data_1MY9 # _entry.id 1MY9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1MY9 pdb_00001my9 10.2210/pdb1my9/pdb RCSB RCSB017306 ? ? WWPDB D_1000017306 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1MY9 _pdbx_database_status.recvd_initial_deposition_date 2002-10-04 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Liu, H.' 1 'Matsugami, A.' 2 'Katahira, M.' 3 'Uesugi, S.' 4 # _citation.id primary _citation.title 'A Dimeric RNA Quadruplex Architecture Comprised of Two G:G(:A):G:G(:A) Hexads, G:G:G:G Tetrads and UUUU Loops' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 322 _citation.page_first 955 _citation.page_last 970 _citation.year 2002 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12367521 _citation.pdbx_database_id_DOI '10.1016/S0022-2836(02)00876-8' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Liu, H.' 1 ? primary 'Matsugami, A.' 2 ? primary 'Katahira, M.' 3 ? primary 'Uesugi, S.' 4 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-R(*GP*GP*AP*GP*GP*UP*UP*UP*UP*GP*GP*AP*GP*G)-3'" _entity.formula_weight 4599.764 _entity.pdbx_number_of_molecules 2 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details 'K+ CATION STABILIZED' # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGAGGUUUUGGAGG _entity_poly.pdbx_seq_one_letter_code_can GGAGGUUUUGGAGG _entity_poly.pdbx_strand_id A,B _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 G n 1 6 U n 1 7 U n 1 8 U n 1 9 U n 1 10 G n 1 11 G n 1 12 A n 1 13 G n 1 14 G n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1MY9 _struct_ref.pdbx_db_accession 1MY9 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1MY9 A 1 ? 14 ? 1MY9 1 ? 14 ? 1 14 2 1 1MY9 B 1 ? 14 ? 1MY9 15 ? 28 ? 15 28 # 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 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.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 2 2 '2D NOESY' 3 2 2 '2D TOCSY' 4 2 2 DQF-COSY # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature_units 1 283 ambient 6.5 '16 mM KCl' ? K 2 305.5 ambient 6.5 '16 mM KCl' ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1.6 mM RNA, 10 mM sodium phosphate buffer (pH 6.5), 16 mM KCl' '95% H2O/5% D2O' 2 '1.6 mM RNA, 10 mM sodium phosphate buffer (pH 6.5), 16 mM KCl' '100% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model DRX _pdbx_nmr_spectrometer.field_strength 600 # _pdbx_nmr_refine.entry_id 1MY9 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1MY9 _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _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 1MY9 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal X-PLOR 3.851 'structure solution' Brunger 1 X-PLOR 3.851 refinement Brunger 2 # _exptl.entry_id 1MY9 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1MY9 _struct.title ;Solution structure of a K+ cation stabilized dimeric RNA quadruplex containing two G:G(:A):G:G(:A) hexads, G:G:G:G tetrads and UUUU loops ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1MY9 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Parallel RNA quadruplex with a loop, Dimer of two quadruplexes, RNA' # 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 1 ? # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N2 ? ? ? 1_555 A A 3 N7 ? ? A G 1 A A 3 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog2 hydrog ? ? A G 1 N3 ? ? ? 1_555 A A 3 N6 ? ? A G 1 A A 3 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog3 hydrog ? ? A G 1 N1 ? ? ? 