data_1T28 # _entry.id 1T28 # _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 1T28 pdb_00001t28 10.2210/pdb1t28/pdb RCSB RCSB022219 ? ? WWPDB D_1000022219 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.db_id 6115 _pdbx_database_related.details 'chemical shifts' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1T28 _pdbx_database_status.recvd_initial_deposition_date 2004-04-20 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _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 'Thiviyanathan, V.' 1 'Yang, Y.' 2 'Kaluarachchi, K.' 3 'Reynbrand, R.' 4 'Gorenstein, D.G.' 5 'Lemon, S.M.' 6 # _citation.id primary _citation.title 'High resolution structure of a picornaviral internal cis-acting replication element(cre).' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 101 _citation.page_first 12688 _citation.page_last 12693 _citation.year 2004 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15314212 _citation.pdbx_database_id_DOI 10.1073/pnas.0403079101 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Thiviyanathan, V.' 1 ? primary 'Yang, Y.' 2 ? primary 'Kaluarachchi, K.' 3 ? primary 'Reynbrand, R.' 4 ? primary 'Gorenstein, D.G.' 5 ? primary 'Lemon, S.M.' 6 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 34-MER _entity.formula_weight 11040.671 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'CRE of the Human Rhinovirus type 14' _entity.details 'Minimal functional sequence of HRV-14 CRE' # _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 GGUCAUCGUUGAGAAAACGAAACAGACGGUGGCC _entity_poly.pdbx_seq_one_letter_code_can GGUCAUCGUUGAGAAAACGAAACAGACGGUGGCC _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 C n 1 5 A n 1 6 U n 1 7 C n 1 8 G n 1 9 U n 1 10 U n 1 11 G n 1 12 A n 1 13 G n 1 14 A n 1 15 A n 1 16 A n 1 17 A n 1 18 C n 1 19 G n 1 20 A n 1 21 A n 1 22 A n 1 23 C n 1 24 A n 1 25 G n 1 26 A n 1 27 C n 1 28 G n 1 29 G n 1 30 U n 1 31 G n 1 32 G n 1 33 C n 1 34 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 'The RNA sequence was synthesized using T7 system. The sequence occurs in Human Rhinovirus type 14.' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1T28 _struct_ref.pdbx_db_accession 1T28 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1T28 _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 34 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1T28 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 34 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 34 # 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 1 1 3D_13C-separated_NOESY 3 1 1 '15N, and 13C HSQC' # 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 1 298 ambient 6.8 ? ? K 2 298 ambient 6.8 ? ? K 3 298 ambient 6.8 ? ? K 4 298 ambient 6.8 ? ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1.4 mM RNA U-15N,13C, 10 mM phosphate buffer (pH 6.8), 10 mM KCl, 0.02 mM EDTA, 90% H2O, 10% D2O' '90% H2O/10% D2O' 2 '1.8 mM RNA, 8-10 mM phosphate buffer (pH 6.8), 10 mM KCl, 0.02 mM EDTA, 90% H2O, 10% D2O' '90% H2O/10% D2O' 3 '1.8 mM RNA, 8-10 mM phosphate buffer (pH 6.8), 10 mM KCl, 0.4-4 mM Mg2+, 90% H2O, 10% D2O' '90% H2O/10% D2O' 4 '0.8 mM RNA, 15N,13C (only the A residues), 10 mM phosphate buffer (pH 6.8), 10 mM KCl, 0.02 mM EDTA, 100% D2O' '100% D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.field_strength 1 ? Varian UNITYPLUS 600 2 ? Varian UNITYPLUS 750 # _pdbx_nmr_refine.entry_id 1T28 _pdbx_nmr_refine.method 'distance geometry, molecular dynamics, simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1T28 _pdbx_nmr_ensemble.conformers_calculated_total_number 18 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'averaged structure' _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 1T28 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal Felix 2000 processing MSI 1 X-PLOR 3.1 refinement 'Brunger, A.T., et al.,' 2 # _exptl.entry_id 1T28 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _exptl_crystal.density_Matthews ? # _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 1T28 _struct.title 'High resolution structure of a picornaviral internal cis-acting replication element' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 1T28 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'CRE, picornavirus, rhino virus, stem loop, 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 # 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 34 N3 ? ? A G 1 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 34 O2 ? ? A G 1 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 34 N4 ? ? A G 1 A C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 33 N3 ? ? A G 2 A C 33 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog5 hydrog ? ? A U 3 N3 ? ? ? 1_555 A G 32 O6 ? ? A U 3 A G 32 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog6 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 31 N1 ? ? A C 4 A G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 31 O6 ? ? A C 4 A G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 31 N2 ? ? A C 4 A G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 30 N3 ? ? A A 5 A U 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 30 O4 ? ? A A 5 A U 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U 6 N3 ? ? ? 1_555 A G 29 O6 ? ? A U 6 A G 29 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog12 hydrog ? ? A U 6 O2 ? ? ? 1_555 A G 29 N1 ? ? A U 6 A G 29 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog13 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 28 N1 ? ? A C 7 A G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 28 O6 ? ? A C 7 A G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 28 N2 ? ? A C 7 A G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 27 N3 ? ? A G 8 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 27 O2 ? ? A G 8 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 27 N4 ? ? A G 8 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 9 N3 ? ? ? 