data_2TOB # _entry.id 2TOB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.329 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2TOB WWPDB D_1000178692 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2TOB _pdbx_database_status.recvd_initial_deposition_date 1998-06-17 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _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 'Jiang, L.' 1 'Patel, D.J.' 2 # _citation.id primary _citation.title 'Solution structure of the tobramycin-RNA aptamer complex.' _citation.journal_abbrev Nat.Struct.Biol. _citation.journal_volume 5 _citation.page_first 769 _citation.page_last 774 _citation.year 1998 _citation.journal_id_ASTM NSBIEW _citation.country US _citation.journal_id_ISSN 1072-8368 _citation.journal_id_CSD 2024 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9731769 _citation.pdbx_database_id_DOI 10.1038/1804 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Jiang, L.' 1 ? primary 'Patel, D.J.' 2 ? # _cell.entry_id 2TOB _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2TOB _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # 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 ;RNA (5'-R(*AP*CP*UP*UP*GP*GP*UP*UP*UP*AP*GP*GP*UP*AP*AP*UP*GP*AP*GP*U)-3') ; 6426.815 1 ? ? ? ? 2 non-polymer man 3-ammonio-3-deoxy-alpha-D-glucopyranose 180.179 1 ? ? ? ? 3 non-polymer man 2,6-diammonio-2,3,6-trideoxy-alpha-D-glucopyranose 164.203 1 ? ? ? ? 4 non-polymer syn 1,3-DIAMINO-4,5,6-TRIHYDROXY-CYCLOHEXANE 164.203 1 ? ? ? ? # _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 ACUUGGUUUAGGUAAUGAGU _entity_poly.pdbx_seq_one_letter_code_can ACUUGGUUUAGGUAAUGAGU _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 A n 1 2 C n 1 3 U n 1 4 U n 1 5 G n 1 6 G n 1 7 U n 1 8 U n 1 9 U n 1 10 A n 1 11 G n 1 12 G n 1 13 U n 1 14 A n 1 15 A n 1 16 U n 1 17 G n 1 18 A n 1 19 G n 1 20 U 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 20 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2TOB _struct_ref.pdbx_db_accession 2TOB _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 2TOB _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 20 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2TOB _struct_ref_seq.db_align_beg 4 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 23 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 4 _struct_ref_seq.pdbx_auth_seq_align_end 23 # 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 2TB non-polymer . 1,3-DIAMINO-4,5,6-TRIHYDROXY-CYCLOHEXANE ? 'C6 H16 N2 O3 2' 164.203 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 TOA 'D-saccharide, alpha linking' . 3-ammonio-3-deoxy-alpha-D-glucopyranose ? 'C6 H14 N O5 1' 180.179 TOC 'D-saccharide, alpha linking' . 2,6-diammonio-2,3,6-trideoxy-alpha-D-glucopyranose ? 'C6 H16 N2 O3 2' 164.203 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.type _pdbx_nmr_exptl.solution_id 1 1 NOESY 1 2 1 COSY 1 3 1 HMQCNULL 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 6.1 _pdbx_nmr_exptl_sample_conditions.ionic_strength '10mM NA(2)HPO(4)' _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents 'D(2)O/H(2)O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength 1 UNITYPLUS Varian 500 2 UNITYPLUS Varian 600 # _pdbx_nmr_refine.entry_id 2TOB _pdbx_nmr_refine.method 'DISTANCE-RESTRAINED MOLECULAR DYNAMICS' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2TOB _pdbx_nmr_details.text ;D2O: 2D NOESY (50MS,120MS,200MS,300MS MIXING TIMES), PHASE-SENSITIVE COSY, TOCSY, 1H-13C HSQC, 3D NOESY-HMQC (120MS, 300MS MIXING TIMES), 3D HCCH-COSY, 3D HCCH-TOCSY (65MS), 2D HP CORRELATION, C13 FILTERED NOESY ; # _pdbx_nmr_ensemble.entry_id 2TOB _pdbx_nmr_ensemble.conformers_calculated_total_number 40 _pdbx_nmr_ensemble.conformers_submitted_total_number 13 _pdbx_nmr_ensemble.conformer_selection_criteria 'LOWEST NOE AND TOTAL ENERGY' # _pdbx_nmr_representative.entry_id 2TOB _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria ? # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR 3.1 BRUNGER 1 'structure solution' 'VARIAN VNMR' VNMR ? 2 # _exptl.entry_id 2TOB _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2TOB _struct.title 'SOLUTION STRUCTURE OF THE TOBRAMYCIN-RNA APTAMER COMPLEX, NMR, 13 STRUCTURES' _struct.pdbx_descriptor "5'-R(*AP*CP*UP*UP*GP*GP*UP*UP*UP*AP*GP*GP*UP*AP*AP*UP*GP*AP*GP*U)-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2TOB _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'AMINOGLYCOSIDE-RNA RECOGNITION, TOBRAMYCIN, 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 2 ? C N N 3 ? D N N 4 ? # 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 one ? B TOA . C1 ? ? ? 1_555 D 2TB . O6 ? ? A TOA 100 A 2TB 101 1_555 ? ? ? ? ? ? ? 1.402 ? ? covale2 covale one ? D 2TB . O4 ? ? ? 1_555 C TOC . C1 ? ? A 2TB 101 A TOC 102 1_555 ? ? ? ? ? ? ? 1.401 ? ? hydrog1 hydrog ? ? A A 1 N1 ? ? ? 1_555 A U 20 N3 ? ? A A 4 A U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A 1 N6 ? ? ? 1_555 A U 20 O4 ? ? A A 4 A U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 19 N1 ? ? A C 5 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 19 O6 ? ? A C 5 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 19 N2 ? ? A C 5 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 18 N1 ? ? A U 6 A A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 18 N6 ? ? A U 6 A A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 4 N3 ? ? ? 1_555 A G 17 O6 ? ? A U 7 A G 20 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog9 hydrog ? ? A U 4 O2 ? ? ? 1_555 A G 17 N1 ? ? A U 7 A G 20 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog10 hydrog ? ? A G 5 O6 ? ? ? 1_555 A U 16 N3 ? ? A G 8 A U 19 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog11 hydrog ? ? A G 6 N1 ? ? ? 1_555 A A 15 N1 ? ? A G 9 A A 18 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog12 hydrog ? ? A G 6 O6 ? ? ? 1_555 A A 15 N6 ? ? A G 9 A A 18 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog13 hydrog ? ? A G 6 N1 ? ? ? 1_555 A U 16 O2 ? ? A G 9 A U 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog14 hydrog ? ? A G 6 O6 ? ? ? 1_555 A U 16 N3 ? ? A G 9 A U 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog15 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 14 N1 ? ? A U 10 A A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 14 N6 ? ? A U 10 A A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 8 N3 ? ? ? 1_555 A U 13 O4 ? ? A U 11 A U 16 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog18 hydrog ? ? A U 8 O2 ? ? ? 