data_1TJZ # _entry.id 1TJZ # _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 1TJZ pdb_00001tjz 10.2210/pdb1tjz/pdb RCSB RCSB022704 ? ? WWPDB D_1000022704 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1TJZ _pdbx_database_status.recvd_initial_deposition_date 2004-06-07 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _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 'Flinders, J.' 1 'Dieckmann, T.' 2 # _citation.id primary _citation.title ;The solution structure of the VS ribozyme active site loop reveals a dynamic "hot-spot" ; _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 341 _citation.page_first 935 _citation.page_last 949 _citation.year 2004 _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 15328609 _citation.pdbx_database_id_DOI 10.1016/j.jmb.2004.06.084 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Flinders, J.' 1 ? primary 'Dieckmann, T.' 2 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'VS Ribozyme' _entity.formula_weight 7127.322 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'RNA Loop VI' _entity.details ? # _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 GGUGACGCCGUAAGGCGCAGCC _entity_poly.pdbx_seq_one_letter_code_can GGUGACGCCGUAAGGCGCAGCC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 U n 1 4 G n 1 5 A n 1 6 C n 1 7 G n 1 8 C n 1 9 C n 1 10 G n 1 11 U n 1 12 A n 1 13 A n 1 14 G n 1 15 G n 1 16 C n 1 17 G n 1 18 C n 1 19 A n 1 20 G n 1 21 C n 1 22 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _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 'Synthesized enzymatically from a DNA template using T7 polymerase' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1TJZ _struct_ref.pdbx_db_accession 1TJZ _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1TJZ _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 22 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1TJZ _struct_ref_seq.db_align_beg 5 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 26 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 5 _struct_ref_seq.pdbx_auth_seq_align_end 26 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 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 3 2 '2D NOESY' 3 3 2 DQF-COSY 4 3 2 '2D TOCSY' 5 4 2 3D_13C-separated_NOESY 6 5 2 '2D NOESY' # 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 6.0 ? ? K 2 293 ambient 6.0 ? ? K 3 293 ambient 6.0 '10 mM MgCl2' ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1 mM VSVI RNA, 90% H2O, 10% D2O' '90% H2O/10% D2O' 2 '1 mM VSVI RNA U-15N,13C,' '90% H2O/10% D2O' 3 '1 mM VSVI RNA, 90% H2O, 10% D2O' '100% D2O' 4 '1 mM VSVI RNA U-15N,13C, 100% D2O' '100% D2O' 5 '1 mM VSVI RNA, 100% D2O' '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 1TJZ _pdbx_nmr_refine.method 'The structure calculations utilized standard simulated annealing protocols.' _pdbx_nmr_refine.details ;The final structures are based on a total of 699 restraints: 582 NOE-derived restraints, 52 dihedral angle restraints, 9 planarity restraints, and 56 distance restraints from hydrogen bonds. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1TJZ _pdbx_nmr_details.text 'The structure was determined from restraints derived from homo- and heteronuclear experiments.' # _pdbx_nmr_ensemble.entry_id 1TJZ _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _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 1TJZ _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 XwinNMR 3.5 collection ? 1 Sparky 3.106 'data analysis' ? 2 CNS 1.1 'structure solution' ? 3 XwinNMR 3.5 processing ? 4 CNS 1.1 refinement ? 