1_555 A A 26 N1 ? ? A U 9 A A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 9 O4 ? ? ? 1_555 A A 26 N6 ? ? A U 9 A A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1T28 _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 1T28 _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 GUA A . n A 1 2 G 2 2 2 G GUA A . n A 1 3 U 3 3 3 U URI A . n A 1 4 C 4 4 4 C CYT A . n A 1 5 A 5 5 5 A ADE A . n A 1 6 U 6 6 6 U URI A . n A 1 7 C 7 7 7 C CYT A . n A 1 8 G 8 8 8 G GUA A . n A 1 9 U 9 9 9 U URI A . n A 1 10 U 10 10 10 U URI A . n A 1 11 G 11 11 11 G GUA A . n A 1 12 A 12 12 12 A ADE A . n A 1 13 G 13 13 13 G GUA A . n A 1 14 A 14 14 14 A ADE A . n A 1 15 A 15 15 15 A ADE A . n A 1 16 A 16 16 16 A ADE A . n A 1 17 A 17 17 17 A ADE A . n A 1 18 C 18 18 18 C CYT A . n A 1 19 G 19 19 19 G GUA A . n A 1 20 A 20 20 20 A ADE A . n A 1 21 A 21 21 21 A ADE A . n A 1 22 A 22 22 22 A ADE A . n A 1 23 C 23 23 23 C CYT A . n A 1 24 A 24 24 24 A ADE A . n A 1 25 G 25 25 25 G GUA A . n A 1 26 A 26 26 26 A ADE A . n A 1 27 C 27 27 27 C CYT A . n A 1 28 G 28 28 28 G GUA A . n A 1 29 G 29 29 29 G GUA A . n A 1 30 U 30 30 30 U URI A . n A 1 31 G 31 31 31 G GUA A . n A 1 32 G 32 32 32 G GUA A . n A 1 33 C 33 33 33 C CYT A . n A 1 34 C 34 34 34 C CYT 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 2004-08-10 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 "HO2'" A G 8 ? ? "HO2'" A U 9 ? ? 0.64 2 1 "HO2'" A G 1 ? ? "H5'" A G 2 ? ? 0.78 3 1 "HO2'" A G 8 ? ? "O2'" A U 9 ? ? 1.08 4 1 "HO2'" A C 7 ? ? "H5'" A G 8 ? ? 1.14 5 1 "HO2'" A A 26 ? ? "H5'" A C 27 ? ? 1.16 6 1 "HO2'" A G 29 ? ? "O5'" A U 30 ? ? 1.30 7 1 "O2'" A A 26 ? ? "H5'" A C 27 ? ? 1.30 8 1 "HO2'" A U 30 ? ? "H5'" A G 31 ? ? 1.32 9 1 "HO2'" A C 4 ? ? "O5'" A A 5 ? ? 1.33 10 1 "HO2'" A G 25 ? ? "H5'" A A 26 ? ? 1.33 11 1 "HO2'" A G 32 ? ? "O2'" A C 33 ? ? 1.34 12 1 "HO2'" A U 30 ? ? "O5'" A G 31 ? ? 1.34 13 1 "HO2'" A A 26 ? ? "C5'" A C 27 ? ? 1.41 14 1 "HO2'" A A 5 ? ? "O5'" A U 6 ? ? 1.41 15 1 "HO2'" A A 26 ? ? "O5'" A C 27 ? ? 1.42 16 1 "HO2'" A G 32 ? ? "O4'" A C 33 ? ? 1.47 17 1 "HO2'" A G 8 ? ? "O4'" A U 9 ? ? 1.49 18 1 "O2'" A G 8 ? ? "HO2'" A U 9 ? ? 1.50 19 1 "O2'" A G 1 ? ? "H5'" A G 2 ? ? 1.52 20 1 "HO2'" A U 30 ? ? "C5'" A G 31 ? ? 1.56 21 1 "O2'" A G 1 ? ? "O4'" A G 2 ? ? 1.58 22 1 "HO2'" A C 4 ? ? "C5'" A A 5 ? ? 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 ? ? 118.19 113.10 5.09 0.50 N 2 1 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.98 106.40 -2.42 0.40 N 3 1 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.65 113.10 4.55 0.50 N 4 1 N7 A A 5 ? ? C8 A A 5 ? ? N9 A A 5 ? ? 