data_5KH8 # _entry.id 5KH8 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 5KH8 pdb_00005kh8 10.2210/pdb5kh8/pdb WWPDB D_1000222101 ? ? BMRB 30108 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details . _pdbx_database_related.db_id 30108 _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 5KH8 _pdbx_database_status.recvd_initial_deposition_date 2016-06-14 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Zhang, Q.' 1 ? 'Zhao, B.' 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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nat. Chem. Biol.' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1552-4469 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 13 _citation.language ? _citation.page_first 968 _citation.page_last 974 _citation.title 'An excited state underlies gene regulation of a transcriptional riboswitch.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/nchembio.2427 _citation.pdbx_database_id_PubMed 28719589 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhao, B.' 1 ? primary 'Guffy, S.L.' 2 ? primary 'Williams, B.' 3 ? primary 'Zhang, Q.' 4 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'riboswitch (47-MER)' _entity.formula_weight 15053.960 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGCGAUGGUGUUCGCCAUAAACGCUCUUCGGAGCUAAUGACACCUAC _entity_poly.pdbx_seq_one_letter_code_can GGCGAUGGUGUUCGCCAUAAACGCUCUUCGGAGCUAAUGACACCUAC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 C n 1 4 G n 1 5 A n 1 6 U n 1 7 G n 1 8 G n 1 9 U n 1 10 G n 1 11 U n 1 12 U n 1 13 C n 1 14 G n 1 15 C n 1 16 C n 1 17 A n 1 18 U n 1 19 A n 1 20 A n 1 21 A n 1 22 C n 1 23 G n 1 24 C n 1 25 U n 1 26 C n 1 27 U n 1 28 U n 1 29 C n 1 30 G n 1 31 G n 1 32 A n 1 33 G n 1 34 C n 1 35 U n 1 36 A n 1 37 A n 1 38 U n 1 39 G n 1 40 A n 1 41 C n 1 42 A n 1 43 C n 1 44 C n 1 45 U n 1 46 A n 1 47 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 47 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5KH8 _struct_ref.pdbx_db_accession 5KH8 _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 5KH8 _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 47 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 5KH8 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 47 _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 47 # 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 2 1 '2D 1H-1H NOESY' 1 isotropic 2 1 2 '2D 1H-1H NOESY' 1 isotropic 3 1 2 '2D 1H-1H TOCSY' 1 isotropic 4 2 3 '2D 1H-15N HSQC' 1 isotropic 5 2 3 '2D 1H-13C HSQC' 1 isotropic 7 1 4 '2D 1H-13C HSQC' 1 isotropic 6 1 5 '2D 1H-13C HSQC' 1 isotropic 9 1 6 '2D 1H-13C HSQC' 1 isotropic 8 1 5 '2D HCCH COSY' 1 isotropic 10 1 6 '2D HCCH COSY' 1 isotropic 14 1 5 '3D HCCH-TOCSY' 1 isotropic 13 1 6 '3D HCCH-TOCSY' 1 isotropic 12 1 5 '31P spin-echo' 2 isotropic 11 1 6 '31P spin-echo' 2 isotropic 16 1 5 'CH-HCCH spin-echo' 2 isotropic 18 1 6 'CH-HCCH spin-echo' 2 isotropic 17 1 3 '2D 1H-15N HSQC' 1 anisotropic 15 1 3 '2D 1H-13C HSQC' 1 anisotropic # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.details _pdbx_nmr_exptl_sample_conditions.ionic_strength_err _pdbx_nmr_exptl_sample_conditions.ionic_strength_units _pdbx_nmr_exptl_sample_conditions.label _pdbx_nmr_exptl_sample_conditions.pH_err _pdbx_nmr_exptl_sample_conditions.pH_units _pdbx_nmr_exptl_sample_conditions.pressure_err _pdbx_nmr_exptl_sample_conditions.temperature_err _pdbx_nmr_exptl_sample_conditions.temperature_units 1 303 atm ambient 6.4 80 ? ? mM 303K ? pH ? ? K 2 283 atm ambient 6.4 80 ? ? mM 283K ? pH ? ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 '1.0 mM RNA (47mer), 10 mM magnesium chloride, 10 mM sodium phosphate, 50 mM potassium chloride, 50 uM EDTA, 95% H2O/5% D2O' '95% H2O/5% D2O' 'Unlabeled H2O' solution ? 2 '1.0 mM RNA (47mer), 10 mM magnesium chloride, 10 mM sodium phosphate, 50 mM potassium chloride, 50 uM EDTA, 100% D2O' '100% D2O' 'Unlabeled D2O' solution ? 3 ;1.0 mM [U-100% 13C; U-100% 15N] RNA (47mer), 10 mM magnesium chloride, 10 mM sodium phosphate, 50 mM potassium chloride, 50 uM EDTA, 95% H2O/5% D2O ; '95% H2O/5% D2O' 'Fully labeled H2O' solution ? 4 ;1.0 mM [U-100% 13C; U-100% 15N] RNA (47mer), 10 mM magnesium chloride, 10 mM sodium phosphate, 50 mM potassium chloride, 50 uM EDTA, 100% D2O ; '100% D2O' 'Fully labeled D2O' solution ? 5 ;1.0 mM [U-13C; U-15N]-Gua RNA (47mer), 10 mM magnesium chloride, 10 mM sodium phosphate, 50 mM potassium chloride, 50 uM EDTA, 100% D2O ; '100% D2O' 'G labeled D2O' solution ? 6 ;1.0 mM [U-13C; U-15N]-Ade ;[U-13C; U-15N]-Ura RNA (47mer), 10 mM magnesium chloride, 10 mM sodium phosphate, 50 mM potassium chloride, 50 uM EDTA, 100% D2O ; '100% D2O' 'AU labeled D2O' solution ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.details 1 'AVANCE III' ? Bruker 600 ? 2 'AVANCE III' ? Bruker 500 ? # _pdbx_nmr_ensemble.entry_id 5KH8 _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria ? # _pdbx_nmr_representative.entry_id 5KH8 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 collection TopSpin 3.2 'Bruker Biospin' 2 processing TopSpin 3.2 'Bruker Biospin' 3 'data analysis' TopSpin 3.2 'Bruker Biospin' 4 processing NMRDraw ? 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 5 'data analysis' NMRDraw ? 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 6 'data analysis' Sparky 3.110 Goddard 7 'peak picking' Sparky 3.110 Goddard 8 'chemical shift assignment' Sparky 3.110 Goddard 9 'structure calculation' 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' 10 refinement 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' # _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 5KH8 _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 5KH8 _struct.title 'Solution structures of the apo state fluoride 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 5KH8 _struct_keywords.text 'apo state, pseudoknot, riboswitch aptamer, transcriptional regulation, RNA' _struct_keywords.pdbx_keywords RNA # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 16 N3 ? ? A G 1 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 1 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 1 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 2 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 2 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 2 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 2 N2 ? ? ? 