data_6EZ0 # _entry.id 6EZ0 # _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 6EZ0 pdb_00006ez0 10.2210/pdb6ez0/pdb WWPDB D_1200007478 ? ? BMRB 34199 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB 'the same sequence but without thipphosphates' 2AHT unspecified BMRB ;Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding ; 34199 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 6EZ0 _pdbx_database_status.recvd_initial_deposition_date 2017-11-13 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _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 'Erat, M.C.' 1 ? 'Besic, E.' 2 ? 'Oberhuber, M.' 3 ? 'Johannsen, S.' 4 ? 'Sigel, R.K.O.' 5 ? # loop_ _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 _citation.database_id_Medline _citation.details _citation.id _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_full _citation.journal_issue _citation.journal_volume _citation.language _citation.page_first _citation.page_last _citation.title _citation.year _citation.database_id_CSD _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.unpublished_flag ? ? ? ? ? ? ? GW ? ? primary 'J. Biol. Inorg. Chem.' JJBCFA ? 1432-1327 ? ? 23 ? 167 177 ;Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding. ; 2018 ? 10.1007/s00775-017-1519-3 29218637 ? ? ? ? ? ? ? ? GE ? ? 1 Chembiochem ? ? 1439-4227 ? ? 8 ? 306 314 ;Solution structure of domain 6 from a self-splicing group II intron ribozyme: a Mg(2+) binding site is located close to the stacked branch adenosine. ; 2007 ? 10.1002/cbic.200600459 17200997 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Erat, M.C.' 1 ? primary 'Besic, E.' 2 ? primary 'Oberhuber, M.' 3 ? primary 'Johannsen, S.' 4 ? primary 'Sigel, R.K.O.' 5 ? 1 'Erat, M.C.' 6 ? 1 'Zerbe, O.' 7 ? 1 'Fox, T.' 8 ? 1 'Sigel, R.K.' 9 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'RNA (27-MER)' _entity.formula_weight 8800.562 _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 yes _entity_poly.pdbx_seq_one_letter_code 'GGAGCGGGGG(U37)G(U37)AAACC(U37)A(U37)CGC(U37)CC' _entity_poly.pdbx_seq_one_letter_code_can GGAGCGGGGGUGUAAACCUAUCGCUCC _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 G n 1 5 C n 1 6 G n 1 7 G n 1 8 G n 1 9 G n 1 10 G n 1 11 U37 n 1 12 G n 1 13 U37 n 1 14 A n 1 15 A n 1 16 A n 1 17 C n 1 18 C n 1 19 U37 n 1 20 A n 1 21 U37 n 1 22 C n 1 23 G n 1 24 C n 1 25 U37 n 1 26 C n 1 27 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 27 _pdbx_entity_src_syn.organism_scientific 'Saccharomyces cerevisiae' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 4932 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6EZ0 _struct_ref.pdbx_db_accession 6EZ0 _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 6EZ0 _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 27 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 6EZ0 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 27 _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 27 # 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 U37 'RNA linking' n ;URIDINE 5'-MONOTHIOPHOSPHATE ; ? 'C9 H13 N2 O8 P S' 340.247 # 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 1 1 '2D 1H-1H NOESY' 1 isotropic 2 1 1 '2D 1H-1H TOCSY' 1 isotropic 3 1 1 '2D 1H-13C HSQC aliphatic' 1 isotropic 4 1 1 '2D 1H-13C HSQC aromatic' 1 isotropic 5 2 2 '2D 1H-1H NOESY' 1 isotropic # 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 1 6.7 50 ? ? mM Non-exchangable 0.1 pD ? ? K 2 275 atm 1 6.7 50 ? ? mM Exchangable ? 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 '2 mM alpha-thio-D6-27, 100% D2O' '100% D2O' alpha-thio-D6-27_D2O solution ? 