5 # _exptl.entry_id 1TJZ _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 ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _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 1TJZ _struct.title 'Solution Structure of the Active Site Stem-Loop of the VS Ribozyme' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1TJZ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA hairpin, RNA stem-loop, protonated adenine, GA base pair, RNA' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 22 N3 ? ? A G 5 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 22 O2 ? ? A G 5 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 22 N4 ? ? A G 5 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 6 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 6 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 6 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 A G 20 O6 ? ? A U 7 A G 24 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog8 hydrog ? ? A U 3 O2 ? ? ? 1_555 A G 20 N1 ? ? A U 7 A G 24 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 A A 19 N7 ? ? A G 8 A A 23 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog10 hydrog ? ? A G 4 N3 ? ? ? 1_555 A A 19 N6 ? ? A G 8 A A 23 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog11 hydrog ? ? A A 5 N6 ? ? ? 1_555 A C 18 N3 ? ? A A 9 A C 22 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog12 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 10 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 10 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 10 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 16 N3 ? ? A G 11 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 11 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 11 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 8 N3 ? ? ? 1_555 A G 15 N1 ? ? A C 12 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 8 N4 ? ? ? 1_555 A G 15 O6 ? ? A C 12 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 O2 ? ? ? 1_555 A G 15 N2 ? ? A C 12 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 14 N1 ? ? A C 13 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 14 O6 ? ? A C 13 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 14 N2 ? ? A C 13 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 10 N2 ? ? ? 1_555 A A 13 N7 ? ? A G 14 A A 17 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog25 hydrog ? ? A G 10 N3 ? ? ? 1_555 A A 13 N6 ? ? A G 14 A A 17 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1TJZ _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 1TJZ _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 5 5 G G A . n A 1 2 G 2 6 6 G G A . n A 1 3 U 3 7 7 U U A . n A 1 4 G 4 8 8 G G A . n A 1 5 A 5 9 9 A A A . n A 1 6 C 6 10 10 C C A . n A 1 7 G 7 11 11 G G A . n A 1 8 C 8 12 12 C C A . n A 1 9 C 9 13 13 C C A . n A 1 10 G 10 14 14 G G A . n A 1 11 U 11 15 15 U U A . n A 1 12 A 12 16 16 A A A . n A 1 13 A 13 17 17 A A A . n A 1 14 G 14 18 18 G G A . n A 1 15 G 15 19 19 G G A . n A 1 16 C 16 20 20 C C A . n A 1 17 G 17 21 21 G G A . n A 1 18 C 18 22 22 C C A . n A 1 19 A 19 23 23 A A A . n A 1 20 G 20 24 24 G G A . n A 1 21 C 21 25 25 C C A . n A 1 22 C 22 26 26 C C A . n # _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 # _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 2004-09-28 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-02 # _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' 'Data collection' 4 4 'Structure model' 'Database references' 5 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_nmr_software 3 4 'Structure model' pdbx_struct_assembly 4 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' 3 4 'Structure model' '_pdbx_nmr_software.name' # 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 "O2'" A A 16 ? ? OP2 A A 17 ? ? 1.77 2 2 H61 A A 9 ? ? O2 A C 22 ? ? 1.59 3 2 "O2'" A A 16 ? ? OP2 A A 17 ? ? 1.78 4 3 "O2'" A A 16 ? ? OP2 A A 17 ? ? 1.78 5 4 "H1'" A A 16 ? ? OP2 A A 17 ? ? 1.58 6 4 N2 A G 14 ? ? OP2 A A 17 ? ? 2.19 7 5 "H1'" A A 16 ? ? OP2 A A 17 ? ? 