1_555 A G 4 O6 ? ? A G 1 A G 4 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog4 hydrog ? ? A G 1 N2 ? ? ? 1_555 A G 4 N7 ? ? A G 1 A G 4 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog5 hydrog ? ? A G 1 N7 ? ? ? 1_555 A G 13 N2 ? ? A G 1 A G 13 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog6 hydrog ? ? A G 1 O6 ? ? ? 1_555 A G 13 N1 ? ? A G 1 A G 13 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog7 hydrog ? ? A G 2 N1 ? ? ? 1_555 A G 5 O6 ? ? A G 2 A G 5 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog8 hydrog ? ? A G 2 N2 ? ? ? 1_555 A G 5 N7 ? ? A G 2 A G 5 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog9 hydrog ? ? A G 2 N7 ? ? ? 1_555 A G 14 N2 ? ? A G 2 A G 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog10 hydrog ? ? A G 2 O6 ? ? ? 1_555 A G 14 N1 ? ? A G 2 A G 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog11 hydrog ? ? A G 4 N1 ? ? ? 1_555 A G 10 O6 ? ? A G 4 A G 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog12 hydrog ? ? A G 4 N2 ? ? ? 1_555 A G 10 N7 ? ? A G 4 A G 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog13 hydrog ? ? A G 4 O6 ? ? ? 1_555 B G 13 N1 ? ? A G 4 B G 27 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog14 hydrog ? ? A G 5 N1 ? ? ? 1_555 A G 11 O6 ? ? A G 5 A G 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog15 hydrog ? ? A G 5 N2 ? ? ? 1_555 A G 11 N7 ? ? A G 5 A G 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog16 hydrog ? ? A G 10 N2 ? ? ? 1_555 A A 12 N7 ? ? A G 10 A A 12 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog17 hydrog ? ? A G 10 N3 ? ? ? 1_555 A A 12 N6 ? ? A G 10 A A 12 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog18 hydrog ? ? A G 10 N1 ? ? ? 1_555 A G 13 O6 ? ? A G 10 A G 13 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog19 hydrog ? ? A G 10 N2 ? ? ? 1_555 A G 13 N7 ? ? A G 10 A G 13 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog20 hydrog ? ? A G 11 N1 ? ? ? 1_555 A G 14 O6 ? ? A G 11 A G 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog21 hydrog ? ? A G 11 N2 ? ? ? 1_555 A G 14 N7 ? ? A G 11 A G 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog22 hydrog ? ? A A 12 N6 ? ? ? 1_555 B G 13 N7 ? ? A A 12 B G 27 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog23 hydrog ? ? A G 13 N7 ? ? ? 1_555 B A 12 N6 ? ? A G 13 B A 26 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog24 hydrog ? ? B G 1 N2 ? ? ? 1_555 B A 3 N7 ? ? B G 15 B A 17 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog25 hydrog ? ? B G 1 N3 ? ? ? 1_555 B A 3 N6 ? ? B G 15 B A 17 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog26 hydrog ? ? B G 1 N1 ? ? ? 1_555 B G 4 O6 ? ? B G 15 B G 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog27 hydrog ? ? B G 1 N2 ? ? ? 1_555 B G 4 N7 ? ? B G 15 B G 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog28 hydrog ? ? B G 1 N7 ? ? ? 1_555 B G 13 N2 ? ? B G 15 B G 27 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog29 hydrog ? ? B G 1 O6 ? ? ? 1_555 B G 13 N1 ? ? B G 15 B G 27 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog30 hydrog ? ? B G 2 N1 ? ? ? 1_555 B G 5 O6 ? ? B G 16 B G 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog31 hydrog ? ? B G 2 N2 ? ? ? 1_555 B G 5 N7 ? ? B G 16 B G 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog32 hydrog ? ? B G 2 N7 ? ? ? 1_555 B G 14 N2 ? ? B G 16 B G 28 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog33 hydrog ? ? B G 2 O6 ? ? ? 1_555 B G 14 N1 ? ? B G 16 B G 28 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog34 hydrog ? ? B G 4 N1 ? ? ? 