data_2MTJ # _entry.id 2MTJ # _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 2MTJ pdb_00002mtj 10.2210/pdb2mtj/pdb RCSB RCSB104026 ? ? BMRB 25163 ? ? WWPDB D_1000104026 ? ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 25163 BMRB unspecified . 2MTK PDB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2MTJ _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2014-08-19 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _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 'Bonneau, E.' 1 'Legault, P.' 2 # _citation.id primary _citation.title ;Nuclear Magnetic Resonance Structure of the III-IV-V Three-Way Junction from the Varkud Satellite Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 53 _citation.page_first 6264 _citation.page_last 6275 _citation.year 2014 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25238589 _citation.pdbx_database_id_DOI 10.1021/bi500826n # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Bonneau, E.' 1 ? primary 'Legault, P.' 2 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'RNA (47-MER)' _entity.formula_weight 15117.960 _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 GGACCUCCCGUCCUUGGACGGUCGAGCGAAAGCUUGUGAUUGGUCCG _entity_poly.pdbx_seq_one_letter_code_can GGACCUCCCGUCCUUGGACGGUCGAGCGAAAGCUUGUGAUUGGUCCG _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 A n 1 4 C n 1 5 C n 1 6 U n 1 7 C n 1 8 C n 1 9 C n 1 10 G n 1 11 U n 1 12 C n 1 13 C n 1 14 U n 1 15 U n 1 16 G n 1 17 G n 1 18 A n 1 19 C n 1 20 G n 1 21 G n 1 22 U n 1 23 C n 1 24 G n 1 25 A n 1 26 G n 1 27 C n 1 28 G n 1 29 A n 1 30 A n 1 31 A n 1 32 G n 1 33 C n 1 34 U n 1 35 U n 1 36 G n 1 37 U n 1 38 G n 1 39 A n 1 40 U n 1 41 U n 1 42 G n 1 43 G n 1 44 U n 1 45 C n 1 46 C n 1 47 G 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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'Neurospora crassa' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 5141 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2MTJ _struct_ref.pdbx_db_accession 2MTJ _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GGACCUCCCGUCCUUGGACGGUCGAGCGAAAGCUUGUGAUUGGUCCG _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2MTJ _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 2MTJ _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.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '1D flip-back watergate 1H' 1 2 1 '2D 1H-15N HSQC' 1 3 1 '2D 1H-15N HSQC NH2 only' 1 4 1 '3D 1H-15N NOESY' 2 5 2 '2D 1H-13C HSQC' 2 6 2 '3D 13C-edited HMQC-NOESY' 2 7 2 '3D CT-HCCH-COSY' 2 8 2 '3D HCCH-TOCSY' 2 9 3 '3D 15N-edited NOESY-HSQC' 2 10 3 '2D H(NC)-TOCSY-(C)H for guanosine residues' 2 11 2 '2D 1H-13C HMQC' 2 12 2 '2D 1H-15N MQ-(HC)N(C)H' 1 13 1 '2D 1H-15N CPMG-NOESY' 1 14 1 '2D HNN-COSY' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.temperature_units _pdbx_nmr_exptl_sample_conditions.label _pdbx_nmr_exptl_sample_conditions.pH_units _pdbx_nmr_exptl_sample_conditions.ionic_strength_units 1 55 6.5 ? ? 288 K ? ? ? 2 55 6.5 ? ? 298 K ? ? ? # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details '1.5-2.0 mM [U-100% 15N] J345-1-1, 5mM MgCl2, 90% H2O/10% D2O' 1 '90% H2O/10% D2O' ? ? ? '2.0 mM [U-100% 13C; U-100% 15N] J345-2-2, 5mM MgCl2, 100% D2O' 2 '100% D2O' ? ? ? '2.0 mM [U-100% 13C; U-100% 15N] J345-3-3, 5mM MgCl2, 90% H2O/10% D2O' 3 '90% H2O/10% D2O' ? ? ? # _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model UNITY _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Varian Unity' # _pdbx_nmr_refine.entry_id 2MTJ _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 21 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2MTJ _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2MTJ _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 'data analysis' NMRDraw ? 