data_7PDU # _entry.id 7PDU # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.354 _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 7PDU pdb_00007pdu 10.2210/pdb7pdu/pdb WWPDB D_1292117542 ? ? BMRB 34654 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'Pre-catalytic complex of 10-23 DNAzyme with RNA target' _pdbx_database_related.db_id 34654 _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 7PDU _pdbx_database_status.recvd_initial_deposition_date 2021-08-07 _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Etzkorn, M.' 1 0000-0002-9796-3246 'Borggrafe, J.' 2 0000-0002-7048-3592 'Viegas, A.' 3 0000-0003-1733-136X # _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 Nature _citation.journal_id_ASTM NATUAS _citation.journal_id_CSD 0006 _citation.journal_id_ISSN 1476-4687 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 601 _citation.language ? _citation.page_first 144 _citation.page_last 149 _citation.title 'Time-resolved structural analysis of an RNA-cleaving DNA catalyst.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41586-021-04225-4 _citation.pdbx_database_id_PubMed 34949858 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Borggrafe, J.' 1 ? primary 'Victor, J.' 2 ? primary 'Rosenbach, H.' 3 ? primary 'Viegas, A.' 4 0000-0003-1733-136X primary 'Gertzen, C.G.W.' 5 0000-0002-9562-7708 primary 'Wuebben, C.' 6 0000-0002-7860-3149 primary 'Kovacs, H.' 7 0000-0002-5246-9439 primary 'Gopalswamy, M.' 8 ? primary 'Riesner, D.' 9 ? primary 'Steger, G.' 10 ? primary 'Schiemann, O.' 11 0000-0001-6346-9779 primary 'Gohlke, H.' 12 ? primary 'Span, I.' 13 ? primary 'Etzkorn, M.' 14 0000-0002-9796-3246 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn '10-23 DNAzyme (33-MER)' 10266.592 1 ? ? ? ? 2 polymer syn 'RNA target (19-MER)' 5980.640 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no ;(DT)(DT)(DG)(DG)(DG)(DG)(DT)(DA)(DA)(DG)(DG)(DC)(DT)(DC)(DG)(DC)(DT)(DA)(DC)(DA) (DA)(DC)(DG)(DA)(DG)(DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT) ; TTGGGGTAAGGCTCGCTACAACGAGGTGCATGT A ? 2 polyribonucleotide no no ACAUGCACCGUUACCCCAA ACAUGCACCGUUACCCCAA B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DT n 1 2 DT n 1 3 DG n 1 4 DG n 1 5 DG n 1 6 DG n 1 7 DT n 1 8 DA n 1 9 DA n 1 10 DG n 1 11 DG n 1 12 DC n 1 13 DT n 1 14 DC n 1 15 DG n 1 16 DC n 1 17 DT n 1 18 DA n 1 19 DC n 1 20 DA n 1 21 DA n 1 22 DC n 1 23 DG n 1 24 DA n 1 25 DG n 1 26 DG n 1 27 DT n 1 28 DG n 1 29 DC n 1 30 DA n 1 31 DT n 1 32 DG n 1 33 DT n 2 1 A n 2 2 C n 2 3 A n 2 4 U n 2 5 G n 2 6 C n 2 7 A n 2 8 C n 2 9 C n 2 10 G n 2 11 U n 2 12 U n 2 13 A n 2 14 C n 2 15 C n 2 16 C n 2 17 C n 2 18 A n 2 19 A n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 33 'synthetic construct' ? 32630 ? 2 1 sample 1 19 'synthetic construct' ? 32630 'Part of human PrP mRNA' # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 7PDU 7PDU ? 1 ? 1 2 PDB 7PDU 7PDU ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 7PDU A 1 ? 33 ? 7PDU 1 ? 