1_555 A A 20 N3 ? ? A G 2 A A 20 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog8 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 14 N1 ? ? A C 3 A G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 14 O6 ? ? A C 3 A G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 14 N2 ? ? A C 3 A G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 35 N3 ? ? A A 5 A U 35 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog15 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 35 O2 ? ? A A 5 A U 35 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog16 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 44 N3 ? ? A G 7 A C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 44 O2 ? ? A G 7 A C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 44 N4 ? ? A G 7 A C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 43 N3 ? ? A G 8 A C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 43 O2 ? ? A G 8 A C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 43 N4 ? ? A G 8 A C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 9 N3 ? ? ? 1_555 A A 42 N1 ? ? A U 9 A A 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A U 9 O4 ? ? ? 1_555 A A 42 N6 ? ? A U 9 A A 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 41 N3 ? ? A G 10 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 41 O2 ? ? A G 10 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 41 N4 ? ? A G 10 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 11 N3 ? ? ? 1_555 A A 40 N1 ? ? A U 11 A A 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 11 O4 ? ? ? 1_555 A A 40 N6 ? ? A U 11 A A 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U 12 N3 ? ? ? 1_555 A G 39 O6 ? ? A U 12 A G 39 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog30 hydrog ? ? A U 12 O2 ? ? ? 1_555 A G 39 N1 ? ? A U 12 A G 39 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog31 hydrog ? ? A G 23 N1 ? ? ? 1_555 A C 34 N3 ? ? A G 23 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 23 N2 ? ? ? 1_555 A C 34 O2 ? ? A G 23 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 23 O6 ? ? ? 1_555 A C 34 N4 ? ? A G 23 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 24 N3 ? ? ? 1_555 A G 33 N1 ? ? A C 24 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 24 N4 ? ? ? 1_555 A G 33 O6 ? ? A C 24 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 24 O2 ? ? ? 1_555 A G 33 N2 ? ? A C 24 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A U 25 N3 ? ? ? 1_555 A A 32 N1 ? ? A U 25 A A 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A U 25 O4 ? ? ? 1_555 A A 32 N6 ? ? A U 25 A A 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 26 N3 ? ? ? 1_555 A G 31 N1 ? ? A C 26 A G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 26 N4 ? ? ? 1_555 A G 31 O6 ? ? A C 26 A G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 26 O2 ? ? ? 1_555 A G 31 N2 ? ? A C 26 A G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A U 27 O2 ? ? ? 1_555 A G 30 N1 ? ? A U 27 A G 30 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog43 hydrog ? ? A A 37 N6 ? ? ? 