1 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRDraw ? 2 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 'data analysis' NMRPipe ? 3 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRPipe ? 4 CCPN 'chemical shift assignment' CCPNMR_suite ? 5 CCPN 'data analysis' CCPNMR_suite ? 6 CCPN 'peak picking' CCPNMR_suite ? 7 'Schwieters, Kuszewski, Tjandra and Clore' 'structure solution' 'X-PLOR NIH' ? 8 'Schwieters, Kuszewski, Tjandra and Clore' refinement 'X-PLOR NIH' ? 9 Schrodinger 'structure analysis' PyMOL ? 10 Schrodinger 'structure display' PyMOL ? 11 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2MTJ _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2MTJ _struct.title 'NMR structure of the III-IV-V three-way junction from the VS ribozyme' _struct.pdbx_model_details 'lowest energy, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2MTJ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'VS ribozyme, Three-way junction, Base triple, U-turn Ribose zipper, GAAA tetraloop, CUUG tetraloop, 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 46 N3 ? ? A G 1 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 46 O2 ? ? A G 1 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 46 N4 ? ? A G 1 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 45 N3 ? ? A G 2 A C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 45 O2 ? ? A G 2 A C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 45 N4 ? ? A G 2 A C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 44 N3 ? ? A A 3 A U 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 44 O4 ? ? A A 3 A U 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 43 N1 ? ? A C 4 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 43 O6 ? ? A C 4 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 43 N2 ? ? A C 4 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 42 N1 ? ? A C 5 A G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 42 O6 ? ? A C 5 A G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 42 N2 ? ? A C 5 A G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 6 N3 ? ? ? 1_555 A U 41 O4 ? ? A U 6 A U 41 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog16 hydrog ? ? A C 7 N4 ? ? ? 1_555 A U 22 O4 ? ? A C 7 A U 22 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog17 hydrog ? ? A C 7 O2 ? ? ? 1_555 A U 40 N3 ? ? A C 7 A U 40 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog18 hydrog ? ? A C 8 N3 ? ? ? 1_555 A G 21 N1 ? ? A C 8 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 8 N4 ? ? ? 1_555 A G 21 O6 ? ? A C 8 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 O2 ? ? ? 1_555 A G 21 N2 ? ? A C 8 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 9 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 9 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 9 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 19 N3 ? ? A G 10 A C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 19 O2 ? ? A G 10 A C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 19 N4 ? ? A G 10 A C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 11 N3 ? ? ? 1_555 A A 18 N1 ? ? A U 11 A A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 11 O4 ? ? ? 1_555 A A 18 N6 ? ? A U 11 A A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 12 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 12 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 12 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 16 N1 ? ? A C 13 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 16 O6 ? ? A C 13 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 16 N2 ? ? A C 13 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A U 14 N3 ? ? ? 