data_8XZK # _entry.id 8XZK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.395 _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 8XZK pdb_00008xzk 10.2210/pdb8xzk/pdb WWPDB D_1300044550 ? ? # 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 2024-07-24 2 'Structure model' 1 1 2024-08-21 # _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' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8XZK _pdbx_database_status.recvd_initial_deposition_date 2024-01-21 _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 # _pdbx_contact_author.id 2 _pdbx_contact_author.email aimingren@zju.edu.cn _pdbx_contact_author.name_first Aiming _pdbx_contact_author.name_last Ren _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-5420-4899 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Li, C.Y.' 1 ? 'Ren, A.M.' 2 ? # _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 52 _citation.language ? _citation.page_first 8454 _citation.page_last 8465 _citation.title 'Structure-based characterization and compound identification of the wild-type THF class-II riboswitch.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkae377 _citation.pdbx_database_id_PubMed 38769061 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Li, C.' 1 ? primary 'Xu, X.' 2 ? primary 'Geng, Z.' 3 ? primary 'Zheng, L.' 4 ? primary 'Song, Q.' 5 ? primary 'Shen, X.' 6 ? primary 'Wu, J.' 7 ? primary 'Zhao, J.' 8 ? primary 'Li, H.' 9 ? primary 'He, M.' 10 ? primary 'Tai, X.' 11 ? primary 'Zhang, L.' 12 0000-0001-8139-0474 primary 'Ma, J.' 13 ? primary 'Dong, Y.' 14 ? primary 'Ren, A.' 15 0000-0002-5420-4899 # 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 man 'RNA (53-MER)' 17094.062 1 ? ? ? ? 2 water nat water 18.015 4 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(GDP)GGUGUGUACCGUUCAACUCGUCCCAGCUUCGACUGGGACUACGGGAGCGCCU' _entity_poly.pdbx_seq_one_letter_code_can GGGUGUGUACCGUUCAACUCGUCCCAGCUUCGACUGGGACUACGGGAGCGCCU _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GDP n 1 2 G n 1 3 G n 1 4 U n 1 5 G n 1 6 U n 1 7 G n 1 8 U n 1 9 A n 1 10 C n 1 11 C n 1 12 G n 1 13 U n 1 14 U n 1 15 C n 1 16 A n 1 17 A n 1 18 C n 1 19 U n 1 20 C n 1 21 G n 1 22 U n 1 23 C n 1 24 C n 1 25 C n 1 26 A n 1 27 G n 1 28 C n 1 29 U n 1 30 U n 1 31 C n 1 32 G n 1 33 A n 1 34 C n 1 35 U n 1 36 G n 1 37 G n 1 38 G n 1 39 A n 1 40 C n 1 41 U n 1 42 A n 1 43 C n 1 44 G n 1 45 G n 1 46 G n 1 47 A n 1 48 G n 1 49 C n 1 50 G n 1 51 C n 1 52 C n 1 53 U n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 53 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'unidentified eubacterium clone A70' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 41312 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'in vitro transcription vector pT7-TP(deltai)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 905931 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # 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 GDP 'RNA linking' n "GUANOSINE-5'-DIPHOSPHATE" ? 'C10 H15 N5 O11 P2' 443.201 HOH non-polymer . WATER ? 