353 -1.181 115.354 -124.039 0.078 -1.554 0.799 0.168 -65.902 -61.288 169.388 8 BB_A31G51:C14G15_AA B 31 ? A 15 ? B 51 ? A 14 ? 1 B G 26 1_555 A C 14 1_555 B G 27 1_555 A C 13 1_555 -1.005 -2.306 3.365 -1.561 4.734 28.650 -5.613 1.666 3.002 9.475 3.125 29.071 9 BB_G51G52:C13C14_AA B 51 ? A 14 ? B 52 ? A 13 ? 1 B G 27 1_555 A C 13 1_555 B A 28 1_555 A U 12 1_555 0.465 -1.416 3.062 -3.637 6.372 31.957 -3.484 -1.380 2.670 11.386 6.499 32.767 10 BB_G52A53:U12C13_AA B 52 ? A 13 ? B 53 ? A 12 ? 1 B A 28 1_555 A U 12 1_555 B G 29 1_555 A C 10 1_555 2.245 -1.206 3.260 5.002 12.735 47.640 -2.374 -2.317 3.069 15.399 -6.048 49.455 11 BB_A53G54:C10U12_AA B 53 ? A 12 ? B 54 ? A 10 ? 1 A G 19 1_555 B C 5 1_555 A U 20 1_555 B A 4 1_555 0.222 -1.609 3.047 -3.840 5.656 27.614 -4.418 -1.227 2.618 11.626 7.892 28.431 12 AA_G19U20:A29C30_BB A 19 ? B 30 ? A 20 ? B 29 ? 1 A U 20 1_555 B A 4 1_555 A CBV 21 1_555 B G 3 1_555 0.273 -1.941 3.348 1.820 4.048 23.932 -5.849 -0.089 2.996 9.656 -4.341 24.334 13 AA_U20CBV21:G28A29_BB A 20 ? B 29 ? A 21 ? B 28 ? 1 A CBV 21 1_555 B G 3 1_555 A G 22 1_555 B C 2 1_555 0.802 -2.110 3.730 8.938 3.297 29.283 -4.715 0.489 3.562 6.315 -17.117 30.761 14 AA_CBV21G22:C27G28_BB A 21 ? B 28 ? A 22 ? B 27 ? 1 A G 22 1_555 B C 2 1_555 A C 23 1_555 B G 1 1_555 0.117 -1.999 2.754 -3.143 2.249 37.081 -3.373 -0.526 2.614 3.524 4.926 37.275 15 AA_G22C23:G26C27_BB A 22 ? B 27 ? A 23 ? B 26 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Natural Science Foundation of China (NSFC)' China 32171191 1 'Cancer Research UK' 'United Kingdom' A18604 2 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id NMN _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id NMN _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 3 'MAGNESIUM ION' MG 4 'BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE' NMN 5 water HOH # _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 2 1' _space_group.name_Hall ;P 32 2" ; _space_group.IT_number 154 _space_group.crystal_system trigonal _space_group.id 1 #