33 ? 1 33 2 2 7PDU B 1 ? 19 ? 7PDU 34 ? 52 ? 34 52 # 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 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 1 1 '2D 1H-1H NOESY' 1 isotropic 2 1 1 '2D 1H-1H TOCSY' 1 isotropic 3 1 3 '2D 1H-13C HSQC aliphatic' 2 isotropic 4 1 3 '2D 1H-13C HSQC-TOCSY' 3 isotropic 5 1 3 '3D 1H-13C NOESY aliphatic' 2 isotropic 6 1 2 '2D 1H-1H NOESY' 3 anisotropic 7 1 2 '2D 1H-1H TOCSY' 3 isotropic # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 310.12 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 7.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength 133 _pdbx_nmr_exptl_sample_conditions.details ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.label Tris_buffer _pdbx_nmr_exptl_sample_conditions.pH_err ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err ? _pdbx_nmr_exptl_sample_conditions.temperature_err ? _pdbx_nmr_exptl_sample_conditions.temperature_units 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 '500 uM 110-23 DNAzyme (33-MER), 500 uM RNA target (19-MER), 50 mM n.a. Tris-d11, 100 mM n.a. NaCl, 1 mM n.a. MgCl2, 90% H2O/10% D2O' '90% H2O/10% D2O' "Dz:RNA2'F" solution ;10-23 DNAzyme:RNA complex, RNA target stabilized by 2'F substitution at cleavage site ; 3 ;500 uM [U-13C; U-15N] 110-23 DNAzyme (33-MER), 500 uM RNA target (19-MER), 50 mM n.a. Tris-d11, 100 mM n.a. NaCl, 1 mM n.a. MgCl2, 90% H2O/10% D2O ; '90% H2O/10% D2O' "13C15N_Dz:RNA2'F" solution ;10-23 DNAzyme:RNA complex, RNA target stabilized by 2'F substitution at cleavage site, Dz 13C,15N-enriched ; 2 '750 uM 110-23 DNAzyme (33-MER), 750 uM RNA target (19-MER), 50 mM n.a. Tris-d11, 100 mM n.a. NaCl, 1 mM n.a. MgCl2, 90% H2O/10% D2O' '90% H2O/10% D2O' "6xF-Dz:RNA2'F" solution ;10-23 DNAzyme:RNA complex, RNA target stabilized by 2'F substitution at cleavage site. Six addition fluorinations in Dz sequence ; # 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 HD' ? Bruker 900 ? 2 'AVANCE III HD' ? Bruker 750 ? 3 'AVANCE III HD' ? Bruker 600 ? # _pdbx_nmr_refine.entry_id 7PDU _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 5 # _pdbx_nmr_ensemble.entry_id 7PDU _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 7 _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 7PDU _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 collection TopSpin 4.0.6 'Bruker Biospin' 2 'chemical shift assignment' CARA 1.9.1.5 'Keller and Wuthrich' 3 'peak picking' CARA 1.9.1.5 'Keller and Wuthrich' 4 'peak picking' Sparky 3.114 Goddard 5 'structure calculation' 'X-PLOR NIH' 2.49 '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 7PDU _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 7PDU _struct.title 'Pre-catalytic complex of 10-23 DNAzyme with RNA target' _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 7PDU _struct_keywords.text '10-23 DNAzyme, RNA-cleaving DNAzyme, pre-catalytic complex, DNA-RNA HYBRID' _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' # 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 ? # 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 DT 1 N3 ? ? ? 