'H2 O' 18.015 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GDP 1 1 1 GDP GDP A . n A 1 2 G 2 2 2 G G A . n A 1 3 G 3 3 3 G G A . n A 1 4 U 4 4 4 U U A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 G 7 7 7 G G A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 C 10 10 10 C C A . n A 1 11 C 11 11 11 C C A . n A 1 12 G 12 12 12 G G A . n A 1 13 U 13 13 13 U U A . n A 1 14 U 14 14 14 U U A . n A 1 15 C 15 15 15 C C 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 C 18 18 18 C C A . n A 1 19 U 19 19 19 U U A . n A 1 20 C 20 20 20 C C A . n A 1 21 G 21 21 21 G G A . n A 1 22 U 22 22 22 U U A . n A 1 23 C 23 23 23 C C A . n A 1 24 C 24 24 24 C C A . n A 1 25 C 25 25 25 C C A . n A 1 26 A 26 26 26 A A A . n A 1 27 G 27 27 27 G G A . n A 1 28 C 28 28 28 C C A . n A 1 29 U 29 29 29 U U A . n A 1 30 U 30 30 30 U U A . n A 1 31 C 31 31 31 C C A . n A 1 32 G 32 32 32 G G A . n A 1 33 A 33 33 33 A A A . n A 1 34 C 34 34 34 C C A . n A 1 35 U 35 35 35 U U A . n A 1 36 G 36 36 36 G G A . n A 1 37 G 37 37 37 G G A . n A 1 38 G 38 38 38 G G A . n A 1 39 A 39 39 39 A A A . n A 1 40 C 40 40 40 C C A . n A 1 41 U 41 41 41 U U A . n A 1 42 A 42 42 42 A A A . n A 1 43 C 43 43 43 C C A . n A 1 44 G 44 44 44 G G A . n A 1 45 G 45 45 45 G G A . n A 1 46 G 46 46 46 G G A . n A 1 47 A 47 47 47 A A A . n A 1 48 G 48 48 48 G G A . n A 1 49 C 49 49 49 C C A . n A 1 50 G 50 50 50 G G A . n A 1 51 C 51 51 51 C C A . n A 1 52 C 52 52 52 C C A . n A 1 53 U 53 53 53 U U A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HOH 1 101 2 HOH HOH A . B 2 HOH 2 102 1 HOH HOH A . B 2 HOH 3 103 4 HOH HOH A . B 2 HOH 4 104 3 HOH HOH A . # 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 ? ? ? '(1.18.2_3874: ???)' 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? Aimless ? ? ? . 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-3000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 8XZK _cell.details ? _cell.formula_units_Z ? _cell.length_a 45.282 _cell.length_a_esd ? _cell.length_b 55.624 _cell.length_b_esd ? _cell.length_c 61.903 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 4 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8XZK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8XZK _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 2.34 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 47.40 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '0.08 M Sodium chloride, 0.04 M Sodium cacodylate trihydrate pH 7.0, 30% v/v MPD, 0.012 M Spermine tetrahydrochloride' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 289 # _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 PILATUS 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2022-01-18 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97853 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'SSRF BEAMLINE BL18U1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.97853 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL18U1 _diffrn_source.pdbx_synchrotron_site SSRF # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 8XZK _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.58 _reflns.d_resolution_low 41.37 _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 4721 _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 89.0 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 11.7 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 16.9 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.02 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.098 _reflns.pdbx_Rpim_I_all 0.028 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 55367 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.998 