1_555 A G 16 O6 ? ? A U 14 A G 16 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog36 hydrog ? ? A U 14 O2 ? ? ? 1_555 A G 16 N1 ? ? A U 14 A G 16 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog37 hydrog ? ? A G 21 N2 ? ? ? 1_555 A A 39 N3 ? ? A G 21 A A 39 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog38 hydrog ? ? A U 22 N3 ? ? ? 1_555 A U 40 O4 ? ? A U 22 A U 40 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog39 hydrog ? ? A G 24 N1 ? ? ? 1_555 A U 35 O2 ? ? A G 24 A U 35 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog40 hydrog ? ? A G 24 O6 ? ? ? 1_555 A U 35 N3 ? ? A G 24 A U 35 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog41 hydrog ? ? A A 25 N1 ? ? ? 1_555 A U 34 N3 ? ? A A 25 A U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A A 25 N6 ? ? ? 1_555 A U 34 O4 ? ? A A 25 A U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 26 N1 ? ? ? 1_555 A C 33 N3 ? ? A G 26 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 26 N2 ? ? ? 1_555 A C 33 O2 ? ? A G 26 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 26 O6 ? ? ? 1_555 A C 33 N4 ? ? A G 26 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 27 N3 ? ? ? 1_555 A G 32 N1 ? ? A C 27 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 27 N4 ? ? ? 1_555 A G 32 O6 ? ? A C 27 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 27 O2 ? ? ? 1_555 A G 32 N2 ? ? A C 27 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 28 N2 ? ? ? 1_555 A A 31 N7 ? ? A G 28 A A 31 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog50 hydrog ? ? A G 28 N3 ? ? ? 1_555 A A 31 N6 ? ? A G 28 A A 31 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2MTJ _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 A 3 3 3 A A A . n A 1 4 C 4 4 4 C C A . n A 1 5 C 5 5 5 C C A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 C 8 8 8 C C A . n A 1 9 C 9 9 9 C C 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 C 12 12 12 C C A . n A 1 13 C 13 13 13 C C A . n A 1 14 U 14 14 14 U U A . n A 1 15 U 15 15 15 U U A . n A 1 16 G 16 16 16 G G A . n A 1 17 G 17 17 17 G G A . n A 1 18 A 18 18 18 A A A . n A 1 19 C 19 19 19 C C A . n A 1 20 G 20 20 20 G G 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 G 24 24 24 G G A . n A 1 25 A 25 25 25 A A A . n A 1 26 G 26 26 26 G G A . n A 1 27 C 27 27 27 C C A . n A 1 28 G 28 28 28 G G A . n A 1 29 A 29 29 29 A A A . n A 1 30 A 30 30 30 A A A . n A 1 31 A 31 31 31 A A A . n A 1 32 G 32 32 32 G G A . n A 1 33 C 33 33 33 C C A . n A 1 34 U 34 34 34 U U 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 U 37 37 37 U U 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 U 40 40 40 U U A . n A 1 41 U 41 41 41 U U A . n A 1 42 G 42 42 42 G G A . n A 1 43 G 43 43 43 G G A . n A 1 44 U 44 44 44 U U A . n A 1 45 C 45 45 45 C C A . n A 1 46 C 46 46 46 C C A . n A 1 47 G 47 47 47 G G A . n # _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2014-10-22 2 'Structure model' 1 1 2020-09-30 3 'Structure model' 1 2 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' 'Data collection' 2 2 'Structure model' 'Derived calculations' 3 2 'Structure model' 'Experimental preparation' 4 3 'Structure model' 'Database references' 5 3 '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' ndb_struct_conf_na 2 2 'Structure model' ndb_struct_na_base_pair 3 2 'Structure model' ndb_struct_na_base_pair_step 4 2 'Structure model' pdbx_nmr_exptl_sample 5 2 'Structure model' pdbx_nmr_sample_details 6 2 