1_555 A U 45 O2 ? ? A A 37 A U 45 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog44 hydrog ? ? A A 37 N7 ? ? ? 1_555 A U 45 N3 ? ? A A 37 A U 45 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 5KH8 _atom_sites.fract_transf_matrix[1][1] 1.000000 _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] 1.000000 _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] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A 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 G 8 8 8 G G A . n A 1 9 U 9 9 9 U U A . n A 1 10 G 10 10 10 G G A . n A 1 11 U 11 11 11 U U 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 G 14 14 14 G G A . n A 1 15 C 15 15 15 C C A . n A 1 16 C 16 16 16 C C A . n A 1 17 A 17 17 17 A A A . n A 1 18 U 18 18 18 U U A . n A 1 19 A 19 19 19 A A A . n A 1 20 A 20 20 20 A A A . n A 1 21 A 21 21 21 A A A . n A 1 22 C 22 22 22 C C A . n A 1 23 G 23 23 23 G G A . n A 1 24 C 24 24 24 C C A . n A 1 25 U 25 25 25 U U A . n A 1 26 C 26 26 26 C C A . n A 1 27 U 27 27 27 U U A . n A 1 28 U 28 28 28 U U A . n A 1 29 C 29 29 29 C C A . n A 1 30 G 30 30 30 G G A . n A 1 31 G 31 31 31 G G A . n A 1 32 A 32 32 32 A A A . n A 1 33 G 33 33 33 G G 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 A 36 36 36 A A A . n A 1 37 A 37 37 37 A A A . n A 1 38 U 38 38 38 U U A . n A 1 39 G 39 39 39 G G A . n A 1 40 A 40 40 40 A A A . n A 1 41 C 41 41 41 C C 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 C 44 44 44 C C A . n A 1 45 U 45 45 45 U U A . n A 1 46 A 46 46 46 A A A . n A 1 47 C 47 47 47 C C A . n # _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 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 # _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 ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2017-07-19 2 'Structure model' 1 1 2017-08-02 3 'Structure model' 1 2 2017-08-30 4 'Structure model' 1 3 2017-09-20 5 'Structure model' 1 4 2019-12-25 6 'Structure model' 1 5 2023-06-14 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Author supporting evidence' 4 5 'Structure model' 'Author supporting evidence' 5 5 'Structure model' 'Data collection' 6 6 'Structure model' 'Database references' 7 6 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 3 'Structure model' citation 3 4 'Structure model' pdbx_audit_support 4 5 'Structure model' pdbx_audit_support 5 5 'Structure model' pdbx_nmr_software 6 5 'Structure model' pdbx_nmr_spectrometer 7 6 'Structure model' database_2 8 6 'Structure model' pdbx_database_status # 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_abbrev' 2 2 'Structure model' '_citation.pdbx_database_id_DOI' 3 2 'Structure model' '_citation.pdbx_database_id_PubMed' 4 2 'Structure model' '_citation.title' 5 3 'Structure model' '_citation.journal_volume' 6 3 'Structure model' '_citation.page_first' 7 3 'Structure model' '_citation.page_last' 8 4 'Structure model' '_pdbx_audit_support.funding_organization' 9 5 'Structure model' '_pdbx_audit_support.funding_organization' 10 5 'Structure model' '_pdbx_nmr_software.name' 11 5 'Structure model' '_pdbx_nmr_spectrometer.model' 12 6 'Structure model' '_database_2.pdbx_DOI' 13 6 'Structure