data_6GMY # _entry.id 6GMY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.308 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 6GMY WWPDB D_1200010259 BMRB 34276 # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB . 6FW6 unspecified BMRB 'Tc-DNA/DNA duplex' 34276 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 6GMY _pdbx_database_status.recvd_initial_deposition_date 2018-05-28 _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 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Istrate, A.' 1 0000-0003-3385-497X 'Johannsen, S.' 2 ? 'Istrate, A.' 3 ? 'Sigel, R.K.O.' 4 ? 'Leumann, C.' 5 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 47 _citation.language ? _citation.page_first 4872 _citation.page_last 4882 _citation.title 'NMR solution structure of tricyclo-DNA containing duplexes: insight into enhanced thermal stability and nuclease resistance.' _citation.year 2019 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkz197 _citation.pdbx_database_id_PubMed 30916334 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Istrate, A.' 1 ? primary 'Johannsen, S.' 2 ? primary 'Istrate, A.' 3 ? primary 'Sigel, R.K.O.' 4 ? primary 'Leumann, C.J.' 5 ? # 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 ;Tc-DNA (5'-(*(TCJ)P*(TTK)P*(TCJ)P*(TCS)P*(TCS)P*(TCJ)P*(TTK)P*(TTK)P*(TCY)P*(TCJ))-3') ; 3352.575 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*GP*UP*AP*AP*GP*CP*CP*GP*AP*G)-3') ; 3240.012 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 yes '(F7H)(EAN)(TCJ)(F4Q)(F4Q)(TCJ)(EAN)(EAN)(TCY)(TCJ)' CTCGGCTTAC A ? 2 polyribonucleotide no no GUAAGCCGAG GUAAGCCGAG B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 F7H n 1 2 EAN n 1 3 TCJ n 1 4 F4Q n 1 5 F4Q n 1 6 TCJ n 1 7 EAN n 1 8 EAN n 1 9 TCY n 1 10 TCJ n 2 1 G n 2 2 U n 2 3 A n 2 4 A n 2 5 G n 2 6 C n 2 7 C n 2 8 G n 2 9 A n 2 10 G 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 10 'Homo sapiens' ? 9606 ? 2 1 sample 1 10 'Homo sapiens' ? 9606 ? # 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 6GMY 6GMY ? 1 ? 1 2 PDB 6GMY 6GMY ? 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 6GMY A 1 ? 10 ? 6GMY 1 ? 10 ? 1 10 2 2 6GMY B 1 ? 10 ? 6GMY 11 ? 20 ? 11 20 # 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 EAN 'DNA linking' n ;[(1~{S},2~{R},4~{R},6~{S},8~{R})-8-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl] dihydrogen phosphate ; ? 'C13 H17 N2 O8 P' 360.256 F4Q 'DNA linking' n ;[(1~{S},2~{R},4~{R},6~{S},8~{R})-8-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl] dihydrogen phosphate ; ? 'C13 H16 N5 O7 P' 385.269 F7H 'DNA linking' n '4-azanyl-1-[(1~{S},2~{R},4~{S},6~{S},8~{R})-2,6-bis(oxidanyl)-9-oxatricyclo[4.3.0.0^{2,4}]nonan-8-yl]-5-methyl-pyrimidin-2-one' ? 'C13 H17 N3 O4' 279.292 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 TCJ 'DNA linking' n ;[(1~{S},2~{R},4~{R},6~{S},8~{R})-8-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl] dihydrogen phosphate ; ? 'C13 H18 N3 O7 P' 359.272 TCY 'DNA linking' n ;(2R,3aS,4aR,5aR,5bS)-2-(6-amino-9H-purin-9-yl)-3a-hydroxyhexahydrocyclopropa[4,5]cyclopenta[1,2-b]furan-5a(4H)-yl dihydrogen phosphate ; ? 'C13 H16 N5 O6 P' 369.270 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 2 2 '2D 1H-1H NOESY' 1 isotropic 3 1 1 '2D 1H-1H TOCSY' 1 isotropic 4 1 1 '2D DQF-COSY' 1 isotropic 5 1 1 '2D 1H-13C HSQC' 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 1 298 atm 1 7.05 'NaCl 50 mM, NaH2PO4 10 mM' ? ? 