1.57 8 5 N2 A G 14 ? ? OP2 A A 17 ? ? 2.19 9 6 N2 A G 14 ? ? OP2 A A 17 ? ? 2.19 10 7 "H1'" A A 16 ? ? OP2 A A 17 ? ? 1.59 11 7 N2 A G 14 ? ? OP2 A A 17 ? ? 2.19 12 8 "H1'" A A 16 ? ? OP2 A A 17 ? ? 1.60 13 8 N2 A G 14 ? ? OP2 A A 17 ? ? 2.19 14 9 "O2'" A A 16 ? ? OP2 A A 17 ? ? 1.58 15 9 N2 A G 14 ? ? OP2 A A 17 ? ? 2.17 16 10 "H1'" A A 16 ? ? OP2 A A 17 ? ? 1.59 17 10 N2 A G 14 ? ? OP2 A A 17 ? ? 2.18 18 11 "H1'" A A 16 ? ? OP2 A A 17 ? ? 1.60 19 11 N2 A G 14 ? ? OP2 A A 17 ? ? 2.19 20 12 "O2'" A A 16 ? ? OP2 A A 17 ? ? 1.78 21 13 N2 A G 14 ? ? OP2 A A 17 ? ? 2.19 22 14 "O2'" A A 16 ? ? OP2 A A 17 ? ? 1.79 23 15 "O2'" A A 16 ? ? OP2 A A 17 ? ? 1.76 24 16 "O2'" A A 16 ? ? OP2 A A 17 ? ? 1.75 25 16 N2 A G 14 ? ? OP2 A A 17 ? ? 2.19 26 17 "O2'" A A 16 ? ? OP2 A A 17 ? ? 1.77 27 18 "O2'" A A 16 ? ? OP2 A A 17 ? ? 1.62 28 19 H61 A A 9 ? ? O2 A C 22 ? ? 1.59 29 19 "O2'" A A 16 ? ? OP2 A A 17 ? ? 1.68 30 20 "H1'" A A 16 ? ? OP2 A A 17 ? ? 1.60 31 20 N2 A G 14 ? ? OP2 A A 17 ? ? 2.18 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1TJZ 'double helix' 1TJZ 'a-form double helix' 1TJZ tetraloop 1TJZ 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 22 1_555 0.443 -0.052 0.004 -0.192 0.047 -1.214 1 A_G5:C26_A A 5 ? A 26 ? 19 1 1 A G 2 1_555 A C 21 1_555 0.422 -0.049 0.006 0.079 -0.105 -1.292 2 A_G6:C25_A A 6 ? A 25 ? 19 1 1 A U 3 1_555 A G 20 1_555 2.567 -0.411 0.001 -0.098 -0.035 1.057 3 A_U7:G24_A A 7 ? A 24 ? 28 ? 1 A G 4 1_555 A A 19 1_555 6.668 -3.608 -0.009 -0.022 0.038 -1.622 4 A_G8:A23_A A 8 ? A 23 ? 11 9 1 A A 5 1_555 A C 18 1_555 -1.389 -0.565 0.012 0.554 -0.015 -0.977 5 A_A9:C22_A A 9 ? A 22 ? ? 1 1 A C 6 1_555 A G 17 1_555 0.130 -0.057 0.004 0.254 0.085 -1.629 6 A_C10:G21_A A 10 ? A 21 ? 19 1 1 A G 7 1_555 A C 16 1_555 -0.286 -0.254 0.446 -1.355 -20.022 -4.825 7 A_G11:C20_A A 11 ? A 20 ? 19 1 1 A C 8 1_555 A G 15 1_555 -0.459 -0.055 0.041 -0.219 -1.120 -1.655 8 A_C12:G19_A A 12 ? A 19 ? 19 1 1 A C 9 1_555 A G 14 1_555 0.617 -0.198 -0.008 0.203 -0.173 -1.522 9 A_C13:G18_A A 13 ? A 18 ? 19 1 1 A G 10 1_555 A A 13 1_555 6.218 -5.440 -0.500 16.924 -5.228 -15.644 10 A_G14:A17_A A 14 ? A 17 ? 11 10 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 22 1_555 A G 2 1_555 A C 21 1_555 -0.747 -1.355 3.631 -1.435 36.100 15.855 -5.768 0.961 0.280 67.025 2.665 39.347 1 AA_G5G6:C25C26_AA A 5 ? A 26 ? A 6 ? A 25 ? 1 A G 2 1_555 A C 21 1_555 A U 3 1_555 A G 20 1_555 0.144 -1.088 3.614 3.452 16.200 47.516 -2.520 0.094 3.113 19.428 -4.140 50.162 2 AA_G6U7:G24C25_AA A 6 ? A 25 ? A 7 ? A 24 ? 1 A U 3 1_555 A G 20 1_555 A G 4 1_555 A A 19 1_555 0.385 -0.850 3.995 7.118 -1.542 57.460 -0.777 0.070 4.032 -1.597 -7.372 57.881 3 AA_U7G8:A23G24_AA A 7 ? A 24 ? A 8 ? A 23 ? 1 A G 4 1_555 A A 19 1_555 A A 5 1_555 A C 18 1_555 -0.385 -2.162 3.479 7.980 2.369 -2.371 6.668 23.237 1.900 -21.096 71.064 -8.655 4 AA_G8A9:C22A23_AA A 8 ? A 23 ? A 9 ? A 22 ? 1 A A 5 1_555 A C 18 1_555 A C 6 1_555 A G 17 1_555 0.184 -0.880 4.093 1.168 4.962 41.621 -1.869 -0.107 3.970 6.951 -1.636 41.918 5 AA_A9C10:G21C22_AA A 9 ? A 22 ? A 10 ? A 21 ? 1 A C 6 1_555 A G 17 1_555 A G 7 1_555 A C 16 1_555 0.724 -1.153 2.787 3.189 28.160 41.047 -2.979 -0.683 1.750 35.533 -4.023 49.530 6 AA_C10G11:C20G21_AA A 10 ? A 21 ? A 11 ? A 20 ? 1 A G 7 1_555 A C 16 1_555 A C 8 1_555 A G 15 1_555 -0.530 -1.664 3.145 2.523 14.638 20.486 -7.201 1.798 1.552 35.717 -6.157 25.258 7 AA_G11C12:G19C20_AA A 11 ? A 20 ? A 12 ? A 19 ? 1 A C 8 1_555 A G 15 1_555 A C 9 1_555 A G 14 1_555 0.678 -1.783 3.332 -0.851 13.167 39.625 -3.805 -1.037 2.621 18.801 1.216 41.680 8 AA_C12C13:G18G19_AA A 12 ? A 19 ? A 13 ? A 18 ? 1 A C 9 1_555 A G 14 1_555 A G 10 1_555 A A 13 1_555 -1.689 -1.647 3.092 2.644 -1.199 48.351 -1.921 2.251 3.039 -1.463 -3.224 48.433 9 AA_C13G14:A17G18_AA A 13 ? A 18 ? A 14 ? A 17 ? #