model' '_database_2.pdbx_database_accession' 14 6 'Structure model' '_pdbx_database_status.status_code_nmr_data' # loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 'RNA (47mer)' 1.0 ? mM 'natural abundance' 1 'magnesium chloride' 10 ? mM 'natural abundance' 1 'sodium phosphate' 10 ? mM 'natural abundance' 1 'potassium chloride' 50 ? mM 'natural abundance' 1 EDTA 50 ? uM 'natural abundance' 2 'RNA (47mer)' 1.0 ? mM 'natural abundance' 2 'magnesium chloride' 10 ? mM 'natural abundance' 2 'sodium phosphate' 10 ? mM 'natural abundance' 2 'potassium chloride' 50 ? mM 'natural abundance' 2 EDTA 50 ? uM 'natural abundance' 3 'RNA (47mer)' 1.0 ? mM '[U-100% 13C; U-100% 15N]' 3 'magnesium chloride' 10 ? mM 'natural abundance' 3 'sodium phosphate' 10 ? mM 'natural abundance' 3 'potassium chloride' 50 ? mM 'natural abundance' 3 EDTA 50 ? uM 'natural abundance' 4 'RNA (47mer)' 1.0 ? mM '[U-100% 13C; U-100% 15N]' 4 'magnesium chloride' 10 ? mM 'natural abundance' 4 'sodium phosphate' 10 ? mM 'natural abundance' 4 'potassium chloride' 50 ? mM 'natural abundance' 4 EDTA 50 ? uM 'natural abundance' 5 'RNA (47mer)' 1.0 ? mM '[U-13C; U-15N]-Gua' 5 'magnesium chloride' 10 ? mM 'natural abundance' 5 'sodium phosphate' 10 ? mM 'natural abundance' 5 'potassium chloride' 50 ? mM 'natural abundance' 5 EDTA 50 ? uM 'natural abundance' 6 'RNA (47mer)' 1.0 ? mM '[U-13C; U-15N]-Ade ;[U-13C; U-15N]-Ura' 6 'magnesium chloride' 10 ? mM 'natural abundance' 6 'sodium phosphate' 10 ? mM 'natural abundance' 6 'potassium chloride' 50 ? mM 'natural abundance' 6 EDTA 50 ? uM 'natural abundance' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5KH8 'double helix' 5KH8 'a-form double helix' 5KH8 tetraloop 5KH8 '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 1 1_555 A C 16 1_555 -0.582 0.020 0.033 3.043 3.222 -0.180 1 A_G1:C16_A A 1 ? A 16 ? 19 1 1 A G 2 1_555 A C 15 1_555 -0.923 -0.149 0.004 -1.670 -0.119 0.194 2 A_G2:C15_A A 2 ? A 15 ? 19 1 1 A C 3 1_555 A G 14 1_555 0.096 0.002 0.058 0.451 -11.286 2.832 3 A_C3:G14_A A 3 ? A 14 ? 19 1 1 A G 4 1_555 A C 13 1_555 -0.953 -0.178 -0.252 -0.793 -0.922 3.852 4 A_G4:C13_A A 4 ? A 13 ? 19 1 1 A G 39 1_555 A U 12 1_555 -2.284 -0.272 0.148 0.393 -9.548 -1.556 5 A_G39:U12_A A 39 ? A 12 ? 28 1 1 A A 40 1_555 A U 11 1_555 0.369 0.036 -0.001 -2.322 -8.322 2.404 6 A_A40:U11_A A 40 ? A 11 ? 20 1 1 A C 41 1_555 A G 10 1_555 0.186 0.090 -0.038 -2.381 -2.646 1.974 7 A_C41:G10_A A 41 ? A 10 ? 19 1 1 A A 42 1_555 A U 9 1_555 0.071 0.090 -0.036 0.869 -5.747 0.707 8 A_A42:U9_A A 42 ? A 9 ? 20 1 1 A C 43 1_555 A G 8 1_555 -0.078 0.099 -0.243 4.120 -1.648 3.459 9 A_C43:G8_A A 43 ? A 8 ? 19 1 1 A C 44 1_555 A G 7 1_555 -0.141 0.170 -0.153 5.313 -1.140 1.959 10 A_C44:G7_A A 44 ? A 7 ? 19 1 1 A U 45 1_555 A A 37 1_555 4.399 -2.228 -0.009 -8.929 -0.943 -83.941 11 A_U45:A37_A A 45 ? A 37 ? 24 4 1 A A 5 1_555 A U 35 1_555 0.102 2.123 0.008 3.365 6.357 168.740 12 A_A5:U35_A A 5 ? A 35 ? 21 2 1 A G 23 1_555 A C 34 1_555 0.592 0.050 0.076 -0.676 -9.469 0.189 13 A_G23:C34_A A 23 ? A 34 ? 19 1 1 A C 24 1_555 A G 33 1_555 0.535 -0.005 0.122 -1.904 -3.928 1.081 14 A_C24:G33_A A 24 ? A 33 ? 