1_555 B G 10 O6 ? ? B G 18 B G 24 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog35 hydrog ? ? B G 4 N2 ? ? ? 1_555 B G 10 N7 ? ? B G 18 B G 24 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog36 hydrog ? ? B G 5 N1 ? ? ? 1_555 B G 11 O6 ? ? B G 19 B G 25 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog37 hydrog ? ? B G 5 N2 ? ? ? 1_555 B G 11 N7 ? ? B G 19 B G 25 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog38 hydrog ? ? B G 10 N2 ? ? ? 1_555 B A 12 N7 ? ? B G 24 B A 26 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog39 hydrog ? ? B G 10 N3 ? ? ? 1_555 B A 12 N6 ? ? B G 24 B A 26 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog40 hydrog ? ? B G 10 N1 ? ? ? 1_555 B G 13 O6 ? ? B G 24 B G 27 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog41 hydrog ? ? B G 10 N2 ? ? ? 1_555 B G 13 N7 ? ? B G 24 B G 27 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog42 hydrog ? ? B G 11 N1 ? ? ? 1_555 B G 14 O6 ? ? B G 25 B G 28 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog43 hydrog ? ? B G 11 N2 ? ? ? 1_555 B G 14 N7 ? ? B G 25 B G 28 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1MY9 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1MY9 _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 U 9 9 9 U U A . n A 1 10 G 10 10 10 G G A . n A 1 11 G 11 11 11 G G A . n A 1 12 A 12 12 12 A A A . n A 1 13 G 13 13 13 G G A . n A 1 14 G 14 14 14 G G A . n B 1 1 G 1 15 15 G G B . n B 1 2 G 2 16 16 G G B . n B 1 3 A 3 17 17 A A B . n B 1 4 G 4 18 18 G G B . n B 1 5 G 5 19 19 G G B . n B 1 6 U 6 20 20 U U B . n B 1 7 U 7 21 21 U U B . n B 1 8 U 8 22 22 U U B . n B 1 9 U 9 23 23 U U B . n B 1 10 G 10 24 24 G G B . n B 1 11 G 11 25 25 G G B . n B 1 12 A 12 26 26 A A B . n B 1 13 G 13 27 27 G G B . n B 1 14 G 14 28 28 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 x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2003-10-07 2 'Structure model' 1 1 2008-04-28 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' # 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 4 'Structure model' database_2 2 4 'Structure model' pdbx_struct_assembly 3 4 'Structure model' pdbx_struct_oper_list # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' # 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 1 "HO2'" A G 10 ? ? OP2 A G 11 ? ? 1.37 2 1 "O5'" A G 1 ? ? "H1'" B G 18 ? ? 1.53 3 1 "O4'" A G 10 ? ? H61 A A 12 ? ? 1.55 4 1 "H1'" A G 5 ? ? "O4'" A U 6 ? ? 1.60 # 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 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.41 113.10 4.31 0.50 N 2 1 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.92 106.40 -2.48 0.40 N 3 1 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.64 113.10 4.54 0.50 N 4 1 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.91 106.40 -2.49 0.40 N 5 1 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 117.21 113.80 3.41 0.50 N 6 1 C8 A A 3 ? ? N9 A A 3 ? ? C4 A A 3 ? ? 103.19 105.80 -2.61 0.40 N 7 1 N7 A G 4 ? ? C8 A G 4 ? ? N9 A G 4 ? ? 117.45 113.10 4.35 0.50 N 8 1 C8 A G 4 ? ? N9 A G 4 ? ? C4 A G 4 ? ? 103.69 106.40 -2.71 0.40 N 9 1 N7 A G 5 ? ? C8 A G 5 ? ? N9 A G 5 ? ? 117.69 113.10 4.59 0.50 N 10 1 C8 A G 5 ? ? N9 A G 5 ? ? C4 A G 5 ? ? 103.73 106.40 -2.67 0.40 N 11 1 N7 A G 10 ? ? C8 A G 10 ? ? N9 A G 10 ? ? 117.55 113.10 4.45 0.50 N 12 1 C8 A G 10 ? ? N9 A G 10 ? ? C4 A G 10 ? ? 103.75 106.40 -2.65 0.40 N 13 1 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 117.62 113.10 4.52 0.50 N 14 1 C8 A G 11 ? ? N9 A G 11 ? ? C4 A G 11 ? ? 