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.093 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # _reflns_shell.d_res_high 2.58 _reflns_shell.d_res_low 2.72 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.number_measured_all 1902 _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 188 _reflns_shell.percent_possible_obs 25.4 _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 10.1 _reflns_shell.pdbx_chi_squared 0.72 _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs 1.4 _reflns_shell.pdbx_Rrim_I_all 1.607 _reflns_shell.pdbx_Rpim_I_all 0.477 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.766 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 1.530 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_percent_possible_ellipsoidal ? _reflns_shell.pdbx_percent_possible_spherical ? _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns_shell.pdbx_percent_possible_spherical_anomalous ? _reflns_shell.pdbx_redundancy_anomalous ? _reflns_shell.pdbx_CC_half_anomalous ? _reflns_shell.pdbx_absDiff_over_sigma_anomalous ? _reflns_shell.pdbx_percent_possible_anomalous ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _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 8XZK _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 2.58 _refine.ls_d_res_low 36.55 _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 4609 _refine.ls_number_reflns_R_free 461 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 87.64 _refine.ls_percent_reflns_R_free 10.00 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2053 _refine.ls_R_factor_R_free 0.2627 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1990 _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 1.34 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _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 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _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 34.02 _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 0.30 _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 2.58 _refine_hist.d_res_low 36.55 _refine_hist.number_atoms_solvent 4 _refine_hist.number_atoms_total 1136 _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 1132 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.005 ? 1261 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.100 ? 1963 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 13.958 ? 632 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.044 ? 264 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.006 ? 53 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 2.58 2.95 . . 113 1041 67.00 . . . . 0.3193 . . . . . . . . . . . 0.3947 'X-RAY DIFFRACTION' 2.95 3.72 . . 167 1492 97.00 . . . . 0.2341 . . . . . . . . . . . 0.3235 'X-RAY DIFFRACTION' 3.72 36.55 . . 181 1615 98.00 . . . . 0.1648 . . . . . . . . . . . 0.2140 # _struct.entry_id 8XZK _struct.title 'Crystal structure of folE riboswitch' _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 8XZK _struct_keywords.text 'riboswitch, 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 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 8XZK _struct_ref.pdbx_db_accession 8XZK _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 8XZK _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 53 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 8XZK _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 53 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 53 # _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 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A GDP 1 "O3'" ? ? ? 