2 '0.7 mM na alpha-thio-D6-27, 90% H2O/10% D2O' '90% H2O/10% D2O' alpha-thio-D6-27_H2O solution ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.details 'Cryo TXI' # _pdbx_nmr_refine.entry_id 6EZ0 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 6EZ0 _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.representative_conformer ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 6EZ0 _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 refinement Xplor-NIH ? 'Schwieters, Kuszewski, Tjandra and Clore' 2 'structure calculation' Xplor-NIH ? 'Schwieters, Kuszewski, Tjandra and Clore' 3 'chemical shift assignment' Sparky ? Goddard 4 'peak picking' Sparky ? Goddard # _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 6EZ0 _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 6EZ0 _struct.title ;Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding ; _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 6EZ0 _struct_keywords.text 'thiophosphate group II intron branch-adenosine hairpin tetraloop, 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 covale1 covale both ? A G 10 "O3'" ? ? ? 1_555 A U37 11 P ? ? A G 10 A U37 11 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale2 covale one ? A U37 11 "O3'" ? ? ? 1_555 A G 12 P ? ? A U37 11 A G 12 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale3 covale both ? A G 12 "O3'" ? ? ? 1_555 A U37 13 P ? ? A G 12 A U37 13 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale4 covale one ? A U37 13 "O3'" ? ? ? 1_555 A A 14 P ? ? A U37 13 A A 14 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale5 covale both ? A C 18 "O3'" ? ? ? 1_555 A U37 19 P ? ? A C 18 A U37 19 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale6 covale one ? A U37 19 "O3'" ? ? ? 1_555 A A 20 P ? ? A U37 19 A A 20 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale7 covale both ? A A 20 "O3'" ? ? ? 1_555 A U37 21 P ? ? A A 20 A U37 21 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale8 covale one ? A U37 21 "O3'" ? ? ? 1_555 A C 22 P ? ? A U37 21 A C 22 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale9 covale both ? A C 24 "O3'" ? ? ? 1_555 A U37 25 P ? ? A C 24 A U37 25 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale10 covale one ? A U37 25 "O3'" ? ? ? 1_555 A C 26 P ? ? A U37 25 A C 26 1_555 ? ? ? ? ? ? ? 1.607 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 27 N3 ? ? A G 1 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 27 O2 ? ? A G 1 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 27 N4 ? ? A G 1 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 26 N3 ? ? A G 2 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 26 O2 ? ? A G 2 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 26 N4 ? ? A G 2 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U37 25 N3 ? ? A A 3 A U37 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U37 25 O4 ? ? A A 3 A U37 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 24 N3 ? ? A G 4 A C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 24 O2 ? ? A G 4 A C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 24 N4 ? ? A G 4 A C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 23 N1 ? ? A C 5 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 23 O6 ? ? A C 5 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 23 N2 ? ? A C 5 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 22 N3 ? ? A G 6 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 22 O2 ? ? A G 6 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 22 N4 ? ? A G 6 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 N1 ? ? ? 