103.80 106.40 -2.60 0.40 N 15 1 N7 A A 12 ? ? C8 A A 12 ? ? N9 A A 12 ? ? 117.46 113.80 3.66 0.50 N 16 1 C8 A A 12 ? ? N9 A A 12 ? ? C4 A A 12 ? ? 103.40 105.80 -2.40 0.40 N 17 1 N7 A G 13 ? ? C8 A G 13 ? ? N9 A G 13 ? ? 117.68 113.10 4.58 0.50 N 18 1 C8 A G 13 ? ? N9 A G 13 ? ? C4 A G 13 ? ? 103.61 106.40 -2.79 0.40 N 19 1 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.66 113.10 4.56 0.50 N 20 1 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.77 106.40 -2.63 0.40 N 21 1 N7 B G 15 ? ? C8 B G 15 ? ? N9 B G 15 ? ? 117.46 113.10 4.36 0.50 N 22 1 C8 B G 15 ? ? N9 B G 15 ? ? C4 B G 15 ? ? 103.84 106.40 -2.56 0.40 N 23 1 N7 B G 16 ? ? C8 B G 16 ? ? N9 B G 16 ? ? 117.66 113.10 4.56 0.50 N 24 1 C8 B G 16 ? ? N9 B G 16 ? ? C4 B G 16 ? ? 103.80 106.40 -2.60 0.40 N 25 1 N7 B A 17 ? ? C8 B A 17 ? ? N9 B A 17 ? ? 117.26 113.80 3.46 0.50 N 26 1 C8 B A 17 ? ? N9 B A 17 ? ? C4 B A 17 ? ? 103.22 105.80 -2.58 0.40 N 27 1 N7 B G 18 ? ? C8 B G 18 ? ? N9 B G 18 ? ? 117.48 113.10 4.38 0.50 N 28 1 C8 B G 18 ? ? N9 B G 18 ? ? C4 B G 18 ? ? 103.81 106.40 -2.59 0.40 N 29 1 N7 B G 19 ? ? C8 B G 19 ? ? N9 B G 19 ? ? 117.62 113.10 4.52 0.50 N 30 1 C8 B G 19 ? ? N9 B G 19 ? ? C4 B G 19 ? ? 103.70 106.40 -2.70 0.40 N 31 1 N7 B G 24 ? ? C8 B G 24 ? ? N9 B G 24 ? ? 117.50 113.10 4.40 0.50 N 32 1 C8 B G 24 ? ? N9 B G 24 ? ? C4 B G 24 ? ? 103.81 106.40 -2.59 0.40 N 33 1 N7 B G 25 ? ? C8 B G 25 ? ? N9 B G 25 ? ? 117.59 113.10 4.49 0.50 N 34 1 C8 B G 25 ? ? N9 B G 25 ? ? C4 B G 25 ? ? 103.83 106.40 -2.57 0.40 N 35 1 N7 B A 26 ? ? C8 B A 26 ? ? N9 B A 26 ? ? 117.53 113.80 3.73 0.50 N 36 1 C8 B A 26 ? ? N9 B A 26 ? ? C4 B A 26 ? ? 103.37 105.80 -2.43 0.40 N 37 1 N7 B G 27 ? ? C8 B G 27 ? ? N9 B G 27 ? ? 117.57 113.10 4.47 0.50 N 38 1 C8 B G 27 ? ? N9 B G 27 ? ? C4 B G 27 ? ? 103.74 106.40 -2.66 0.40 N 39 1 N7 B G 28 ? ? C8 B G 28 ? ? N9 B G 28 ? ? 117.66 113.10 4.56 0.50 N 40 1 C8 B G 28 ? ? N9 B G 28 ? ? C4 B G 28 ? ? 103.73 106.40 -2.67 0.40 N # _ndb_struct_conf_na.entry_id 1MY9 _ndb_struct_conf_na.feature '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 G 11 1_555 A G 14 1_555 1.671 2.575 -1.465 -26.724 50.366 -91.374 1 A_G11:G14_A A 11 ? A 14 ? 6 ? 1 A G 1 1_555 A G 13 1_555 -0.529 -3.759 0.328 -16.923 0.605 101.415 2 A_G1:G13_A A 1 ? A 13 ? 6 3 1 A G 4 1_555 B G 13 1_555 -0.459 0.412 2.071 -0.080 34.679 18.244 3 A_G4:G27_B A 4 ? B 27 ? ? ? 1 B G 1 1_555 B G 4 1_555 1.015 3.231 1.211 9.881 -3.519 -84.126 4 B_G15:G18_B B 15 ? B 18 ? 6 3 1 B G 11 1_555 B G 14 1_555 1.684 3.206 -1.152 -18.836 31.990 -88.174 5 B_G25:G28_B B 25 ? B 28 ? 6 ? 1 B G 5 1_555 B G 2 1_555 -2.135 -3.322 -0.086 8.217 -20.933 82.301 6 B_G19:G16_B B 19 ? B 16 ? 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 11 1_555 A G 14 1_555 A G 1 1_555 A G 13 1_555 -0.796 -1.432 -4.341 -16.461 17.480 59.297 -0.309 1.745 -4.248 16.935 15.948 63.562 1 AA_G11G1:G13G14_AA A 11 ? A 14 ? A 1 ? A 13 ? 1 A G 1 1_555 A G 13 1_555 A G 4 1_555 B G 13 1_555 -1.046 -4.148 -1.495 -6.042 0.270 125.788 -2.328 0.610 -1.471 0.151 3.393 125.870 2 AA_G1G4:G27G13_BA A 1 ? A 13 ? A 4 ? B 27 ? 1 A G 4 1_555 B G 13 1_555 B G 1 1_555 B G 4 1_555 -1.558 1.229 -4.499 50.265 -164.158 -40.454 -2.127 -1.244 -0.029 84.679 25.929 -172.195 3 AB_G4G15:G18G27_BB A 4 ? B 27 ? B 15 ? B 18 ? 1 B G 11 1_555 B G 14 1_555 B G 5 1_555 B G 2 1_555 0.603 3.235 -0.479 14.810 -9.374 -176.777 -1.619 0.301 -0.474 4.689 7.408 -176.815 4 BB_G25G19:G16G28_BB B 25 ? B 28 ? B 19 ? B 16 ? #