1_555 B A 19 N1 ? ? A DT 1 B A 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DT 1 O4 ? ? ? 1_555 B A 19 N6 ? ? A DT 1 B A 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B A 18 N1 ? ? A DT 2 B A 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B A 18 N6 ? ? A DT 2 B A 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B C 15 N3 ? ? A DG 5 B C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B C 15 O2 ? ? A DG 5 B C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B C 15 N4 ? ? A DG 5 B C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B C 16 N3 ? ? A DG 5 B C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B C 16 O2 ? ? A DG 5 B C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B C 16 N4 ? ? A DG 5 B C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B C 14 N3 ? ? A DG 6 B C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B C 14 O2 ? ? A DG 6 B C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B C 14 N4 ? ? A DG 6 B C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B A 13 N1 ? ? A DT 7 B A 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B A 13 N6 ? ? A DT 7 B A 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B U 12 N3 ? ? A DA 8 B U 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B U 12 O4 ? ? A DA 8 B U 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B U 11 N3 ? ? A DA 9 B U 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B U 11 O4 ? ? A DA 9 B U 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 26 N1 ? ? ? 1_555 B C 8 N3 ? ? A DG 26 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 26 N2 ? ? ? 1_555 B C 8 O2 ? ? A DG 26 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 26 O6 ? ? ? 1_555 B C 8 N4 ? ? A DG 26 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DT 27 N3 ? ? ? 1_555 B A 7 N1 ? ? A DT 27 B A 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DT 27 O4 ? ? ? 1_555 B A 7 N6 ? ? A DT 27 B A 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 28 N1 ? ? ? 1_555 B C 6 N3 ? ? A DG 28 B C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 28 N2 ? ? ? 1_555 B C 6 O2 ? ? A DG 28 B C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 28 O6 ? ? ? 1_555 B C 6 N4 ? ? A DG 28 B C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 29 N3 ? ? ? 1_555 B G 5 N1 ? ? A DC 29 B G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 29 N4 ? ? ? 1_555 B G 5 O6 ? ? A DC 29 B G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 29 O2 ? ? ? 1_555 B G 5 N2 ? ? A DC 29 B G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DA 30 N1 ? ? ? 1_555 B U 4 N3 ? ? A DA 30 B U 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DA 30 N6 ? ? ? 1_555 B U 4 O4 ? ? A DA 30 B U 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DT 31 N3 ? ? ? 1_555 B A 3 N1 ? ? A DT 31 B A 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DT 31 O4 ? ? ? 