1_555 A A 20 N1 ? ? A G 7 A A 20 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog19 hydrog ? ? A G 7 O6 ? ? ? 1_555 A A 20 N6 ? ? A G 7 A A 20 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog20 hydrog ? ? A G 8 N1 ? ? ? 1_555 A U37 19 O2 ? ? A G 8 A U37 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog21 hydrog ? ? A G 8 O6 ? ? ? 1_555 A U37 19 N3 ? ? A G 8 A U37 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog22 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 18 N3 ? ? A G 9 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 18 O2 ? ? A G 9 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 18 N4 ? ? A G 9 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 17 N3 ? ? A G 10 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 17 O2 ? ? A G 10 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 17 N4 ? ? A G 10 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U37 11 N3 ? ? ? 1_555 A A 16 N1 ? ? A U37 11 A A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U37 11 O4 ? ? ? 1_555 A A 16 N6 ? ? A U37 11 A A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 12 N2 ? ? ? 1_555 A A 15 N1 ? ? A G 12 A A 15 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog31 hydrog ? ? A G 12 N3 ? ? ? 1_555 A A 15 N6 ? ? A G 12 A A 15 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 6EZ0 _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 S # 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 G 4 4 4 G G A . n A 1 5 C 5 5 5 C C A . n A 1 6 G 6 6 6 G G A . n A 1 7 G 7 7 7 G G A . n A 1 8 G 8 8 8 G G A . n A 1 9 G 9 9 9 G G A . n A 1 10 G 10 10 10 G G A . n A 1 11 U37 11 11 11 U37 U37 A . n A 1 12 G 12 12 12 G G A . n A 1 13 U37 13 13 13 U37 U37 A . n A 1 14 A 14 14 14 A A A . n A 1 15 A 15 15 15 A A A . n A 1 16 A 16 16 16 A A A . n A 1 17 C 17 17 17 C C A . n A 1 18 C 18 18 18 C C A . n A 1 19 U37 19 19 19 U37 U37 A . n A 1 20 A 20 20 20 A A A . n A 1 21 U37 21 21 21 U37 U37 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 U37 25 25 25 U37 U37 A . n A 1 26 C 26 26 26 C C A . n A 1 27 C 27 27 27 C C A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details 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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2350 ? 1 MORE 4 ? 1 'SSA (A^2)' 5110 ? # _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 2018-01-03 2 'Structure model' 1 1 2018-01-17 3 'Structure model' 1 2 2019-05-08 4 'Structure model' 1 3 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' 'Data collection' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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' pdbx_nmr_software 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_database_status 5 4 'Structure model' pdbx_nmr_spectrometer # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation.year' 5 3 'Structure model' '_pdbx_nmr_software.name' 6 4 'Structure model' '_database_2.pdbx_DOI' 7 4 'Structure model' '_database_2.pdbx_database_accession' 8 4 'Structure model' '_pdbx_database_status.status_code_nmr_data' 9 4 'Structure model' '_pdbx_nmr_spectrometer.model' # 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 alpha-thio-D6-27 2 ? mM 'natural abundance' 2 alpha-thio-D6-27 0.7 ? mM na # 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 4 HB A U37 21 ? ? "O5'" A C 22 ? ? 1.58 2 7 HB A U37 21 ? ? "O5'" A C 22 ? ? 1.31 3 12 HB A U37 21 ? ? "O5'" A C 22 ? ? 1.29 4 16 HB A U37 21 ? ? "O5'" A C 22 ? ? 1.53 5 19 HB A U37 21 ? ? "O5'" A C 22 ? ? 