'Structure model' pdbx_nmr_software 7 2 'Structure model' struct_conn 8 3 'Structure model' database_2 9 3 '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' '_ndb_struct_na_base_pair.buckle' 2 2 'Structure model' '_ndb_struct_na_base_pair.opening' 3 2 'Structure model' '_ndb_struct_na_base_pair.propeller' 4 2 'Structure model' '_ndb_struct_na_base_pair.shear' 5 2 'Structure model' '_ndb_struct_na_base_pair.stagger' 6 2 'Structure model' '_ndb_struct_na_base_pair.stretch' 7 2 'Structure model' '_ndb_struct_na_base_pair_step.helical_rise' 8 2 'Structure model' '_ndb_struct_na_base_pair_step.helical_twist' 9 2 'Structure model' '_ndb_struct_na_base_pair_step.inclination' 10 2 'Structure model' '_ndb_struct_na_base_pair_step.rise' 11 2 'Structure model' '_ndb_struct_na_base_pair_step.roll' 12 2 'Structure model' '_ndb_struct_na_base_pair_step.shift' 13 2 'Structure model' '_ndb_struct_na_base_pair_step.slide' 14 2 'Structure model' '_ndb_struct_na_base_pair_step.tilt' 15 2 'Structure model' '_ndb_struct_na_base_pair_step.tip' 16 2 'Structure model' '_ndb_struct_na_base_pair_step.twist' 17 2 'Structure model' '_ndb_struct_na_base_pair_step.x_displacement' 18 2 'Structure model' '_ndb_struct_na_base_pair_step.y_displacement' 19 2 'Structure model' '_pdbx_nmr_sample_details.contents' 20 2 'Structure model' '_pdbx_nmr_software.name' 21 3 'Structure model' '_database_2.pdbx_DOI' 22 3 'Structure model' '_database_2.pdbx_database_accession' 23 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' # loop_ _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 _pdbx_nmr_exptl_sample.solution_id J345-1-1 2 1.5-2.0 mM '[U-100% 15N]' 1 J345-2-2 2.0 ? mM '[U-100% 13C; U-100% 15N]' 2 J345-3-3 2.0 ? mM '[U-100% 13C; U-100% 15N]' 3 MgCl2-1 5 ? mM ? 4 MgCl2-2 5 ? mM ? 5 MgCl2-3 5 ? mM ? 6 # 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 2 "HO2'" A G 10 ? ? "O4'" A U 11 ? ? 1.57 2 4 "HO2'" A G 16 ? ? "O4'" A G 17 ? ? 1.58 3 4 "HO2'" A G 10 ? ? "O4'" A U 11 ? ? 1.59 4 5 "HO2'" A U 14 ? ? "O5'" A U 15 ? ? 1.58 5 6 "HO2'" A G 21 ? ? "O5'" A U 22 ? ? 1.52 6 6 H3 A U 37 ? ? OP1 A U 40 ? ? 1.55 7 7 H3 A U 22 ? ? O4 A U 40 ? ? 1.58 8 13 "HO2'" A U 14 ? ? "O5'" A U 15 ? ? 1.59 9 14 "HO2'" A U 6 ? ? "O5'" A C 7 ? ? 1.47 10 14 H3 A U 37 ? ? OP2 A U 40 ? ? 1.52 11 16 H3 A U 22 ? ? O4 A U 40 ? ? 1.55 12 18 H3 A U 37 ? ? OP2 A U 40 ? ? 1.55 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2MTJ 'double helix' 2MTJ 'a-form double helix' 2MTJ tetraloop 2MTJ 'mismatched base pair' 2MTJ '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 G 1 1_555 A C 46 1_555 -0.231 -0.142 0.593 9.493 19.447 2.394 1 A_G1:C46_A A 1 ? A 46 ? 19 1 1 A G 2 1_555 A C 45 1_555 0.022 -0.058 -0.752 -20.526 0.201 -0.608 2 A_G2:C45_A A 2 ? A 45 ? 19 1 1 A A 3 1_555 A U 44 1_555 -0.008 -0.130 -0.037 4.305 -18.040 0.016 3 A_A3:U44_A A 3 ? A 44 ? 20 1 1 A C 4 1_555 A G 43 1_555 0.101 -0.214 -1.019 7.104 -9.973 1.669 4 A_C4:G43_A A 4 ? A 43 ? 19 1 1 A C 5 1_555 A G 42 1_555 0.105 -0.323 -0.961 -9.672 -5.141 2.550 5 A_C5:G42_A A 5 ? A 42 ? 19 1 1 A U 6 1_555 A U 41 1_555 2.494 -2.110 2.022 -6.082 13.229 -22.669 6 A_U6:U41_A A 6 ? A 41 ? ? ? 1 A C 7 1_555 A U 22 1_555 1.221 0.342 0.259 7.059 -11.933 -42.902 7 A_C7:U22_A A 7 ? A 22 ? ? ? 1 A C 8 1_555 A G 21 1_555 0.283 -0.313 -1.179 6.763 -6.627 1.890 8 A_C8:G21_A A 8 ? A 21 ? 19 1 1 A C 9 1_555 A G 20 1_555 -0.070 -0.168 -0.498 -10.140 5.418 -0.953 9 A_C9:G20_A A 9 ? A 20 ? 19 1 1 A G 10 1_555 A C 19 1_555 0.157 -0.172 -0.817 -8.337 12.254 -2.539 10 A_G10:C19_A A 10 ? A 19 ? 19 1 1 A U 11 1_555 A A 18 1_555 -0.238 -0.203 0.784 -1.917 -17.996 -4.520 11 A_U11:A18_A A 11 ? A 18 ? 