117.73 113.80 3.93 0.50 N 5 1 N7 A G 8 ? ? C8 A G 8 ? ? N9 A G 8 ? ? 118.00 113.10 4.90 0.50 N 6 1 "C4'" A U 9 ? ? "C3'" A U 9 ? ? "O3'" A U 9 ? ? 91.13 109.40 -18.27 2.10 N 7 1 "C4'" A U 9 ? ? "C3'" A U 9 ? ? "C2'" A U 9 ? ? 34.07 102.60 -68.53 1.00 N 8 1 "C3'" A U 9 ? ? "C2'" A U 9 ? ? "C1'" A U 9 ? ? 110.48 101.50 8.98 0.80 N 9 1 "O4'" A U 9 ? ? "C1'" A U 9 ? ? "C2'" A U 9 ? ? 38.94 105.80 -66.86 1.00 N 10 1 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 118.04 113.10 4.94 0.50 N 11 1 N7 A A 12 ? ? C8 A A 12 ? ? N9 A A 12 ? ? 117.97 113.80 4.17 0.50 N 12 1 N7 A G 13 ? ? C8 A G 13 ? ? N9 A G 13 ? ? 118.04 113.10 4.94 0.50 N 13 1 N7 A A 14 ? ? C8 A A 14 ? ? N9 A A 14 ? ? 117.89 113.80 4.09 0.50 N 14 1 N7 A A 15 ? ? C8 A A 15 ? ? N9 A A 15 ? ? 117.90 113.80 4.10 0.50 N 15 1 N7 A A 16 ? ? C8 A A 16 ? ? N9 A A 16 ? ? 117.95 113.80 4.15 0.50 N 16 1 N7 A A 17 ? ? C8 A A 17 ? ? N9 A A 17 ? ? 117.92 113.80 4.12 0.50 N 17 1 N7 A G 19 ? ? C8 A G 19 ? ? N9 A G 19 ? ? 118.03 113.10 4.93 0.50 N 18 1 N7 A A 20 ? ? C8 A A 20 ? ? N9 A A 20 ? ? 117.98 113.80 4.18 0.50 N 19 1 N7 A A 21 ? ? C8 A A 21 ? ? N9 A A 21 ? ? 118.08 113.80 4.28 0.50 N 20 1 N7 A A 22 ? ? C8 A A 22 ? ? N9 A A 22 ? ? 117.87 113.80 4.07 0.50 N 21 1 "C2'" A C 23 ? ? "C3'" A C 23 ? ? "O3'" A C 23 ? ? 92.24 109.50 -17.26 2.20 N 22 1 N7 A A 24 ? ? C8 A A 24 ? ? N9 A A 24 ? ? 118.06 113.80 4.26 0.50 N 23 1 "O4'" A G 25 ? ? "C1'" A G 25 ? ? N9 A G 25 ? ? 113.28 108.50 4.78 0.70 N 24 1 N7 A G 25 ? ? C8 A G 25 ? ? N9 A G 25 ? ? 118.03 113.10 4.93 0.50 N 25 1 C8 A G 25 ? ? N9 A G 25 ? ? C4 A G 25 ? ? 103.76 106.40 -2.64 0.40 N 26 1 N7 A A 26 ? ? C8 A A 26 ? ? N9 A A 26 ? ? 117.79 113.80 3.99 0.50 N 27 1 "C4'" A G 28 ? ? "C3'" A G 28 ? ? "C2'" A G 28 ? ? 89.25 102.60 -13.35 1.00 N 28 1 "C3'" A G 28 ? ? "C2'" A G 28 ? ? "C1'" A G 28 ? ? 109.01 101.50 7.51 0.80 N 29 1 "O4'" A G 28 ? ? "C1'" A G 28 ? ? "C2'" A G 28 ? ? 93.32 105.80 -12.48 1.00 N 30 1 "O4'" A G 28 ? ? "C1'" A G 28 ? ? N9 A G 28 ? ? 113.66 108.50 5.16 0.70 N 31 1 N7 A G 28 ? ? C8 A G 28 ? ? N9 A G 28 ? ? 118.06 113.10 4.96 0.50 N 32 1 C8 A G 28 ? ? N9 A G 28 ? ? C4 A G 28 ? ? 103.84 106.40 -2.56 0.40 N 33 1 N7 A G 29 ? ? C8 A G 29 ? ? N9 A G 29 ? ? 117.77 113.10 4.67 0.50 N 34 1 C8 A G 29 ? ? N9 A G 29 ? ? C4 A G 29 ? ? 103.88 106.40 -2.52 0.40 N 35 1 N7 A G 31 ? ? C8 A G 31 ? ? N9 A G 31 ? ? 117.85 113.10 4.75 0.50 N 36 1 N7 A G 32 ? ? C8 A G 32 ? ? N9 A G 32 ? ? 117.87 113.10 4.77 0.50 N 37 1 "C4'" A C 33 ? ? "C3'" A C 33 ? ? "O3'" A C 33 ? ? 90.15 109.40 -19.25 2.10 N 38 1 "C4'" A C 33 ? ? "C3'" A C 33 ? ? "C2'" A C 33 ? ? 31.08 102.60 -71.52 1.00 N 39 1 "C3'" A C 33 ? ? "C2'" A C 33 ? ? "C1'" A C 33 ? ? 112.38 101.50 10.88 0.80 N 40 1 "O4'" A C 33 ? ? "C1'" A C 33 ? ? "C2'" A C 33 ? ? 41.33 105.80 -64.47 1.00 N 41 1 N1 A C 33 ? ? "C1'" A C 33 ? ? "C2'" A C 33 ? ? 