1_555 B A 3 N6 ? ? A DT 31 B A 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A DG 32 N1 ? ? ? 1_555 B C 2 N3 ? ? A DG 32 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A DG 32 N2 ? ? ? 1_555 B C 2 O2 ? ? A DG 32 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A DG 32 O6 ? ? ? 1_555 B C 2 N4 ? ? A DG 32 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A DT 33 N3 ? ? ? 1_555 B A 1 N1 ? ? A DT 33 B A 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A DT 33 O4 ? ? ? 1_555 B A 1 N6 ? ? A DT 33 B A 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A DT 33 N3 ? ? ? 1_555 B C 2 N3 ? ? A DT 33 B C 35 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog41 hydrog ? ? A DT 33 O4 ? ? ? 1_555 B C 2 N4 ? ? A DT 33 B C 35 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 7PDU _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 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 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # 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 DT 1 1 1 DT THY A . n A 1 2 DT 2 2 2 DT THY A . n A 1 3 DG 3 3 3 DG GUA A . n A 1 4 DG 4 4 4 DG GUA A . n A 1 5 DG 5 5 5 DG GUA A . n A 1 6 DG 6 6 6 DG GUA A . n A 1 7 DT 7 7 7 DT THY A . n A 1 8 DA 8 8 8 DA ADE A . n A 1 9 DA 9 9 9 DA ADE A . n A 1 10 DG 10 10 10 DG GUA A . n A 1 11 DG 11 11 11 DG GUA A . n A 1 12 DC 12 12 12 DC CYT A . n A 1 13 DT 13 13 13 DT THY A . n A 1 14 DC 14 14 14 DC CYT A . n A 1 15 DG 15 15 15 DG GUA A . n A 1 16 DC 16 16 16 DC CYT A . n A 1 17 DT 17 17 17 DT THY A . n A 1 18 DA 18 18 18 DA ADE A . n A 1 19 DC 19 19 19 DC CYT A . n A 1 20 DA 20 20 20 DA ADE A . n A 1 21 DA 21 21 21 DA ADE A . n A 1 22 DC 22 22 22 DC CYT A . n A 1 23 DG 23 23 23 DG GUA A . n A 1 24 DA 24 24 24 DA ADE A . n A 1 25 DG 25 25 25 DG GUA A . n A 1 26 DG 26 26 26 DG GUA A . n A 1 27 DT 27 27 27 DT THY A . n A 1 28 DG 28 28 28 DG GUA A . n A 1 29 DC 29 29 29 DC CYT A . n A 1 30 DA 30 30 30 DA ADE A . n A 1 31 DT 31 31 31 DT THY A . n A 1 32 DG 32 32 32 DG GUA A . n A 1 33 DT 33 33 33 DT THY A . n B 2 1 A 1 34 34 A ADE B . n B 2 2 C 2 35 35 C CYT B . n B 2 3 A 3 36 36 A ADE B . n B 2 4 U 4 37 37 U URI B . n B 2 5 G 5 38 38 G GUA B . n B 2 6 C 6 39 39 C CYT B . n B 2 7 A 7 40 40 A ADE B . n B 2 8 C 8 41 41 C CYT B . n B 2 9 C 9 42 42 C CYT B . n B 2 10 G 10 43 43 G GUA B . n B 2 11 U 11 44 44 U URI B . n B 2 12 U 12 45 45 U URI B . n B 2 13 A 13 46 46 A ADE B . n B 2 14 C 14 47 47 C CYT B . n B 2 15 C 15 48 48 C CYT B . n B 2 16 C 16 49 49 C CYT B . n B 2 17 C 17 50 50 C CYT B . n B 2 18 A 18 51 51 A ADE B . n B 2 19 A 19 52 52 A ADE B . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email Manuel.Etzkorn@hhu.de _pdbx_contact_author.name_first Manuel _pdbx_contact_author.name_last Etzkorn _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-9796-3246 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 2021-12-15 2 'Structure model' 1 1 2022-01-26 # _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' # 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 2 'Structure model' citation_author # 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.