1_555 A G 2 P ? ? A GDP 1 A G 2 1_555 ? ? ? ? ? ? ? 1.563 ? ? hydrog1 hydrog ? ? A GDP 1 N2 ? ? ? 1_555 A U 53 O2 ? ? A GDP 1 A U 53 1_555 ? ? ? ? ? ? 'GDP-U MISPAIR' ? ? ? hydrog2 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 52 N3 ? ? A G 2 A C 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 52 O2 ? ? A G 2 A C 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 52 N4 ? ? A G 2 A C 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 51 N3 ? ? A G 3 A C 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 51 O2 ? ? A G 3 A C 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 51 N4 ? ? A G 3 A C 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 4 N3 ? ? ? 1_555 A G 50 O6 ? ? A U 4 A G 50 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog9 hydrog ? ? A U 4 O2 ? ? ? 1_555 A G 50 N1 ? ? A U 4 A G 50 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog10 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 49 N3 ? ? A G 5 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 49 O2 ? ? A G 5 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 49 N4 ? ? A G 5 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 6 N3 ? ? ? 1_555 A G 48 O6 ? ? A U 6 A G 48 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog14 hydrog ? ? A U 6 O2 ? ? ? 1_555 A G 48 N1 ? ? A U 6 A G 48 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog15 hydrog ? ? A G 7 N2 ? ? ? 1_555 A A 47 N7 ? ? A G 7 A A 47 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog16 hydrog ? ? A G 7 N3 ? ? ? 1_555 A A 47 N6 ? ? A G 7 A A 47 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog17 hydrog ? ? A A 9 N6 ? ? ? 1_555 A G 46 N3 ? ? A A 9 A G 46 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog18 hydrog ? ? A A 9 N7 ? ? ? 1_555 A G 46 N2 ? ? A A 9 A G 46 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog19 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 45 N1 ? ? A C 10 A G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 45 O6 ? ? A C 10 A G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 45 N2 ? ? A C 10 A G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N3 ? ? ? 1_555 A G 44 N1 ? ? A C 11 A G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 N4 ? ? ? 1_555 A G 44 O6 ? ? A C 11 A G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 O2 ? ? ? 1_555 A G 44 N2 ? ? A C 11 A G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 43 N3 ? ? A G 12 A C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 43 O2 ? ? A G 12 A C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 43 N4 ? ? A G 12 A C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 13 O2 ? ? ? 1_555 A A 16 N6 ? ? A U 13 A A 16 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog29 hydrog ? ? A U 13 N3 ? ? ? 1_555 A A 42 N1 ? ? A U 13 A A 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 13 O4 ? ? ? 1_555 A A 42 N6 ? ? A U 13 A A 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 17 N7 ? ? A U 14 A A 17 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog32 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 17 N6 ? ? A U 14 A A 17 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog33 hydrog ? ? A A 16 N6 ? ? ? 