1_555 A U 13 N3 ? ? A U 11 A U 16 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 2TOB _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 2TOB _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 A 1 4 4 A A A . n A 1 2 C 2 5 5 C C A . n A 1 3 U 3 6 6 U U A . n A 1 4 U 4 7 7 U U A . n A 1 5 G 5 8 8 G G A . n A 1 6 G 6 9 9 G G A . n A 1 7 U 7 10 10 U U A . n A 1 8 U 8 11 11 U U A . n A 1 9 U 9 12 12 U U A . n A 1 10 A 10 13 13 A A A . n A 1 11 G 11 14 14 G G A . n A 1 12 G 12 15 15 G G A . n A 1 13 U 13 16 16 U U A . n A 1 14 A 14 17 17 A A A . n A 1 15 A 15 18 18 A A A . n A 1 16 U 16 19 19 U U A . n A 1 17 G 17 20 20 G G A . n A 1 18 A 18 21 21 A A A . n A 1 19 G 19 22 22 G G A . n A 1 20 U 20 23 23 U U A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 TOA 1 100 100 TOA TOA A . C 3 TOC 1 102 102 TOC TOC A . D 4 2TB 1 101 101 2TB 2TB A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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 1999-06-22 2 'Structure model' 1 1 2008-03-25 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2020-06-24 5 'Structure model' 2 0 2020-07-29 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 5 'Structure model' repository Remediation 'Carbohydrate remediation' ? # 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' 5 4 'Structure model' Other 6 4 'Structure model' 'Source and taxonomy' 7 5 'Structure model' 'Atomic model' 8 5 'Structure model' 'Data collection' 9 5 'Structure model' 'Derived calculations' 10 5 'Structure model' 'Structure summary' # 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' ndb_struct_na_base_pair 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_entity_src_syn 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_ref 8 4 'Structure model' struct_ref_seq 9 5 'Structure model' atom_site 10 5 'Structure model' chem_comp 11 5 'Structure model' entity 12 5 'Structure model' pdbx_chem_comp_identifier 13 5 'Structure model' pdbx_entity_nonpoly 14 5 'Structure model' struct_site 15 5 'Structure model' struct_site_gen # 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' '_ndb_struct_na_base_pair.hbond_type_12' 2 4 'Structure model' '_pdbx_database_status.process_site' 3 5 'Structure model' '_atom_site.auth_atom_id' 4 5 'Structure model' '_atom_site.label_atom_id' 5 5 'Structure model' '_chem_comp.name' 6 5 'Structure model' '_chem_comp.type' 7 5 'Structure model' '_entity.pdbx_description' 8 5 'Structure model' '_pdbx_entity_nonpoly.name' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' 3.1 ? 1 X-PLOR refinement 3.1 ? 2 X-PLOR phasing 3.1 ? 3 # 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 H3 A U 7 ? ? O6 A G 20 ? ? 1.51 2 1 OP2 A G 15 ? ? HN21 A TOC 102 ? ? 1.56 3 1 O6 A G 9 ? ? H61 A A 18 ? ? 1.58 4 1 "HO2'" A A 17 ? ? "O4'" A A 18 ? ? 1.59 5 2 "HO2'" A G 14 ? ? OP1 A U 16 ? ? 1.52 6 2 H3 A U 7 ? ? O6 A G 20 ? ? 1.53 7 2 "HO2'" A G 15 ? ? OP2 A U 16 ? ? 1.55 8 2 O4 A U 7 ? ? HN32 A TOA 100 ? ? 1.56 9 3 "HO2'" A G 15 ? ? OP2 A U 16 ? ? 1.50 10 3 "HO2'" A G 14 ? ? OP1 A U 16 ? ? 1.52 11 3 H3 A U 7 ? ? O6 A G 20 ? ? 1.53 12 3 O6 A G 9 ? ? H61 A A 18 ? ? 1.56 13 3 H3 A U 11 ? ? O4 A U 16 ? ? 1.59 14 4 H3 A U 7 ? ? O6 A G 20 ? ? 1.50 15 4 "HO2'" A G 15 ? ? OP2 A U 16 ? ? 1.53 16 4 "HO2'" A G 14 ? ? OP1 A U 16 ? ? 1.56 17 4 HN23 A TOC 102 ? ? O5 A 2TB 101 ? ? 1.58 18 4 O6 A G 9 ? ? H61 A A 18 ? ? 1.59 19 4 O6 A G 8 ? ? H3 A U 19 ? ? 1.60 20 5 OP2 A G 15 ? ? HN21 A TOC 102 ? ? 1.53 21 5 OP2 A U 10 ? ? HN31 A 2TB 101 ? ? 1.57 22 5 HN23 A TOC 102 ? ? O5 A 2TB 101 ? ? 1.59 23 6 H3 A U 7 ? ? O6 A G 20 ? ? 1.49 24 6 "HO2'" A G 15 ? ? OP2 A U 16 ? ? 1.57 25 7 "HO2'" A G 15 ? ? OP2 A U 16 ? ? 1.50 26 7 "HO2'" A G 14 ? ? OP1 A U 16 ? ? 1.51 27 7 H3 A U 7 ? ? O6 A G 20 ? ? 1.55 28 7 OP2 A G 8 ? ? HN13 A 2TB 101 ? ? 1.57 29 8 "HO2'" A G 15 ? ? OP2 A U 16 ? ? 1.50 30 8 H3 A U 7 ? ? O6 A G 20 ? ? 1.55 31 9 O6 A G 9 ? ? H61 A A 18 ? ? 1.50 32 9 OP2 A G 15 ? ? HN22 A TOC 102 ? ? 1.51 33 9 O4 A U 7 ? ? HN31 A TOA 100 ? ? 