123.03 114.00 9.03 1.30 N 42 1 "O4'" A C 33 ? ? "C1'" A C 33 ? ? N1 A C 33 ? ? 100.09 108.20 -8.11 0.80 N 43 1 "C3'" A C 34 ? ? "C2'" A C 34 ? ? "C1'" A C 34 ? ? 107.79 101.50 6.29 0.80 N # 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 G A 25 ? ? 0.049 'SIDE CHAIN' 2 1 G A 29 ? ? 0.048 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1T28 'double helix' 1T28 'b-form double helix' 1T28 'hairpin loop' 1T28 '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 34 1_555 -1.566 -0.695 0.647 -3.303 35.248 12.735 1 A_G1:C34_A A 1 ? A 34 ? 19 1 1 A G 2 1_555 A C 33 1_555 1.898 -0.525 1.303 9.826 -2.056 -18.625 2 A_G2:C33_A A 2 ? A 33 ? ? 1 1 A U 3 1_555 A G 32 1_555 1.557 -0.600 -1.576 -17.893 20.549 -21.781 3 A_U3:G32_A A 3 ? A 32 ? ? ? 1 A C 4 1_555 A G 31 1_555 -0.364 -0.603 -1.953 12.089 -6.076 9.181 4 A_C4:G31_A A 4 ? A 31 ? 19 1 1 A A 5 1_555 A U 30 1_555 -0.700 -0.317 -1.444 -5.879 -8.158 12.815 5 A_A5:U30_A A 5 ? A 30 ? 20 1 1 A U 6 1_555 A G 29 1_555 2.431 -0.385 -1.326 -3.271 -20.301 26.109 6 A_U6:G29_A A 6 ? A 29 ? 28 1 1 A C 7 1_555 A G 28 1_555 -0.376 -0.256 -0.713 -3.554 19.900 -10.138 7 A_C7:G28_A A 7 ? A 28 ? 19 1 1 A G 8 1_555 A C 27 1_555 0.059 -0.655 -1.770 -2.557 -5.485 -9.300 8 A_G8:C27_A A 8 ? A 27 ? 19 1 1 A U 9 1_555 A A 26 1_555 -1.155 0.251 -0.615 14.548 9.754 -11.710 9 A_U9:A26_A A 9 ? A 26 ? 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 G 1 1_555 A C 34 1_555 A G 2 1_555 A C 33 1_555 -1.626 -0.533 3.283 4.149 3.421 27.169 -1.907 4.360 2.919 7.193 -8.723 27.686 1 AA_G1G2:C33C34_AA A 1 ? A 34 ? A 2 ? A 33 ? 1 A G 2 1_555 A C 33 1_555 A U 3 1_555 A G 32 1_555 -1.194 -0.217 5.617 17.755 31.838 27.106 -5.002 4.188 2.818 47.654 -26.575 45.150 2 AA_G2U3:G32C33_AA A 2 ? A 33 ? A 3 ? A 32 ? 1 A U 3 1_555 A G 32 1_555 A C 4 1_555 A G 31 1_555 1.335 0.639 2.871 0.728 16.747 12.597 -5.292 -3.367 2.288 53.279 -2.316 20.941 3 AA_U3C4:G31G32_AA A 3 ? A 32 ? A 4 ? A 31 ? 1 A C 4 1_555 A G 31 1_555 A A 5 1_555 A U 30 1_555 0.104 -0.191 4.715 -2.888 15.666 26.871 -4.636 -0.982 3.975 30.540 5.631 31.163 4 AA_C4A5:U30G31_AA A 4 ? A 31 ? A 5 ? A 30 ? 1 A A 5 1_555 A U 30 1_555 A U 6 1_555 A G 29 1_555 0.839 0.709 3.173 3.503 26.291 40.593 -1.311 -0.738 3.125 33.894 -4.516 48.182 5 AA_A5U6:G29U30_AA A 5 ? A 30 ? A 6 ? A 29 ? 1 A U 6 1_555 A G 29 1_555 A C 7 1_555 A G 28 1_555 -1.116 0.288 3.295 -2.608 24.151 21.171 -4.152 1.512 2.492 49.231 5.317 32.117 6 AA_U6C7:G28G29_AA A 6 ? A 29 ? A 7 ? A 28 ? 1 A C 7 1_555 A G 28 1_555 A G 8 1_555 A C 27 1_555 0.355 0.579 4.210 7.584 28.985 20.737 -4.833 0.938 2.963 54.248 -14.194 36.302 7 AA_C7G8:C27G28_AA A 7 ? A 28 ? A 8 ? A 27 ? 1 A G 8 1_555 A C 27 1_555 A U 9 1_555 A A 26 1_555 0.394 -0.124 3.205 -5.590 8.633 17.618 -4.055 -3.512 2.616 25.552 16.546 20.380 8 AA_G8U9:A26C27_AA A 8 ? A 27 ? A 9 ? A 26 ? #