data_7KUC # _entry.id 7KUC # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 7KUC pdb_00007kuc 10.2210/pdb7kuc/pdb WWPDB D_1000252738 ? ? BMRB 30817 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB 'Other VEGF Readthrough Domain' 7KUB unspecified BMRB 'Ax1 Domain of VEGF Readthrough Element' 30817 unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 7KUC _pdbx_database_status.recvd_initial_deposition_date 2020-11-24 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs REL _pdbx_database_status.status_code_nmr_data REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID ;D'Souza, V.M. ; 1 0000-0002-5397-9481 'Wagner, N.O.' 2 0000-0001-8200-3878 'Edwards, J.M.' 3 0000-0001-7123-2472 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Stop codon readthrough in VEGF-A is regulated by complex signals' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wagner, N.O.' 1 ? primary 'Edwards, J.E.' 2 ? primary 'Abramovich, J.' 3 ? primary 'Gupta, P.' 4 ? primary 'Swaminathan, H.' 5 ? primary 'Rouskin, S.' 6 ? primary ;D'Souza, V.M. ; 7 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'VEGF Ax1' _entity.formula_weight 5215.198 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _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 GGAGGAAGGAGCCUCC _entity_poly.pdbx_seq_one_letter_code_can GGAGGAAGGAGCCUCC _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 A n 1 4 G n 1 5 G n 1 6 A n 1 7 A n 1 8 G n 1 9 G n 1 10 A n 1 11 G n 1 12 C n 1 13 C n 1 14 U n 1 15 C n 1 16 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 16 _pdbx_entity_src_syn.organism_scientific 'Bos taurus' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9913 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7KUC _struct_ref.pdbx_db_accession 7KUC _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 7KUC _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 16 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7KUC _struct_ref_seq.db_align_beg 582 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 597 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 582 _struct_ref_seq.pdbx_auth_seq_align_end 597 # 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.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 2D_NOESY 1 anisotropic 2 2 2 1H-13C_HMQC 2 anisotropic 3 3 3 2D_NOESY 1 anisotropic # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.details _pdbx_nmr_exptl_sample_conditions.ionic_strength_err _pdbx_nmr_exptl_sample_conditions.ionic_strength_units _pdbx_nmr_exptl_sample_conditions.label _pdbx_nmr_exptl_sample_conditions.pH_err _pdbx_nmr_exptl_sample_conditions.pH_units _pdbx_nmr_exptl_sample_conditions.pressure_err _pdbx_nmr_exptl_sample_conditions.temperature_err _pdbx_nmr_exptl_sample_conditions.temperature_units 1 311 ? ambient 5.6 '50MM KCL' ? ? mM Condition_1 ? pH ? ? K 2 311 ? ambient 5.6 '50MM KCL' ? ? mM Condition_2 ? pH ? ? K 3 278 ? ambient 5.6 '50MM KCL' ? ? mM Condition_3 ? pH ? ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 '1 mM RNA, 100% D2O' '100% D2O' D2O_NOESY_sample solution ? 2 '1 mM [U-13C] RNA, 100% D2O' '100% D2O' HMQC_sample solution ? 3 '1 mM RNA, 10%D2O 90%H2O' '10%D2O 90%H2O' H2O_NOESY_sample solution ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.details 1 Ascend800 ? Bruker 800 ? 2 UltraShield700Plus ? Bruker 700 ? # _pdbx_nmr_refine.entry_id 7KUC _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ;First round of structure calculation was conducted with distance and dihedral angle restraints only. Second round was performed with electrostatics using both high temperature annealing and low temperature annealing. ; _pdbx_nmr_refine.software_ordinal 3 # _pdbx_nmr_ensemble.entry_id 7KUC _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria '10 structures for lowest energy' _pdbx_nmr_ensemble.representative_conformer ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 7KUC _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 4 processing NMRDraw ? 