1.55 34 9 H3 A U 7 ? ? O6 A G 20 ? ? 1.56 35 9 "HO2'" A A 17 ? ? "O4'" A A 18 ? ? 1.59 36 10 HN22 A TOC 102 ? ? O5 A 2TB 101 ? ? 1.47 37 10 H3 A U 7 ? ? O6 A G 20 ? ? 1.58 38 11 H3 A U 7 ? ? O6 A G 20 ? ? 1.48 39 11 "HO2'" A G 15 ? ? OP2 A U 16 ? ? 1.57 40 11 OP2 A G 8 ? ? HN12 A 2TB 101 ? ? 1.59 41 12 "HO2'" A G 15 ? ? OP2 A U 16 ? ? 1.50 42 12 "HO2'" A G 14 ? ? OP1 A U 16 ? ? 1.52 43 12 O6 A G 9 ? ? H61 A A 18 ? ? 1.52 44 12 H3 A U 7 ? ? O6 A G 20 ? ? 1.53 45 12 OP2 A G 15 ? ? HN21 A TOC 102 ? ? 1.53 46 12 O4 A U 7 ? ? HN33 A TOA 100 ? ? 1.58 47 12 HN23 A TOC 102 ? ? O5 A 2TB 101 ? ? 1.59 48 13 O4 A U 7 ? ? HN32 A TOA 100 ? ? 1.51 49 13 "HO2'" A G 15 ? ? OP2 A U 16 ? ? 1.54 50 13 HN22 A TOC 102 ? ? O5 A 2TB 101 ? ? 1.56 51 13 OP2 A G 8 ? ? HN11 A 2TB 101 ? ? 1.56 52 13 OP2 A G 15 ? ? HN23 A TOC 102 ? ? 1.59 53 13 O6 A G 8 ? ? H3 A U 19 ? ? 1.59 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2TOB 'double helix' 2TOB 'a-form double helix' 2TOB 'hairpin loop' 2TOB '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 A 1 1_555 A U 20 1_555 0.131 -0.115 0.394 2.987 -7.322 5.314 1 A_A4:U23_A A 4 ? A 23 ? 20 1 1 A C 2 1_555 A G 19 1_555 0.501 -0.215 -0.076 15.780 -18.968 -6.275 2 A_C5:G22_A A 5 ? A 22 ? 19 1 1 A U 3 1_555 A A 18 1_555 -0.327 -0.166 -0.084 6.120 -6.299 -1.711 3 A_U6:A21_A A 6 ? A 21 ? 20 1 1 A U 4 1_555 A G 17 1_555 2.405 -0.809 0.114 5.881 -9.369 -12.004 4 A_U7:G20_A A 7 ? A 20 ? 28 1 1 A G 5 1_555 A U 16 1_555 -2.430 -0.126 -0.629 -1.092 -6.653 -73.920 5 A_G8:U19_A A 8 ? A 19 ? ? ? 1 A G 6 1_555 A A 15 1_555 -0.017 1.327 -0.149 7.006 14.962 -24.398 6 A_G9:A18_A A 9 ? A 18 ? 8 1 1 A U 7 1_555 A A 14 1_555 0.246 -0.045 -0.176 8.646 2.450 3.279 7 A_U10:A17_A A 10 ? A 17 ? 20 1 1 A U 8 1_555 A U 13 1_555 2.926 -1.884 0.033 15.979 -11.237 4.325 8 A_U11:U16_A A 11 ? A 16 ? 16 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 A 1 1_555 A U 20 1_555 A C 2 1_555 A G 19 1_555 -0.148 -1.176 2.817 4.015 -1.379 32.762 -1.867 0.850 2.825 -2.432 -7.081 33.028 1 AA_A4C5:G22U23_AA A 4 ? A 23 ? A 5 ? A 22 ? 1 A C 2 1_555 A G 19 1_555 A U 3 1_555 A A 18 1_555 -0.842 -1.725 3.093 -5.244 12.040 36.427 -3.917 0.701 2.512 18.536 8.072 38.646 2 AA_C5U6:A21G22_AA A 5 ? A 22 ? A 6 ? A 21 ? 1 A U 3 1_555 A A 18 1_555 A U 4 1_555 A G 17 1_555 1.171 -1.929 2.994 -1.219 2.861 41.928 -2.953 -1.745 2.829 3.991 1.701 42.038 3 AA_U6U7:G20A21_AA A 6 ? A 21 ? A 7 ? A 20 ? 1 A U 4 1_555 A G 17 1_555 A G 5 1_555 A U 16 1_555 -3.204 -1.980 2.935 0.132 16.042 20.947 -7.340 7.059 1.134 37.782 -0.312 26.330 4 AA_U7G8:U19G20_AA A 7 ? A 20 ? A 8 ? A 19 ? 1 A G 5 1_555 A U 16 1_555 A G 6 1_555 A A 15 1_555 0.899 -2.367 2.948 -5.681 3.178 40.620 -3.666 -1.808 2.620 4.543 8.121 41.117 5 AA_G8G9:A18U19_AA A 8 ? A 19 ? A 9 ? A 18 ? 1 A G 6 1_555 A A 15 1_555 A U 7 1_555 A A 14 1_555 0.911 -1.933 3.123 -3.496 7.278 25.356 -5.841 -2.767 2.342 16.069 7.719 26.590 6 AA_G9U10:A17A18_AA A 9 ? A 18 ? A 10 ? A 17 ? 1 A U 7 1_555 A A 14 1_555 A U 8 1_555 A U 13 1_555 0.194 -1.615 2.698 -2.721 2.636 43.662 -2.367 -0.470 2.585 3.537 3.651 43.818 7 AA_U10U11:U16A17_AA A 10 ? A 17 ? A 11 ? A 16 ? # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier TOA 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-Glcp3N TOC 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-3-deoxy-GlcpN6N # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 3-ammonio-3-deoxy-alpha-D-glucopyranose TOA 3 2,6-diammonio-2,3,6-trideoxy-alpha-D-glucopyranose TOC 4 1,3-DIAMINO-4,5,6-TRIHYDROXY-CYCLOHEXANE 2TB #