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.journal_volume' 7 2 'Structure model' '_citation.page_first' 8 2 'Structure model' '_citation.page_last' 9 2 'Structure model' '_citation.pdbx_database_id_DOI' 10 2 'Structure model' '_citation.pdbx_database_id_PubMed' 11 2 'Structure model' '_citation.title' 12 2 'Structure model' '_citation.year' # 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 '110-23 DNAzyme (33-MER)' 500 ? uM none 1 'RNA target (19-MER)' 500 ? uM none 1 Tris-d11 50 ? mM n.a. 1 NaCl 100 ? mM n.a. 1 MgCl2 1 ? mM n.a. 3 '110-23 DNAzyme (33-MER)' 500 ? uM '[U-13C; U-15N]' 3 'RNA target (19-MER)' 500 ? uM none 3 Tris-d11 50 ? mM n.a. 3 NaCl 100 ? mM n.a. 3 MgCl2 1 ? mM n.a. 2 '110-23 DNAzyme (33-MER)' 750 ? uM none 2 'RNA target (19-MER)' 750 ? uM none 2 Tris-d11 50 ? mM n.a. 2 NaCl 100 ? mM n.a. 2 MgCl2 1 ? mM n.a. # 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 H21 A DG 3 ? ? O2 B C 50 ? ? 1.60 2 4 N3 A DA 8 ? ? "O3'" A DG 11 ? ? 2.07 3 4 O2 A DT 7 ? ? O4 B U 45 ? ? 2.13 4 7 "H4'" A DG 28 ? ? OP1 A DC 29 ? ? 1.53 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 6 ? ? "C4'" A DG 6 ? ? "C3'" A DG 6 ? ? 101.60 104.50 -2.90 0.40 N 2 1 "C1'" B C 42 ? ? "O4'" B C 42 ? ? "C4'" B C 42 ? ? 105.44 109.70 -4.26 0.70 N 3 2 "C1'" A DT 2 ? ? "O4'" A DT 2 ? ? "C4'" A DT 2 ? ? 103.46 110.10 -6.64 1.00 N 4 2 "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? "C3'" A DG 4 ? ? 102.05 104.50 -2.45 0.40 N 5 2 "C1'" A DG 4 ? ? "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? 103.59 110.10 -6.51 1.00 N 6 2 "C1'" A DG 5 ? ? "O4'" A DG 5 ? ? "C4'" A DG 5 ? ? 103.67 110.10 -6.43 1.00 N 7 2 "C1'" A DA 18 ? ? "O4'" A DA 18 ? ? "C4'" A DA 18 ? ? 103.36 110.10 -6.74 1.00 N 8 2 "C1'" A DA 24 ? ? "O4'" A DA 24 ? ? "C4'" A DA 24 ? ? 101.20 110.10 -8.90 1.00 N 9 2 "C1'" B A 40 ? ? "O4'" B A 40 ? ? "C4'" B A 40 ? ? 105.16 109.70 -4.54 0.70 N 10 2 "C1'" B G 43 ? ? "O4'" B G 43 ? ? "C4'" B G 43 ? ? 105.09 109.70 -4.61 0.70 N 11 2 "C3'" B U 44 ? ? "C2'" B U 44 ? ? "C1'" B U 44 ? ? 96.18 101.30 -5.12 0.70 N 12 3 "C1'" A DG 4 ? ? "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? 103.89 110.10 -6.21 1.00 N 13 3 "C3'" A DT 27 ? ? "C2'" A DT 27 ? ? "C1'" A DT 27 ? ? 97.46 102.40 -4.94 0.80 N 14 3 "C3'" B A 52 ? ? "C2'" B A 52 ? ? "C1'" B A 52 ? ? 96.65 101.30 -4.65 0.70 N 15 4 "C1'" A DG 4 ? ? "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? 104.01 110.10 -6.09 1.00 N 16 4 "C4'" A DG 6 ? ? "C3'" A DG 6 ? ? "C2'" A DG 6 ? ? 96.64 102.20 -5.56 0.70 N 17 4 "O4'" A DA 9 ? ? "C4'" A DA 9 ? ? "C3'" A DA 9 ? ? 100.68 104.50 -3.82 0.40 N 18 4 "O4'" A DC 29 ? ? "C4'" A DC 29 ? ? "C3'" A DC 29 ? ? 100.25 104.50 -4.25 0.40 N 19 4 "C1'" A DC 29 ? ? "O4'" A DC 29 ? ? "C4'" A DC 29 ? ? 102.42 110.10 -7.68 1.00 N 20 4 "C3'" B C 50 ? ? "C2'" B C 50 ? ? "C1'" B C 50 ? ? 