'Not defined' 'D2O 298K' ? pH ? ? K 2 283 atm 1 7.05 'NaCl 50 mM, NaH2PO4 10 mM' ? ? 'Not defined' 'H2O 283K' ? pH ? ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 '0.5 mM tc-DNA/RNA, 50 mM NaCl, 10 mM NaH2PO4, 100% D2O' '100% D2O' D2O solution ? 2 '0.5 mM tc-DNA/RNA, 50 mM NaCl, 10 mM NaH2PO4, 90% H2O/10% D2O' '90% H2O/10% D2O' H2O solution ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model AvanceII _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 700 _pdbx_nmr_spectrometer.details ? # loop_ _pdbx_nmr_refine.entry_id _pdbx_nmr_refine.method _pdbx_nmr_refine.details _pdbx_nmr_refine.software_ordinal 6GMY 'simulated annealing' ? 1 6GMY 'simulated annealing' ? 2 # _pdbx_nmr_ensemble.entry_id 6GMY _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the least restraint violations' _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 6GMY _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 refinement CNS ? 'Brunger, Adams, Clore, Gros, Nilges and Read' 2 refinement GROMOS ? 'van Gunsteren and Berendsen' 3 'chemical shift assignment' Sparky ? Goddard 4 processing NMRPipe ? 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' # _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 6GMY _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 6GMY _struct.title 'Tc-DNA/RNA duplex' _struct.pdbx_descriptor ;Tc-DNA (5'-(*(TCJ)P*(TTK)P*(TCJ)P*(TCS)P*(TCS)P*(TCJ)P*(TTK)P*(TTK)P*(TCY)P*(TCJ))-3'), RNA (5'-R(*GP*UP*AP*AP*GP*CP*CP*GP*AP*G)-3') ; _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 6GMY _struct_keywords.text 'tricyclo-DNA, Modified nucleic acids, Modified oligonucleotide, Tc-DNA, 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 covale1 covale one ? A F7H 1 "O3'" ? ? ? 1_555 A EAN 2 P ? ? A F7H 1 A EAN 2 1_555 ? ? ? ? ? ? ? 1.621 ? covale2 covale one ? A EAN 2 "O3'" ? ? ? 1_555 A TCJ 3 P ? ? A EAN 2 A TCJ 3 1_555 ? ? ? ? ? ? ? 1.629 ? covale3 covale one ? A TCJ 3 "O3'" ? ? ? 1_555 A F4Q 4 P ? ? A TCJ 3 A F4Q 4 1_555 ? ? ? ? ? ? ? 1.625 ? covale4 covale one ? A F4Q 4 "O3'" ? ? ? 1_555 A F4Q 5 P ? ? A F4Q 4 A F4Q 5 1_555 ? ? ? ? ? ? ? 1.630 ? covale5 covale one ? A F4Q 5 "O3'" ? ? ? 1_555 A TCJ 6 P ? ? A F4Q 5 A TCJ 6 1_555 ? ? ? ? ? ? ? 1.620 ? covale6 covale one ? A TCJ 6 "O3'" ? ? ? 1_555 A EAN 7 P ? ? A TCJ 6 A EAN 7 1_555 ? ? ? ? ? ? ? 1.623 ? covale7 covale one ? A EAN 7 "O3'" ? ? ? 1_555 A EAN 8 P ? ? A EAN 7 A EAN 8 1_555 ? ? ? ? ? ? ? 1.617 ? covale8 covale one ? A EAN 8 "O3'" ? ? ? 1_555 A TCY 9 P ? ? A EAN 8 A TCY 9 1_555 ? ? ? ? ? ? ? 1.627 ? covale9 covale both ? A TCY 9 "O3'" ? ? ? 1_555 A TCJ 10 P ? ? A TCY 9 A TCJ 10 1_555 ? ? ? ? ? ? ? 1.636 ? hydrog1 hydrog ? ? A EAN 2 N3 ? ? ? 1_555 B A 9 N1 ? ? A EAN 2 B A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A EAN 2 O4 ? ? ? 1_555 B A 9 N6 ? ? A EAN 2 B A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A TCJ 3 N3 ? ? ? 1_555 B G 8 N1 ? ? A TCJ 3 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A TCJ 3 N4 ? ? ? 1_555 B G 8 O6 ? ? A TCJ 3 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A TCJ 3 O2 ? ? ? 1_555 B G 8 N2 ? ? A TCJ 3 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A F4Q 4 N1 ? ? ? 1_555 B C 7 N3 ? ? A F4Q 4 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A F4Q 4 N2 ? ? ? 1_555 B C 7 O2 ? ? A F4Q 4 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A F4Q 4 O6 ? ? ? 