19 1 1 A U 25 1_555 A A 32 1_555 0.660 0.064 0.024 0.240 -3.347 -1.088 15 A_U25:A32_A A 25 ? A 32 ? 20 1 1 A C 26 1_555 A G 31 1_555 1.294 -0.396 -0.009 2.943 -0.229 2.706 16 A_C26:G31_A A 26 ? A 31 ? 19 1 1 A U 27 1_555 A G 30 1_555 1.355 -4.316 0.030 1.308 -6.793 -99.916 17 A_U27:G30_A A 27 ? A 30 ? ? 6 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 16 1_555 A G 2 1_555 A C 15 1_555 0.201 -1.658 3.447 -3.266 20.002 29.960 -5.263 -0.746 1.963 34.209 5.585 36.040 1 AA_G1G2:C15C16_AA A 1 ? A 16 ? A 2 ? A 15 ? 1 A G 2 1_555 A C 15 1_555 A C 3 1_555 A G 14 1_555 -0.017 -1.235 3.913 1.061 -4.605 31.989 -1.222 0.259 4.044 -8.299 -1.912 32.327 2 AA_G2C3:G14C15_AA A 2 ? A 15 ? A 3 ? A 14 ? 1 A C 3 1_555 A G 14 1_555 A G 4 1_555 A C 13 1_555 -0.086 -0.924 3.886 -1.105 9.701 30.801 -3.639 -0.070 3.445 17.714 2.017 32.275 3 AA_C3G4:C13G14_AA A 3 ? A 14 ? A 4 ? A 13 ? 1 A G 4 1_555 A C 13 1_555 A G 39 1_555 A U 12 1_555 -0.308 -2.489 3.337 -4.227 7.513 19.002 -9.743 -0.761 2.217 21.390 12.033 20.850 4 AA_G4G39:U12C13_AA A 4 ? A 13 ? A 39 ? A 12 ? 1 A G 39 1_555 A U 12 1_555 A A 40 1_555 A U 11 1_555 -0.251 -1.056 3.397 -1.515 7.991 45.348 -2.047 0.189 3.183 10.267 1.947 46.033 5 AA_G39A40:U11U12_AA A 39 ? A 12 ? A 40 ? A 11 ? 1 A A 40 1_555 A U 11 1_555 A C 41 1_555 A G 10 1_555 -0.140 -1.530 3.255 0.184 15.050 29.043 -5.042 0.278 2.214 27.781 -0.340 32.637 6 AA_A40C41:G10U11_AA A 40 ? A 11 ? A 41 ? A 10 ? 1 A C 41 1_555 A G 10 1_555 A A 42 1_555 A U 9 1_555 0.312 -1.066 3.462 0.537 13.484 30.161 -4.159 -0.458 2.753 24.434 -0.974 32.978 7 AA_C41A42:U9G10_AA A 41 ? A 10 ? A 42 ? A 9 ? 1 A A 42 1_555 A U 9 1_555 A C 43 1_555 A G 8 1_555 0.285 -1.355 3.409 1.025 12.486 27.286 -5.088 -0.349 2.565 24.872 -2.041 29.975 8 AA_A42C43:G8U9_AA A 42 ? A 9 ? A 43 ? A 8 ? 1 A C 43 1_555 A G 8 1_555 A C 44 1_555 A G 7 1_555 0.558 -1.653 3.493 -1.419 10.979 30.006 -4.954 -1.266 2.708 20.355 2.630 31.939 9 AA_C43C44:G7G8_AA A 43 ? A 8 ? A 44 ? A 7 ? 1 A C 44 1_555 A G 7 1_555 A U 45 1_555 A A 37 1_555 -2.153 -2.215 3.578 7.004 12.690 76.935 -2.123 1.910 3.067 10.115 -5.583 78.080 10 AA_C44U45:A37G7_AA A 44 ? A 7 ? A 45 ? A 37 ? 1 A A 5 1_555 A U 35 1_555 A G 23 1_555 A C 34 1_555 4.016 0.103 1.040 -101.242 146.233 -44.352 -1.011 1.344 2.431 -73.664 -51.000 -178.018 11 AA_A5G23:C34U35_AA A 5 ? A 35 ? A 23 ? A 34 ? 1 A G 23 1_555 A C 34 1_555 A C 24 1_555 A G 33 1_555 -0.013 -1.554 3.289 0.234 9.349 33.270 -3.984 0.055 2.764 15.941 -0.398 34.523 12 AA_G23C24:G33C34_AA A 23 ? A 34 ? A 24 ? A 33 ? 1 A C 24 1_555 A G 33 1_555 A U 25 1_555 A A 32 1_555 -0.019 -1.274 3.680 2.126 1.685 29.018 -2.942 0.555 3.591 3.353 -4.231 29.142 13 AA_C24U25:A32G33_AA A 24 ? A 33 ? A 25 ? A 32 ? 1 A U 25 1_555 A A 32 1_555 A C 26 1_555 A G 31 1_555 0.418 -1.230 3.612 0.176 5.160 31.543 -3.239 -0.725 3.375 9.412 -0.321 31.952 14 AA_U25C26:G31A32_AA A 25 ? A 32 ? A 26 ? A 31 ? 1 A C 26 1_555 A G 31 1_555 A U 27 1_555 A G 30 1_555 -0.679 -1.181 3.289 8.034 9.716 92.219 -0.995 0.617 3.129 6.716 -5.554 92.884 15 AA_C26U27:G30G31_AA A 26 ? A 31 ? A 27 ? A 30 ? # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number 'R01 GM114432' _pdbx_audit_support.ordinal 1 #