1_555 A C 43 O2 ? ? A A 16 A C 43 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog34 hydrog ? ? A A 17 N6 ? ? ? 1_555 A A 42 N3 ? ? A A 17 A A 42 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog35 hydrog ? ? A G 21 N1 ? ? ? 1_555 A C 40 N3 ? ? A G 21 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 21 N2 ? ? ? 1_555 A C 40 O2 ? ? A G 21 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 21 O6 ? ? ? 1_555 A C 40 N4 ? ? A G 21 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A U 22 N3 ? ? ? 1_555 A A 39 N1 ? ? A U 22 A A 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A U 22 O4 ? ? ? 1_555 A A 39 N6 ? ? A U 22 A A 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 23 N3 ? ? ? 1_555 A G 38 N1 ? ? A C 23 A G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 23 N4 ? ? ? 1_555 A G 38 O6 ? ? A C 23 A G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 23 O2 ? ? ? 1_555 A G 38 N2 ? ? A C 23 A G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 24 N3 ? ? ? 1_555 A G 37 N1 ? ? A C 24 A G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 24 N4 ? ? ? 1_555 A G 37 O6 ? ? A C 24 A G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 24 O2 ? ? ? 1_555 A G 37 N2 ? ? A C 24 A G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 25 N3 ? ? ? 1_555 A G 36 N1 ? ? A C 25 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 25 N4 ? ? ? 1_555 A G 36 O6 ? ? A C 25 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 25 O2 ? ? ? 1_555 A G 36 N2 ? ? A C 25 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A A 26 N1 ? ? ? 1_555 A U 35 N3 ? ? A A 26 A U 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A A 26 N6 ? ? ? 1_555 A U 35 O4 ? ? A A 26 A U 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A G 27 N1 ? ? ? 1_555 A C 34 N3 ? ? A G 27 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A G 27 N2 ? ? ? 1_555 A C 34 O2 ? ? A G 27 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A G 27 O6 ? ? ? 1_555 A C 34 N4 ? ? A G 27 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A C 28 N3 ? ? ? 1_555 A G 32 N1 ? ? A C 28 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A C 28 N4 ? ? ? 1_555 A G 32 O6 ? ? A C 28 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A C 28 O2 ? ? ? 1_555 A G 32 N2 ? ? A C 28 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 "O2'" A C 28 ? ? OP2 A U 30 ? ? 2.15 2 1 O6 A G 3 ? ? O A HOH 101 ? ? 2.15 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "C3'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 GDP _pdbx_validate_rmsd_angle.auth_seq_id_1 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 "O3'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 GDP _pdbx_validate_rmsd_angle.auth_seq_id_2 1 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 P _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 G _pdbx_validate_rmsd_angle.auth_seq_id_3 2 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 109.36 _pdbx_validate_rmsd_angle.angle_target_value 119.70 _pdbx_validate_rmsd_angle.angle_deviation -10.34 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.20 _pdbx_validate_rmsd_angle.linker_flag Y # _pdbx_entry_details.entry_id 8XZK _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.has_protein_modification ? # 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 GDP PB P N N 111 GDP O1B O N N 112 GDP O2B O N N 113 GDP O3B O N N 114 GDP O3A O N N 115 GDP PA P N N 116 GDP O1A O N N 117 GDP O2A O N N 118 GDP "O5'" O N N 119 GDP "C5'" C N N 120 GDP "C4'" C N R 121 GDP "O4'" O N N 122 GDP "C3'" C N S 123 GDP "O3'" O N N 124 GDP "C2'" C N R 125 GDP "O2'" O N N 126 GDP "C1'" C N R 127 GDP N9 N Y N 128 GDP C8 C Y N 129 GDP N7 N Y N 130 GDP C5 C Y N 131 GDP C6 C N N 132 GDP O6 O N N 133 GDP N1 N N N 134 GDP C2 C N N 135 GDP N2 N N N 136 GDP N3 N N N 137 GDP C4 C Y N 138 GDP HOB2 H N N 139 GDP HOB3 H N N 140 GDP HOA2 H N N 141 GDP "H5'" H N N 142 GDP "H5''" H N N 143 GDP "H4'" H N N 144 GDP "H3'" H N N 145 GDP "HO3'" H N N 146 GDP "H2'" H N N 147 GDP "HO2'" H N N 148 GDP "H1'" H N N 149 GDP H8 H N N 150 GDP HN1 H N N 151 GDP HN21 H N N 152 GDP HN22 H N N 153 HOH O O N N 154 HOH H1 H N N 155 HOH H2 H N N 156 U OP3 O N N 157 U P P N N 158 U OP1 O N N 159 U OP2 O N N 160 U "O5'" O N N 161 U "C5'" C N N 162 U "C4'" C N R 163 U "O4'" O N N 164 U "C3'" C N S 165 U "O3'" O N N 166 U "C2'" C N R 167 U "O2'" O N N 168 U "C1'" C N R 169 U N1 N N N 170 U C2 C N N 171 U O2 O N N 172 U N3 N N N 173 U C4 C N N 174 U O4 O N N 175 U C5 C N N 176 U C6 C N N 177 U HOP3 H N N 178 U HOP2 H N N 179 U "H5'" H N N 180 U "H5''" H N N 181 U "H4'" H N N 182 U "H3'" H N N 183 U "HO3'" H N N 184 U "H2'" H N N 185 U "HO2'" H N N 186 U "H1'" H N N 187 U H3 H N N 188 U H5 H N N 189 U H6 H N N 190 # 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 GDP PB O1B doub N N 116 GDP PB O2B sing N N 117 GDP PB O3B sing N N 118 GDP PB O3A sing N N 119 GDP O2B HOB2 sing N N 120 GDP O3B HOB3 sing N N 121 GDP O3A PA sing N N 122 GDP PA O1A doub N N 123 GDP PA O2A sing N N 124 GDP PA "O5'" sing N N 125 GDP O2A HOA2 sing N N 126 GDP "O5'" "C5'" sing N N 127 GDP "C5'" "C4'" sing N N 128 GDP "C5'" "H5'" sing N N 129 GDP "C5'" "H5''" sing N N 130 GDP "C4'" "O4'" sing N N 131 GDP "C4'" "C3'" sing N N 132 GDP "C4'" "H4'" sing N N 133 GDP "O4'" "C1'" sing N N 134 GDP "C3'" "O3'" sing N N 135 GDP "C3'" "C2'" sing N N 136 GDP "C3'" "H3'" sing N N 137 GDP "O3'" "HO3'" sing N N 138 GDP "C2'" "O2'" sing N N 139 GDP "C2'" "C1'" sing N N 140 GDP "C2'" "H2'" sing N N 141 GDP "O2'" "HO2'" sing N N 142 GDP "C1'" N9 sing N N 143 GDP "C1'" "H1'" sing N N 144 GDP N9 C8 sing Y N 145 GDP N9 C4 sing Y N 146 GDP C8 N7 doub Y N 147 GDP C8 H8 sing N N 148 GDP N7 C5 sing Y N 149 GDP C5 C6 sing N N 150 GDP C5 C4 doub Y N 151 GDP C6 O6 doub N N 152 GDP C6 N1 sing N N 153 GDP N1 C2 sing N N 154 GDP N1 HN1 sing N N 155 GDP C2 N2 sing N N 156 GDP C2 N3 doub N N 157 GDP N2 HN21 sing N N 158 GDP N2 HN22 sing N N 159 GDP N3 C4 sing N N 160 HOH O H1 sing N N 161 HOH O H2 sing N N 162 U OP3 P sing N N 163 U OP3 HOP3 sing N N 164 U P OP1 doub N N 165 U P OP2 sing N N 166 U P "O5'" sing N N 167 U OP2 HOP2 sing N N 168 U "O5'" "C5'" sing N N 169 U "C5'" "C4'" sing N N 170 U "C5'" "H5'" sing N N 171 U "C5'" "H5''" sing N N 172 U "C4'" "O4'" sing N N 173 U "C4'" "C3'" sing N N 174 U "C4'" "H4'" sing N N 175 U "O4'" "C1'" sing N N 176 U "C3'" "O3'" sing N N 177 U "C3'" "C2'" sing N N 178 U "C3'" "H3'" sing N N 179 U "O3'" "HO3'" sing N N 180 U "C2'" "O2'" sing N N 181 U "C2'" "C1'" sing N N 182 U "C2'" "H2'" sing N N 183 U "O2'" "HO2'" sing N N 184 U "C1'" N1 