1.38 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 6EZ0 'double helix' 6EZ0 'a-form double helix' 6EZ0 tetraloop 6EZ0 'bulge loop' 6EZ0 '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 27 1_555 0.344 -0.019 0.008 0.330 -0.069 1.990 1 A_G1:C27_A A 1 ? A 27 ? 19 1 1 A G 2 1_555 A C 26 1_555 0.483 -0.119 -0.040 -0.313 0.387 -0.346 2 A_G2:C26_A A 2 ? A 26 ? 19 1 1 A A 3 1_555 A U37 25 1_555 -0.189 0.079 -0.006 -0.170 0.164 -0.185 3 A_A3:U3725_A A 3 ? A 25 ? 20 1 1 A G 4 1_555 A C 24 1_555 0.370 -0.086 -0.018 -0.015 0.276 -2.897 4 A_G4:C24_A A 4 ? A 24 ? 19 1 1 A C 5 1_555 A G 23 1_555 -0.559 -0.179 -0.025 0.002 0.184 -2.114 5 A_C5:G23_A A 5 ? A 23 ? 19 1 1 A G 6 1_555 A C 22 1_555 0.538 -0.205 -0.018 -1.779 -2.178 -0.653 6 A_G6:C22_A A 6 ? A 22 ? 19 1 1 A G 7 1_555 A A 20 1_555 1.509 -0.256 -2.194 17.269 -3.559 -41.498 7 A_G7:A20_A A 7 ? A 20 ? 8 1 1 A G 8 1_555 A U37 19 1_555 -1.799 -0.455 -0.031 -0.212 0.520 -11.458 8 A_G8:U3719_A A 8 ? A 19 ? 28 1 1 A G 9 1_555 A C 18 1_555 -0.055 -0.116 0.007 -0.231 0.050 -1.989 9 A_G9:C18_A A 9 ? A 18 ? 19 1 1 A G 10 1_555 A C 17 1_555 -0.450 -0.236 -0.048 -0.522 -0.590 -1.090 10 A_G10:C17_A A 10 ? A 17 ? 19 1 1 A U37 11 1_555 A A 16 1_555 -0.646 0.054 -0.001 -0.545 0.744 -6.405 11 A_U3711:A16_A A 11 ? A 16 ? 20 1 1 A G 12 1_555 A A 15 1_555 4.001 -3.037 -0.017 0.120 -0.388 -65.642 12 A_G12:A15_A A 12 ? A 15 ? 10 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 27 1_555 A G 2 1_555 A C 26 1_555 0.192 -0.993 3.534 1.185 6.891 35.254 -2.647 -0.133 3.292 11.241 -1.933 35.919 1 AA_G1G2:C26C27_AA A 1 ? A 27 ? A 2 ? A 26 ? 1 A G 2 1_555 A C 26 1_555 A A 3 1_555 A U37 25 1_555 -0.368 -1.562 3.262 0.335 14.898 25.996 -5.733 0.774 2.075 30.169 -0.679 29.901 2 AA_G2A3:U3725C26_AA A 2 ? A 26 ? A 3 ? A 25 ? 1 A A 3 1_555 A U37 25 1_555 A G 4 1_555 A C 24 1_555 -0.461 -1.251 3.090 0.458 20.092 36.894 -3.555 0.687 2.154 29.242 -0.667 41.845 3 AA_A3G4:C24U3725_AA A 3 ? A 25 ? A 4 ? A 24 ? 1 A G 4 1_555 A C 24 1_555 A C 5 1_555 A G 23 1_555 0.406 -1.983 3.422 -0.611 1.874 23.638 -5.456 -1.195 3.245 4.564 1.487 23.719 4 AA_G4C5:G23C24_AA A 4 ? A 24 ? A 5 ? A 23 ? 1 A C 5 1_555 A G 23 1_555 A G 6 1_555 A C 22 1_555 -1.169 -0.601 3.426 -0.762 8.274 38.580 -1.901 1.640 3.256 12.349 1.137 39.431 5 AA_C5G6:C22G23_AA A 5 ? A 23 ? A 6 ? A 22 ? 1 A G 6 1_555 A C 22 1_555 A G 7 1_555 A A 20 1_555 -0.397 -1.173 4.821 -10.064 -2.812 54.411 -1.016 -0.456 4.869 -3.044 10.894 55.330 6 AA_G6G7:A20C22_AA A 6 ? A 22 ? A 7 ? A 20 ? 1 A G 7 1_555 A A 20 1_555 A G 8 1_555 A U37 19 1_555 1.274 -1.920 3.999 -10.591 3.639 22.128 -5.683 -6.483 2.762 8.794 25.593 24.769 7 AA_G7G8:U3719A20_AA A 7 ? A 20 ? A 8 ? A 19 ? 1 A G 8 1_555 A U37 19 1_555 A G 9 1_555 A C 18 1_555 0.065 -1.034 3.514 -2.434 7.181 40.269 -2.301 -0.372 3.281 10.320 3.498 40.948 8 AA_G8G9:C18U3719_AA A 8 ? A 19 ? A 9 ? A 18 ? 1 A G 9 1_555 A C 18 1_555 A G 10 1_555 A C 17 1_555 -0.642 -0.551 3.147 -2.276 23.187 37.928 -2.748 0.653 2.468 32.236 3.164 44.286 9 AA_G9G10:C17C18_AA A 9 ? A 18 ? A 10 ? A 17 ? 1 A G 10 1_555 A C 17 1_555 A U37 11 1_555 A A 16 1_555 -0.549 -1.622 4.425 -5.852 -8.976 26.994 -0.367 -0.776 4.725 -18.338 11.956 29.006 10 AA_G10U3711:A16C17_AA A 10 ? A 17 ? A 11 ? A 16 ? 1 A U37 11 1_555 A A 16 1_555 A G 12 1_555 A A 15 1_555 1.621 -1.059 3.508 18.157 9.130 101.890 -0.820 -0.745 3.610 5.839 -11.612 103.341 11 AA_U3711G12:A15A16_AA A 11 ? A 16 ? A 12 ? A 15 ? # _pdbx_audit_support.funding_organization 'Swiss National Science Foundation' _pdbx_audit_support.country Switzerland _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _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 ? #