97.09 101.30 -4.21 0.70 N 21 5 "C3'" A DA 8 ? ? "C2'" A DA 8 ? ? "C1'" A DA 8 ? ? 97.45 102.40 -4.95 0.80 N 22 5 "C3'" B C 42 ? ? "C2'" B C 42 ? ? "C1'" B C 42 ? ? 96.85 101.30 -4.45 0.70 N 23 5 "C3'" B C 50 ? ? "C2'" B C 50 ? ? "C1'" B C 50 ? ? 97.02 101.30 -4.28 0.70 N 24 6 "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? "C3'" A DG 4 ? ? 101.88 104.50 -2.62 0.40 N 25 6 "C1'" A DG 4 ? ? "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? 103.81 110.10 -6.29 1.00 N 26 6 "C1'" A DA 18 ? ? "O4'" A DA 18 ? ? "C4'" A DA 18 ? ? 102.17 110.10 -7.93 1.00 N 27 6 "C3'" B A 51 ? ? "C2'" B A 51 ? ? "C1'" B A 51 ? ? 93.79 101.30 -7.51 0.70 N 28 7 "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? "C3'" A DG 4 ? ? 101.92 104.50 -2.58 0.40 N 29 7 "C1'" A DG 4 ? ? "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? 103.79 110.10 -6.31 1.00 N 30 7 "C1'" A DA 8 ? ? "O4'" A DA 8 ? ? "C4'" A DA 8 ? ? 103.49 110.10 -6.61 1.00 N 31 7 "C1'" B A 34 ? ? "O4'" B A 34 ? ? "C4'" B A 34 ? ? 102.97 109.70 -6.73 0.70 N 32 7 "C3'" B A 36 ? ? "C2'" B A 36 ? ? "C1'" B A 36 ? ? 96.71 101.30 -4.59 0.70 N 33 7 "C1'" B G 43 ? ? "O4'" B G 43 ? ? "C4'" B G 43 ? ? 105.33 109.70 -4.37 0.70 N 34 7 "C3'" B A 52 ? ? "C2'" B A 52 ? ? "C1'" B A 52 ? ? 96.79 101.30 -4.51 0.70 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7PDU 'double helix' 7PDU 'a-form double 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 DT 1 1_555 B A 19 1_555 -0.270 -1.754 -1.850 -43.342 10.710 -17.490 1 A_DT1:A52_B A 1 ? B 52 ? 20 1 1 A DT 2 1_555 B A 18 1_555 0.005 -0.108 -0.425 15.935 15.813 3.098 2 A_DT2:A51_B A 2 ? B 51 ? 20 1 1 A DG 5 1_555 B C 15 1_555 0.163 -0.108 -0.455 -7.585 18.875 0.455 3 A_DG5:C48_B A 5 ? B 48 ? 19 1 1 A DG 6 1_555 B C 14 1_555 -0.501 -0.208 -0.273 2.219 16.384 -0.231 4 A_DG6:C47_B A 6 ? B 47 ? 19 1 1 A DT 7 1_555 B A 13 1_555 -0.145 -0.114 -1.104 30.943 -9.474 -4.502 5 A_DT7:A46_B A 7 ? B 46 ? 20 1 1 A DA 8 1_555 B U 12 1_555 -0.355 -0.171 1.269 33.402 25.883 12.976 6 A_DA8:U45_B A 8 ? B 45 ? 20 1 1 A DA 9 1_555 B U 11 1_555 0.231 -0.781 -1.208 7.540 49.088 -27.231 7 A_DA9:U44_B A 9 ? B 44 ? 20 1 1 A DG 26 1_555 B C 8 1_555 -0.535 -0.200 -0.301 36.150 -7.836 9.969 8 A_DG26:C41_B A 26 ? B 41 ? 19 1 1 A DT 27 1_555 B A 7 1_555 0.375 -0.207 -1.219 29.539 -25.041 12.811 9 A_DT27:A40_B A 27 ? B 40 ? 20 1 1 A DG 28 1_555 B C 6 1_555 -0.701 -0.490 1.145 23.339 41.192 21.650 10 A_DG28:C39_B A 28 ? B 39 ? 19 1 1 A DC 29 1_555 B G 5 1_555 0.485 -0.084 0.215 28.102 -1.841 2.164 11 A_DC29:G38_B A 29 ? B 38 ? 19 1 1 A DA 30 1_555 B U 4 1_555 0.437 0.075 0.641 43.546 -33.596 0.432 12 A_DA30:U37_B A 30 ? B 37 ? 20 1 1 A DT 31 1_555 B A 3 1_555 0.173 -0.154 -0.781 26.732 -33.357 6.436 13 A_DT31:A36_B A 31 ? B 36 ? 20 1 1 A DG 32 1_555 B C 2 1_555 0.038 -0.446 -1.259 -11.485 11.983 -5.741 14 A_DG32:C35_B A 32 ? B 35 ? 19 1 1 A DT 33 1_555 B A 1 1_555 -0.387 -0.744 -1.777 18.320 15.681 -21.892 15 A_DT33:A34_B A 33 ? B 34 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DT 1 1_555 B A 19 1_555 A DT 2 1_555 B A 18 1_555 1.854 -0.571 3.424 5.577 -23.794 15.092 5.457 -2.195 2.646 -57.216 -13.411 28.663 1 AA_DT1DT2:A51A52_BB A 1 ? B 52 ? A 2 ? B 51 ? 