sing N N 185 U "C1'" "H1'" sing N N 186 U N1 C2 sing N N 187 U N1 C6 sing N N 188 U C2 O2 doub N N 189 U C2 N3 sing N N 190 U N3 C4 sing N N 191 U N3 H3 sing N N 192 U C4 O4 doub N N 193 U C4 C5 sing N N 194 U C5 C6 doub N N 195 U C5 H5 sing N N 196 U C6 H6 sing N N 197 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8XZK 'double helix' 8XZK 'a-form double helix' 8XZK 'hairpin loop' 8XZK 'bulge loop' 8XZK 'mismatched base pair' 8XZK 'quadruple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A GDP 1 1_555 A U 53 1_555 -0.581 0.507 -0.357 -9.672 8.199 -6.324 1 A_GDP1:U53_A A 1 ? A 53 ? ? ? 1 A G 2 1_555 A C 52 1_555 -0.246 -0.242 0.310 7.126 -6.303 0.209 2 A_G2:C52_A A 2 ? A 52 ? 19 1 1 A G 3 1_555 A C 51 1_555 0.110 -0.157 -0.308 -10.232 -12.471 -0.736 3 A_G3:C51_A A 3 ? A 51 ? 19 1 1 A U 4 1_555 A G 50 1_555 2.363 -0.615 0.321 -10.922 -5.863 -2.512 4 A_U4:G50_A A 4 ? A 50 ? 28 1 1 A G 5 1_555 A C 49 1_555 0.305 -0.101 -0.074 -7.341 -8.057 2.291 5 A_G5:C49_A A 5 ? A 49 ? 19 1 1 A U 6 1_555 A G 48 1_555 2.508 -0.788 -0.004 -2.111 3.154 -4.958 6 A_U6:G48_A A 6 ? A 48 ? 28 1 1 A G 7 1_555 A A 47 1_555 6.926 -4.818 0.313 16.199 0.421 -5.062 7 A_G7:A47_A A 7 ? A 47 ? 11 10 1 A A 9 1_555 A G 46 1_555 -6.911 -3.866 0.860 -17.292 -12.228 5.764 8 A_A9:G46_A A 9 ? A 46 ? 11 9 1 A C 10 1_555 A G 45 1_555 0.334 -0.169 0.028 -1.727 -3.910 2.793 9 A_C10:G45_A A 10 ? A 45 ? 19 1 1 A C 11 1_555 A G 44 1_555 0.277 -0.169 0.059 6.209 -16.768 0.747 10 A_C11:G44_A A 11 ? A 44 ? 19 1 1 A G 12 1_555 A C 43 1_555 -0.517 -0.355 0.428 -6.589 -17.489 -0.907 11 A_G12:C43_A A 12 ? A 43 ? 19 1 1 A U 13 1_555 A A 42 1_555 0.138 0.034 0.538 -12.095 -8.798 4.808 12 A_U13:A42_A A 13 ? A 42 ? 20 1 1 A G 21 1_555 A C 40 1_555 -0.345 -0.381 0.131 -0.132 -14.854 1.798 13 A_G21:C40_A A 21 ? A 40 ? 19 1 1 A U 22 1_555 A A 39 1_555 -0.079 -0.428 0.175 -1.543 -12.183 -2.590 14 A_U22:A39_A A 22 ? A 39 ? 20 1 1 A C 23 1_555 A G 38 1_555 -0.199 0.090 -0.061 5.547 -15.771 6.070 15 A_C23:G38_A A 23 ? A 38 ? 19 1 1 A C 24 1_555 A G 37 1_555 0.174 -0.381 0.037 2.447 -7.379 0.119 16 A_C24:G37_A A 24 ? A 37 ? 19 1 1 A C 25 1_555 A G 36 1_555 -0.126 -0.147 0.233 0.063 -6.077 1.282 17 A_C25:G36_A A 25 ? A 36 ? 19 1 1 A A 26 1_555 A U 35 1_555 -0.363 -0.184 0.021 2.675 -15.890 0.497 18 A_A26:U35_A A 26 ? A 35 ? 20 1 1 A G 27 1_555 A C 34 1_555 -0.512 -0.161 0.194 -8.341 -16.845 -0.420 19 A_G27:C34_A A 27 ? A 34 ? 19 1 1 A C 28 1_555 A G 32 1_555 -0.200 0.087 -0.035 0.862 1.456 2.599 20 A_C28:G32_A A 28 ? A 32 ? 19 1 1 A U 14 1_555 A A 17 1_555 -0.575 3.535 0.419 3.727 7.583 -70.416 21 A_U14:A17_A A 14 ? A 17 ? 23 3 # 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 GDP 1 1_555 A U 53 1_555 A G 2 1_555 A C 52 1_555 0.512 -1.602 2.841 -8.409 7.141 31.467 -3.745 -2.013 2.228 12.689 14.942 33.299 1 AA_GDP1G2:C52U53_AA A 1 ? A 53 ? A 2 ? A 52 ? 1 A G 2 1_555 A C 52 1_555 A G 3 1_555 A C 51 1_555 0.036 -1.845 3.604 3.636 10.052 34.976 -4.370 0.458 2.968 16.261 -5.883 36.524 2 AA_G2G3:C51C52_AA A 2 ? A 52 ? A 3 ? A 51 ? 1 A G 3 1_555 A C 51 1_555 A U 4 1_555 A G 50 1_555 -0.137 -1.493 3.278 -3.002 2.002 41.921 -2.285 -0.118 3.208 2.793 4.187 42.069 3 AA_G3U4:G50C51_AA A 3 ? A 51 ? A 4 ? A 50 ? 1 A U 4 1_555 A G 50 1_555 A G 5 1_555 A C 49 1_555 -0.082 -1.868 2.907 6.176 6.415 27.090 -5.002 1.328 2.337 13.247 -12.755 28.490 4 AA_U4G5:C49G50_AA A 4 ? A 50 ? A 5 ? A 49 ? 