1_555 B C 7 N4 ? ? A F4Q 4 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A F4Q 5 N1 ? ? ? 1_555 B C 6 N3 ? ? A F4Q 5 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A F4Q 5 N2 ? ? ? 1_555 B C 6 O2 ? ? A F4Q 5 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A F4Q 5 O6 ? ? ? 1_555 B C 6 N4 ? ? A F4Q 5 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A TCJ 6 N3 ? ? ? 1_555 B G 5 N1 ? ? A TCJ 6 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A TCJ 6 N4 ? ? ? 1_555 B G 5 O6 ? ? A TCJ 6 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A TCJ 6 O2 ? ? ? 1_555 B G 5 N2 ? ? A TCJ 6 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A EAN 7 N3 ? ? ? 1_555 B A 4 N1 ? ? A EAN 7 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A EAN 7 O4 ? ? ? 1_555 B A 4 N6 ? ? A EAN 7 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A EAN 8 N3 ? ? ? 1_555 B A 3 N1 ? ? A EAN 8 B A 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A EAN 8 O4 ? ? ? 1_555 B A 3 N6 ? ? A EAN 8 B A 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A TCY 9 N1 ? ? ? 1_555 B U 2 N3 ? ? A TCY 9 B U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A TCY 9 N6 ? ? ? 1_555 B U 2 O4 ? ? A TCY 9 B U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 6GMY _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 F7H 1 1 1 F7H TCJ A . n A 1 2 EAN 2 2 2 EAN TTK A . n A 1 3 TCJ 3 3 3 TCJ TCJ A . n A 1 4 F4Q 4 4 4 F4Q TCS A . n A 1 5 F4Q 5 5 5 F4Q TCS A . n A 1 6 TCJ 6 6 6 TCJ TCJ A . n A 1 7 EAN 7 7 7 EAN TTK A . n A 1 8 EAN 8 8 8 EAN TTK A . n A 1 9 TCY 9 9 9 TCY TCY A . n A 1 10 TCJ 10 10 10 TCJ TCJ A . n B 2 1 G 1 11 11 G G B . n B 2 2 U 2 12 12 U U B . n B 2 3 A 3 13 13 A A B . n B 2 4 A 4 14 14 A A B . n B 2 5 G 5 15 15 G G B . n B 2 6 C 6 16 16 C C B . n B 2 7 C 7 17 17 C C B . n B 2 8 G 8 18 18 G G B . n B 2 9 A 9 19 19 A A B . n B 2 10 G 10 20 20 G G B . n # _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 2018-06-13 2 'Structure model' 1 1 2019-04-03 3 'Structure model' 1 2 2019-05-08 4 'Structure model' 2 0 2019-05-15 5 'Structure model' 2 1 2019-05-22 # _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 ? # 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' 'Database references' 3 3 'Structure model' 'Data collection' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Polymer sequence' 6 5 'Structure model' 'Data collection' 7 5 'Structure model' '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 3 2 'Structure model' pdbx_database_proc 4 3 'Structure model' pdbx_nmr_software 5 4 'Structure model' entity_poly 6 4 'Structure model' pdbx_seq_map_depositor_info 7 5 'Structure model' citation 8 5 'Structure model' database_PDB_rev 9 5 'Structure model' database_PDB_rev_record 10 5 'Structure model' pdbx_database_proc # 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.pdbx_database_id_DOI' 7 2 'Structure model' '_citation.pdbx_database_id_PubMed' 8 2 'Structure model' '_citation.title' 9 2 'Structure model' '_citation.year' 10 2 'Structure model' '_citation_author.name' 11 3 'Structure model' '_pdbx_nmr_software.name' 12 4 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 13 4 'Structure model' '_pdbx_seq_map_depositor_info.one_letter_code' 14 5 'Structure model' '_citation.journal_volume' 15 5 'Structure model' '_citation.page_first' 16 5 'Structure model' '_citation.page_last' # 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 tc-DNA/RNA 0.5 ? mM 'natural abundance' 1 NaCl 50 ? mM 'natural abundance' 1 NaH2PO4 10 ? mM 'natural abundance' 2 tc-DNA/RNA 0.5 ? mM 'natural abundance' 2 NaCl 50 ? mM 'natural abundance' 2 NaH2PO4 10 ? mM 'natural abundance' # 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 "C3'" B G 11 ? ? "O3'" B G 11 ? ? P B U 12 ? ? 