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 1 'chemical shift assignment' NMRViewJ ? 'Bruce A. Johnson' 2 'structure calculation' CYANA ? 'Guntert, Mumenthaler and Wuthrich' 3 refinement 'X-PLOR NIH' 3.1 'Schwieters, Kuszewski, Tjandra and Clore' # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 7KUC _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 7KUC _struct.title 'Ax1 Domain of VEGF Readthrough Element' _struct.pdbx_model_details 'NMR Structure' _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7KUC _struct_keywords.text 'Stop codon readthrough, VEGF mRNA, stem-loop, RNA' _struct_keywords.pdbx_keywords 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 ? # 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 16 N3 ? ? A G 582 A C 597 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 582 A C 597 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 582 A C 597 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 583 A C 596 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 583 A C 596 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 583 A C 596 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 14 N3 ? ? A A 584 A U 595 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 14 O4 ? ? A A 584 A U 595 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 585 A C 594 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 585 A C 594 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 585 A C 594 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 12 N3 ? ? A G 586 A C 593 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 12 O2 ? ? A G 586 A C 593 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 12 N4 ? ? A G 586 A C 593 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 6 N1 ? ? ? 1_555 A G 11 N1 ? ? A A 587 A G 592 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog16 hydrog ? ? A A 6 N6 ? ? ? 1_555 A G 11 O6 ? ? A A 587 A G 592 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog17 hydrog ? ? A A 7 N3 ? ? ? 1_555 A A 10 N6 ? ? A A 588 A A 591 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 7KUC _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _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 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # 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 1 582 582 G GUA A . n A 1 2 G 2 583 583 G GUA A . n A 1 3 A 3 584 584 A ADE A . n A 1 4 G 4 585 585 G GUA A . n A 1 5 G 5 586 586 G GUA A . n A 1 6 A 6 587 587 A ADE A . n A 1 7 A 7 588 588 A ADE A . n A 1 8 G 8 589 589 G GUA A . n A 1 9 G 9 590 590 G GUA A . n A 1 10 A 10 591 591 A ADE A . n A 1 11 G 11 592 592 G GUA A . n A 1 12 C 12 593 593 C CYT A . n A 1 13 C 13 594 594 C CYT A . n A 1 14 U 14 595 595 U URI A . n A 1 15 C 15 596 596 C CYT A . n A 1 16 C 16 597 597 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 ? _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 2022-06-01 2 'Structure model' 1 1 2023-06-14 # _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 ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group Other # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category pdbx_database_status # _pdbx_audit_revision_item.ordinal 1 _pdbx_audit_revision_item.revision_ordinal 2 _pdbx_audit_revision_item.data_content_type 'Structure model' _pdbx_audit_revision_item.item '_pdbx_database_status.status_code_nmr_data' # loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 RNA 1 ? mM 'natural abundance' 2 RNA 1 ? mM '[U-13C]' 3 RNA 1 ? mM 'natural abundance' # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C1'" A G 590 ? ? "O4'" A G 590 ? ? "C4'" A G 590 ? ? 