1 A G 5 1_555 A C 49 1_555 A U 6 1_555 A G 48 1_555 -0.011 -1.276 3.080 2.844 9.102 36.407 -3.043 0.349 2.686 14.269 -4.459 37.594 5 AA_G5U6:G48C49_AA A 5 ? A 49 ? A 6 ? A 48 ? 1 A U 6 1_555 A G 48 1_555 A G 7 1_555 A A 47 1_555 -0.108 -1.089 2.919 4.137 4.690 55.898 -1.390 0.320 2.813 4.986 -4.398 56.219 6 AA_U6G7:A47G48_AA A 6 ? A 48 ? A 7 ? A 47 ? 1 A G 7 1_555 A A 47 1_555 A A 9 1_555 A G 46 1_555 -2.076 -0.142 5.788 8.707 13.797 4.250 -13.992 15.609 0.276 63.845 -40.294 16.855 7 AA_G7A9:G46A47_AA A 7 ? A 47 ? A 9 ? A 46 ? 1 A A 9 1_555 A G 46 1_555 A C 10 1_555 A G 45 1_555 0.354 -0.314 2.941 -0.524 11.491 58.569 -0.831 -0.380 2.837 11.623 0.531 59.589 8 AA_A9C10:G45G46_AA A 9 ? A 46 ? A 10 ? A 45 ? 1 A C 10 1_555 A G 45 1_555 A C 11 1_555 A G 44 1_555 0.025 -1.607 2.993 1.302 6.143 27.397 -4.555 0.213 2.577 12.758 -2.704 28.094 9 AA_C10C11:G44G45_AA A 10 ? A 45 ? A 11 ? A 44 ? 1 A C 11 1_555 A G 44 1_555 A G 12 1_555 A C 43 1_555 0.271 -1.920 3.243 -2.023 11.561 29.567 -5.381 -0.823 2.324 21.611 3.781 31.763 10 AA_C11G12:C43G44_AA A 11 ? A 44 ? A 12 ? A 43 ? 1 A G 12 1_555 A C 43 1_555 A U 13 1_555 A A 42 1_555 0.005 -1.345 3.344 -1.227 6.542 37.167 -2.915 -0.164 3.070 10.164 1.907 37.737 11 AA_G12U13:A42C43_AA A 12 ? A 43 ? A 13 ? A 42 ? 1 A U 13 1_555 A A 42 1_555 A G 21 1_555 A C 40 1_555 -2.764 -2.852 5.880 1.366 2.907 78.328 -2.400 2.254 5.747 2.301 -1.081 78.383 12 AA_U13G21:C40A42_AA A 13 ? A 42 ? A 21 ? A 40 ? 1 A G 21 1_555 A C 40 1_555 A U 22 1_555 A A 39 1_555 -0.612 -1.436 3.290 -3.286 6.173 33.186 -3.432 0.534 3.027 10.661 5.674 33.894 13 AA_G21U22:A39C40_AA A 21 ? A 40 ? A 22 ? A 39 ? 1 A U 22 1_555 A A 39 1_555 A C 23 1_555 A G 38 1_555 0.507 -1.310 2.988 1.855 5.689 32.251 -3.185 -0.616 2.747 10.132 -3.303 32.787 14 AA_U22C23:G38A39_AA A 22 ? A 39 ? A 23 ? A 38 ? 1 A C 23 1_555 A G 38 1_555 A C 24 1_555 A G 37 1_555 0.131 -1.833 3.326 0.355 6.042 32.868 -4.157 -0.170 2.953 10.567 -0.621 33.405 15 AA_C23C24:G37G38_AA A 23 ? A 38 ? A 24 ? A 37 ? 1 A C 24 1_555 A G 37 1_555 A C 25 1_555 A G 36 1_555 -0.061 -2.013 3.255 -0.333 5.418 27.070 -5.454 0.053 2.806 11.430 0.702 27.599 16 AA_C24C25:G36G37_AA A 24 ? A 37 ? A 25 ? A 36 ? 1 A C 25 1_555 A G 36 1_555 A A 26 1_555 A U 35 1_555 0.470 -1.720 3.097 4.396 9.311 29.384 -4.776 -0.136 2.492 17.685 -8.350 31.098 17 AA_C25A26:U35G36_AA A 25 ? A 36 ? A 26 ? A 35 ? 1 A A 26 1_555 A U 35 1_555 A G 27 1_555 A C 34 1_555 0.244 -1.542 3.426 0.462 7.406 35.134 -3.565 -0.330 3.052 12.102 -0.755 35.885 18 AA_A26G27:C34U35_AA A 26 ? A 35 ? A 27 ? A 34 ? 1 A G 27 1_555 A C 34 1_555 A C 28 1_555 A G 32 1_555 -0.695 -1.155 2.940 2.409 5.468 26.822 -3.583 1.970 2.587 11.604 -5.112 27.468 19 AA_G27C28:G32C34_AA A 27 ? A 34 ? A 28 ? A 32 ? # _pdbx_audit_support.funding_organization 'National Natural Science Foundation of China (NSFC)' _pdbx_audit_support.country China _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _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 8XZE _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 8XZK _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.022084 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.017978 _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] 0.016154 _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 C MG N O P # loop_