128.54 119.70 8.84 1.20 Y 2 4 "C3'" B G 11 ? ? "O3'" B G 11 ? ? P B U 12 ? ? 128.43 119.70 8.73 1.20 Y 3 5 "C3'" B G 11 ? ? "O3'" B G 11 ? ? P B U 12 ? ? 128.16 119.70 8.46 1.20 Y # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 A B 19 ? ? 0.061 'SIDE CHAIN' 2 2 C B 17 ? ? 0.089 'SIDE CHAIN' 3 2 A B 19 ? ? 0.057 'SIDE CHAIN' 4 4 C B 16 ? ? 0.093 'SIDE CHAIN' 5 5 G B 20 ? ? 0.062 'SIDE CHAIN' 6 7 C B 16 ? ? 0.067 'SIDE CHAIN' 7 8 C B 16 ? ? 0.084 'SIDE CHAIN' 8 10 C B 16 ? ? 0.080 'SIDE CHAIN' 9 10 G B 18 ? ? 0.049 'SIDE CHAIN' # _ndb_struct_conf_na.entry_id 6GMY _ndb_struct_conf_na.feature '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 EAN 2 1_555 B A 9 1_555 0.049 -0.184 0.885 -6.331 -14.620 0.636 1 A_EAN2:A19_B A 2 ? B 19 ? 20 1 1 A TCJ 3 1_555 B G 8 1_555 0.217 -0.085 0.245 0.907 -19.087 -0.414 2 A_TCJ3:G18_B A 3 ? B 18 ? 19 1 1 A F4Q 4 1_555 B C 7 1_555 -0.114 -0.086 0.113 -5.774 -12.824 -0.642 3 A_F4Q4:C17_B A 4 ? B 17 ? 19 1 1 A F4Q 5 1_555 B C 6 1_555 -0.156 -0.068 -0.101 -10.210 -12.363 0.057 4 A_F4Q5:C16_B A 5 ? B 16 ? 19 1 1 A TCJ 6 1_555 B G 5 1_555 -0.026 -0.007 0.183 -1.001 -10.327 1.298 5 A_TCJ6:G15_B A 6 ? B 15 ? 19 1 1 A EAN 7 1_555 B A 4 1_555 -0.004 -0.006 0.191 -6.651 -11.242 -2.800 6 A_EAN7:A14_B A 7 ? B 14 ? 20 1 1 A EAN 8 1_555 B A 3 1_555 0.101 0.009 -0.074 -1.854 -8.549 -3.629 7 A_EAN8:A13_B A 8 ? B 13 ? 20 1 1 A TCY 9 1_555 B U 2 1_555 -0.257 0.023 0.020 6.020 1.992 9.844 8 A_TCY9:U12_B A 9 ? B 12 ? 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 EAN 2 1_555 B A 9 1_555 A TCJ 3 1_555 B G 8 1_555 0.188 -1.685 2.869 7.975 0.475 32.846 -2.967 0.814 2.812 0.824 -13.850 33.778 1 AA_EAN2TCJ3:G18A19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A TCJ 3 1_555 B G 8 1_555 A F4Q 4 1_555 B C 7 1_555 -0.029 -1.539 3.392 1.498 7.897 31.703 -4.077 0.307 2.930 14.171 -2.688 32.680 2 AA_TCJ3F4Q4:C17G18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A F4Q 4 1_555 B C 7 1_555 A F4Q 5 1_555 B C 6 1_555 -0.579 -1.763 3.277 1.703 5.944 33.353 -3.932 1.253 2.897 10.248 -2.936 33.905 3 AA_F4Q4F4Q5:C16C17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A F4Q 5 1_555 B C 6 1_555 A TCJ 6 1_555 B G 5 1_555 0.121 -2.124 3.094 0.771 -2.783 30.873 -3.451 -0.082 3.271 -5.213 -1.445 31.005 4 AA_F4Q5TCJ6:G15C16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A TCJ 6 1_555 B G 5 1_555 A EAN 7 1_555 B A 4 1_555 -0.118 -2.065 3.425 3.680 -1.379 32.163 -3.445 0.898 3.473 -2.477 -6.612 32.396 5 AA_TCJ6EAN7:A14G15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A EAN 7 1_555 B A 4 1_555 A EAN 8 1_555 B A 3 1_555 -0.179 -1.975 3.148 4.237 0.106 30.541 -3.735 1.127 3.089 0.199 -7.995 30.827 6 AA_EAN7EAN8:A13A14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A EAN 8 1_555 B A 3 1_555 A TCY 9 1_555 B U 2 1_555 0.412 -1.281 3.144 -2.446 2.169 30.229 -2.852 -1.248 3.005 4.144 4.673 30.401 7 AA_EAN8TCY9:U12A13_BB A 8 ? B 13 ? A 9 ? B 12 ? # _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 'mass spectrometry' _pdbx_struct_assembly_auth_evidence.details ? #