20 1 1 A C 12 1_555 A G 17 1_555 -0.013 -0.249 -0.966 -3.818 1.194 0.060 12 A_C12:G17_A A 12 ? A 17 ? 19 1 1 A C 13 1_555 A G 16 1_555 0.167 -0.327 0.855 11.678 17.230 9.222 13 A_C13:G16_A A 13 ? A 16 ? 19 1 1 A G 24 1_555 A U 35 1_555 -2.454 -0.440 -0.119 -5.284 8.959 -1.890 14 A_G24:U35_A A 24 ? A 35 ? 28 1 1 A A 25 1_555 A U 34 1_555 0.125 -0.130 -0.495 0.310 -1.904 -0.853 15 A_A25:U34_A A 25 ? A 34 ? 20 1 1 A G 26 1_555 A C 33 1_555 -0.092 -0.161 -0.502 -0.717 -20.494 3.488 16 A_G26:C33_A A 26 ? A 33 ? 19 1 1 A C 27 1_555 A G 32 1_555 -0.018 -0.153 0.506 7.412 9.245 2.481 17 A_C27:G32_A A 27 ? A 32 ? 19 1 1 A G 28 1_555 A A 31 1_555 5.865 -3.975 1.499 30.961 16.088 15.315 18 A_G28:A31_A A 28 ? A 31 ? 11 9 # 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 46 1_555 A G 2 1_555 A C 45 1_555 -1.237 -2.349 5.477 9.001 -1.725 28.436 -3.971 5.474 4.991 -3.401 -17.749 29.847 1 AA_G1G2:C45C46_AA A 1 ? A 46 ? A 2 ? A 45 ? 1 A G 2 1_555 A C 45 1_555 A A 3 1_555 A U 44 1_555 0.092 -1.445 2.530 -1.555 5.036 28.706 -3.675 -0.431 2.241 10.051 3.104 29.176 2 AA_G2A3:U44C45_AA A 2 ? A 45 ? A 3 ? A 44 ? 1 A A 3 1_555 A U 44 1_555 A C 4 1_555 A G 43 1_555 0.065 -0.652 3.544 4.364 16.246 33.966 -3.200 0.489 2.932 25.931 -6.966 37.794 3 AA_A3C4:G43U44_AA A 3 ? A 44 ? A 4 ? A 43 ? 1 A C 4 1_555 A G 43 1_555 A C 5 1_555 A G 42 1_555 0.781 -1.285 4.844 -1.095 2.229 27.599 -3.470 -2.018 4.694 4.659 2.290 27.708 4 AA_C4C5:G42G43_AA A 4 ? A 43 ? A 5 ? A 42 ? 1 A C 5 1_555 A G 42 1_555 A U 6 1_555 A U 41 1_555 -1.568 -1.090 4.075 -14.071 2.063 40.740 -1.754 0.303 4.306 2.860 19.509 43.051 5 AA_C5U6:U41G42_AA A 5 ? A 42 ? A 6 ? A 41 ? 1 A U 6 1_555 A U 41 1_555 A C 7 1_555 A U 22 1_555 2.397 -4.329 3.025 4.773 3.323 50.554 -5.254 -2.485 2.954 3.877 -5.568 50.866 6 AA_U6C7:U22U41_AA A 6 ? A 41 ? A 7 ? A 22 ? 1 A C 7 1_555 A U 22 1_555 A C 8 1_555 A G 21 1_555 1.934 -2.606 3.486 4.367 2.424 19.454 -8.688 -3.359 3.483 7.026 -12.656 20.079 7 AA_C7C8:G21U22_AA A 7 ? A 22 ? A 8 ? A 21 ? 1 A C 8 1_555 A G 21 1_555 A C 9 1_555 A G 20 1_555 -0.273 -1.370 4.798 -5.265 5.192 33.950 -3.443 -0.706 4.536 8.762 8.887 34.723 8 AA_C8C9:G20G21_AA A 8 ? A 21 ? A 9 ? A 20 ? 1 A C 9 1_555 A G 20 1_555 A G 10 1_555 A C 19 1_555 -0.645 -2.247 3.561 3.115 10.733 23.423 -7.776 2.241 2.229 24.714 -7.173 25.919 9 AA_C9G10:C19G20_AA A 9 ? A 20 ? A 10 ? A 19 ? 1 A G 10 1_555 A C 19 1_555 A U 11 1_555 A A 18 1_555 -0.394 -0.855 3.884 -5.517 1.491 27.391 -2.191 -0.745 3.837 3.106 11.492 27.970 10 AA_G10U11:A18C19_AA A 10 ? A 19 ? A 11 ? A 18 ? 1 A U 11 1_555 A A 18 1_555 A C 12 1_555 A G 17 1_555 0.530 -0.381 3.909 7.376 14.798 36.107 -2.635 0.251 3.534 22.482 -11.206 39.598 11 AA_U11C12:G17A18_AA A 11 ? A 18 ? A 12 ? A 17 ? 1 A C 12 1_555 A G 17 1_555 A C 13 1_555 A G 16 1_555 0.425 -1.183 3.429 -11.519 7.944 18.844 -5.473 -4.758 2.160 20.924 30.343 23.433 12 AA_C12C13:G16G17_AA A 12 ? A 17 ? A 13 ? A 16 ? 1 A G 24 1_555 A U 35 1_555 A A 25 1_555 A U 34 1_555 -0.990 -1.582 3.717 5.089 -5.255 32.129 -1.758 2.746 3.726 -9.344 -9.050 32.929 13 AA_G24A25:U34U35_AA A 24 ? A 35 ? A 25 ? A 34 ? 1 A A 25 1_555 A U 34 1_555 A G 26 1_555 A C 33 1_555 0.040 -0.722 3.860 2.290 13.366 31.985 -3.556 0.334 3.300 23.006 -3.941 34.672 14 AA_A25G26:C33U34_AA A 25 ? A 34 ? A 26 ? A 33 ? 1 A G 26 1_555 A C 33 1_555 A C 27 1_555 A G 32 1_555 0.220 -1.161 3.764 -9.253 0.982 25.069 -2.803 -3.207 3.419 2.168 20.441 26.714 15 AA_G26C27:G32C33_AA A 26 ? A 33 ? A 27 ? A 32 ? 1 A C 27 1_555 A G 32 1_555 A G 28 1_555 A A 31 1_555 0.096 0.177 2.574 -3.305 15.574 51.424 -0.581 -0.272 2.516 17.476 3.708 53.672 16 AA_C27G28:A31G32_AA A 27 ? A 32 ? A 28 ? A 31 ? #