1 A DG 5 1_555 B C 15 1_555 A DG 6 1_555 B C 14 1_555 -0.034 -1.815 3.351 -5.032 -5.993 19.171 -2.158 -2.338 3.636 -17.101 14.360 20.693 2 AA_DG5DG6:C47C48_BB A 5 ? B 48 ? A 6 ? B 47 ? 1 A DG 6 1_555 B C 14 1_555 A DT 7 1_555 B A 13 1_555 -1.306 -0.510 2.732 9.083 7.594 35.147 -1.592 3.000 2.186 12.157 -14.541 37.028 3 AA_DG6DT7:A46C47_BB A 6 ? B 47 ? A 7 ? B 46 ? 1 A DT 7 1_555 B A 13 1_555 A DA 8 1_555 B U 12 1_555 0.415 -1.175 3.210 -18.932 34.334 26.273 -3.795 -1.800 0.823 50.315 27.744 46.907 4 AA_DT7DA8:U45A46_BB A 7 ? B 46 ? A 8 ? B 45 ? 1 A DA 8 1_555 B U 12 1_555 A DA 9 1_555 B U 11 1_555 -5.331 -1.167 1.676 -19.278 48.703 42.805 -2.371 4.332 1.769 49.676 19.663 66.673 5 AA_DA8DA9:U44U45_BB A 8 ? B 45 ? A 9 ? B 44 ? 1 A DG 26 1_555 B C 8 1_555 A DT 27 1_555 B A 7 1_555 -0.456 -0.096 3.264 2.299 12.886 33.685 -1.966 1.059 2.993 21.266 -3.793 36.070 6 AA_DG26DT27:A40C41_BB A 26 ? B 41 ? A 27 ? B 40 ? 1 A DT 27 1_555 B A 7 1_555 A DG 28 1_555 B C 6 1_555 -0.498 -0.985 3.238 -22.804 45.720 22.163 -3.526 -0.694 0.739 60.934 30.392 55.393 7 AA_DT27DG28:C39A40_BB A 27 ? B 40 ? A 28 ? B 39 ? 1 A DG 28 1_555 B C 6 1_555 A DC 29 1_555 B G 5 1_555 -1.049 1.214 3.825 10.635 12.723 23.040 -1.057 5.102 3.272 27.712 -23.164 28.321 8 AA_DG28DC29:G38C39_BB A 28 ? B 39 ? A 29 ? B 38 ? 1 A DC 29 1_555 B G 5 1_555 A DA 30 1_555 B U 4 1_555 0.598 -0.136 2.846 -3.375 -2.413 27.984 0.204 -1.899 2.758 -4.956 6.932 28.284 9 AA_DC29DA30:U37G38_BB A 29 ? B 38 ? A 30 ? B 37 ? 1 A DA 30 1_555 B U 4 1_555 A DT 31 1_555 B A 3 1_555 0.397 -1.326 3.527 4.568 10.698 35.769 -3.499 -0.002 3.046 16.876 -7.207 37.554 10 AA_DA30DT31:A36U37_BB A 30 ? B 37 ? A 31 ? B 36 ? 1 A DT 31 1_555 B A 3 1_555 A DG 32 1_555 B C 2 1_555 -0.560 -1.800 4.376 -4.880 22.842 27.590 -6.723 0.092 2.331 40.018 8.549 36.003 11 AA_DT31DG32:C35A36_BB A 31 ? B 36 ? A 32 ? B 35 ? 1 A DG 32 1_555 B C 2 1_555 A DT 33 1_555 B A 1 1_555 -0.861 -1.535 2.674 5.271 2.821 25.726 -3.937 2.963 2.277 6.229 -11.639 26.400 12 AA_DG32DT33:A34C35_BB A 32 ? B 35 ? A 33 ? B 34 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'German Research Foundation (DFG)' 'European Union' 'ET 103/2-1' 1 'German Research Foundation (DFG)' 'European Union' 'ET 103/2-2' 2 'German Research Foundation (DFG)' 'European Union' 'ET 103/4-1' 3 'German Research Foundation (DFG)' 'European Union' 'ET 103/5-1' 4 'H2020 Marie Curie Actions of the European Commission' 'European Union' 'N 660258' 5 # loop_ _pdbx_struct_assembly_auth_evidence.id _pdbx_struct_assembly_auth_evidence.assembly_id _pdbx_struct_assembly_auth_evidence.experimental_support _pdbx_struct_assembly_auth_evidence.details 1 1 'native gel electrophoresis' 'Characteristic band for Dz:RNA in native PAGE' 2 1 'NMR Distance Restraints' 'Characteristic imino peaks visible only after hybridization' #