105.31 109.70 -4.39 0.70 N 2 2 "C1'" A G 590 ? ? "O4'" A G 590 ? ? "C4'" A G 590 ? ? 104.95 109.70 -4.75 0.70 N 3 3 "C1'" A G 590 ? ? "O4'" A G 590 ? ? "C4'" A G 590 ? ? 104.83 109.70 -4.87 0.70 N 4 4 "C1'" A G 590 ? ? "O4'" A G 590 ? ? "C4'" A G 590 ? ? 105.03 109.70 -4.67 0.70 N 5 5 "C1'" A G 590 ? ? "O4'" A G 590 ? ? "C4'" A G 590 ? ? 105.21 109.70 -4.49 0.70 N 6 6 "C1'" A G 590 ? ? "O4'" A G 590 ? ? "C4'" A G 590 ? ? 105.17 109.70 -4.53 0.70 N 7 7 "C1'" A G 590 ? ? "O4'" A G 590 ? ? "C4'" A G 590 ? ? 104.74 109.70 -4.96 0.70 N 8 8 "C1'" A G 590 ? ? "O4'" A G 590 ? ? "C4'" A G 590 ? ? 105.49 109.70 -4.21 0.70 N 9 9 "C1'" A G 590 ? ? "O4'" A G 590 ? ? "C4'" A G 590 ? ? 105.12 109.70 -4.58 0.70 N 10 10 "C1'" A G 590 ? ? "O4'" A G 590 ? ? "C4'" A G 590 ? ? 105.14 109.70 -4.56 0.70 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7KUC 'double helix' 7KUC 'a-form double helix' 7KUC 'hairpin loop' 7KUC '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 16 1_555 -0.220 0.026 -0.073 -0.074 -6.183 1.055 1 A_G582:C597_A A 582 ? A 597 ? 19 1 1 A G 2 1_555 A C 15 1_555 -0.159 -0.011 -0.133 -0.258 -9.713 2.918 2 A_G583:C596_A A 583 ? A 596 ? 19 1 1 A A 3 1_555 A U 14 1_555 0.108 -0.114 0.010 -3.476 -12.302 0.697 3 A_A584:U595_A A 584 ? A 595 ? 20 1 1 A G 4 1_555 A C 13 1_555 0.023 0.018 -0.030 -6.150 -7.415 1.871 4 A_G585:C594_A A 585 ? A 594 ? 19 1 1 A G 5 1_555 A C 12 1_555 0.088 0.070 -0.160 -3.783 3.304 -2.687 5 A_G586:C593_A A 586 ? A 593 ? 19 1 1 A A 6 1_555 A G 11 1_555 1.215 1.130 0.327 20.520 23.972 -14.871 6 A_A587:G592_A A 587 ? A 592 ? 8 1 1 A A 7 1_555 A A 10 1_555 6.975 -4.605 -0.733 25.701 12.010 -16.931 7 A_A588:A591_A A 588 ? A 591 ? ? 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 1 1_555 A C 16 1_555 A G 2 1_555 A C 15 1_555 0.207 -1.668 3.183 0.181 9.364 30.677 -4.541 -0.346 2.576 17.203 -0.332 32.042 1 AA_G582G583:C596C597_AA A 582 ? A 597 ? A 583 ? A 596 ? 1 A G 2 1_555 A C 15 1_555 A A 3 1_555 A U 14 1_555 -0.015 -1.569 3.274 -0.669 8.101 33.475 -3.847 -0.073 2.828 13.812 1.141 34.420 2 AA_G583A584:U595C596_AA A 583 ? A 596 ? A 584 ? A 595 ? 1 A A 3 1_555 A U 14 1_555 A G 4 1_555 A C 13 1_555 0.025 -1.613 3.232 0.068 8.929 32.415 -4.142 -0.033 2.705 15.628 -0.119 33.590 3 AA_A584G585:C594U595_AA A 584 ? A 595 ? A 585 ? A 594 ? 1 A G 4 1_555 A C 13 1_555 A G 5 1_555 A C 12 1_555 -0.145 -1.733 3.225 1.101 11.940 30.638 -4.887 0.425 2.394 21.587 -1.991 32.849 4 AA_G585G586:C593C594_AA A 585 ? A 594 ? A 586 ? A 593 ? 1 A G 5 1_555 A C 12 1_555 A A 6 1_555 A G 11 1_555 -0.720 -1.505 2.918 0.293 8.284 28.776 -4.336 1.444 2.393 16.248 -0.574 29.922 5 AA_G586A587:G592C593_AA A 586 ? A 593 ? A 587 ? A 592 ? 1 A A 6 1_555 A G 11 1_555 A A 7 1_555 A A 10 1_555 -0.331 -1.178 3.587 6.248 6.604 50.830 -1.834 0.834 3.360 7.623 -7.213 51.583 6 AA_A587A588:A591G592_AA A 587 ? A 592 ? A 588 ? A 591 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Howard Hughes Medical Institute (HHMI)' 'United States' 55108516 1 'National Science Foundation (NSF, United States)' 'United States' 1144152 2 # loop_ _pdbx_struct_assembly_auth_evidence.id _pdbx_struct_assembly_auth_evidence.assembly_id _pdbx_struct_assembly_auth_evidence.experimental_support _pdbx_struct_assembly_auth_evidence.details 1 1 'native gel electrophoresis' ? 2 1 'isothermal titration calorimetry' ? #