data_5UF3 # _entry.id 5UF3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.283 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5UF3 WWPDB D_1000223105 BMRB 30224 # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'Structure Effects of the Four-Adenine Loop of the Coliphage GA Replicase RNA Operator' _pdbx_database_related.db_id 30224 _pdbx_database_related.content_type 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 5UF3 _pdbx_database_status.recvd_initial_deposition_date 2017-01-03 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Chang, A.T.' 1 ? 'Tran, M.' 2 ? 'DeJong, E.' 3 ? 'Nikonowicz, E.P.' 4 ? # _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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Biochemistry _citation.journal_id_ASTM BICHAW _citation.journal_id_CSD 0033 _citation.journal_id_ISSN 1520-4995 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 56 _citation.language ? _citation.page_first 2690 _citation.page_last 2700 _citation.title 'Structure and Dynamics of the Tetra-A Loop and (A-A)-U Sequence Motif within the Coliphage GA Replicase RNA Operator.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.biochem.7b00123 _citation.pdbx_database_id_PubMed 28488852 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Chang, A.T.' 1 primary 'Tran, M.' 2 primary 'Nikonowicz, E.P.' 3 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'phage GA operator RNA hairpin' _entity.formula_weight 7394.496 _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 GGACAUAAGGAAAACCUAUGUCC _entity_poly.pdbx_seq_one_letter_code_can GGACAUAAGGAAAACCUAUGUCC _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 C n 1 5 A n 1 6 U n 1 7 A n 1 8 A n 1 9 G n 1 10 G n 1 11 A n 1 12 A n 1 13 A n 1 14 A n 1 15 C n 1 16 C n 1 17 U n 1 18 A n 1 19 U n 1 20 G n 1 21 U n 1 22 C n 1 23 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 23 _pdbx_entity_src_syn.organism_scientific 'Enterobacteria phage GA' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 12018 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5UF3 _struct_ref.pdbx_db_accession 5UF3 _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 5UF3 _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 23 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 5UF3 _struct_ref_seq.db_align_beg 1 _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 1 _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 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 2 '2D 1H-1H NOESY' 1 isotropic 2 1 1 '3D 1H-13C NOESY' 1 isotropic 3 1 1 '2D 1H-13C HSQC' 1 isotropic 4 1 1 '3D HCCH-TOCSY' 1 isotropic 5 2 3 '2D 1H-15N HSQC' 1 isotropic 6 1 5 '2D 1H-31P HetCor' 2 isotropic 7 1 1 '2D 1H-13C CTEP' 2 isotropic 8 1 6 '2D 1H-13C HSQC' 1 isotropic 9 1 4 '2D 1H-13C HSQC' 1 anisotropic 10 2 3 '3D 1H-15N NOESY' 1 isotropic 11 1 1 '2D 1H-13C H(N)CO' 1 isotropic 12 1 1 '2D 1H-15N HSQC' 1 isotropic 13 1 1 '2D 1H-13C H(CN)CO' 1 isotropic 14 1 1 '2D 1H-13C C(C)H-COSY' 1 isotropic # 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 1 298 atm 1 6.8 20 '100% D2O' ? mM condition_1 ? pH* ? ? K 2 285 atm 1 6.8 20 '90% H2O, 10% D2O' ? mM condition_2 ? 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 [U-13C; U-15N] phage GA operator RNA hairpin, 10 mM potassium phosphate, 10 mM potassium chloride, 0.02 mM EDTA, 100% D2O' '100% D2O' phageGA_15N13C_D2O solution ? 2 '1.5 mM phage GA operator RNA hairpin, 10 mM potassium phosphate, 10 mM potassium chloride, 0.02 mM EDTA, 100% D2O' '100% D2O' phageGA_nl_D2O solution ? 3 ;1 mM [U-13C; U-15N] phage GA operator RNA hairpin, 10 mM potassium chloride, 10 mM potassium phosphate, 0.02 mM EDTA, 90% H2O/10% D2O ; '90% H2O/10% D2O' phageGA_15N13C_H2O solution ? 4 ;0.3 mM [U-13C; U-15N] phage GA operator RNA hairpin, 10 mM potassium chloride, 10 mM potassium phosphate, 15 mg/mL Pf1 phage, 100% D2O ; '100% D2O' phageGA_Pf1 solution ? 5 '1.2 mM 2H, 40%-85% phage GA operator RNA hairpin, 10 mM potassium chloride, 10 mM potassium phosphate, 0.02 mM EDTA, 100% D2O' '100% D2O' phageGA_fract_D solution ;deuteration achieved by culturing cells in 90% D2O and sodium acetate. See Nikonowicz, EP. Methods Enzymol. 338:320-341 (2001). ; 6 '1.1 mM 13C, 4%-20% phage GA operator RNA hairpin, 10 mM potassium chloride, 10 mM potassium phosphate, 0.02 mM na EDTA, 100% D2O' '100% D2O' phageGA_fract_C solution ;Fractional 13-C enrichment achieved by culturing cells on 20% [13C-C2, 12C-C1], 80% [U-12C] sodium acetate. See Nikonowicz, EP. Methods Enzymol. 338:320-341 (2001). ; # 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 INOVA ? Varian 600 ? 2 INOVA ? Varian 500 ? # _pdbx_nmr_refine.details 'RNA ff1 force field' _pdbx_nmr_refine.entry_id 5UF3 _pdbx_nmr_refine.method ? _pdbx_nmr_refine.software_ordinal 5 # _pdbx_nmr_ensemble.entry_id 5UF3 _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 8 _pdbx_nmr_ensemble.conformer_selection_criteria ? # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 processing Felix ? 'Accelrys Software Inc.' 5 refinement 'X-PLOR NIH' 2.43 'Schwieters, Kuszewski, Tjandra and Clore' 6 'structure calculation' 'X-PLOR NIH' 2.43 '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 5UF3 _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 5UF3 _struct.title 'Structure Effects of the Four-Adenine Loop of the Coliphage GA Replicase RNA Operator' _struct.pdbx_descriptor 'phage GA operator RNA hairpin' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 5UF3 _struct_keywords.text 'phage, RNA hairpin, tetraloop, (A-A)-U motif, 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 hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 1 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 1 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 1 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 22 N3 ? ? A G 2 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 22 O2 ? ? A G 2 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 22 N4 ? ? A G 2 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 21 N3 ? ? A A 3 A U 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 21 O4 ? ? A A 3 A U 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 4 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 4 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 4 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 19 N3 ? ? A A 5 A U 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 19 O4 ? ? A A 5 A U 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 18 N1 ? ? A U 6 A A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 18 N6 ? ? A U 6 A A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A A 7 N1 ? ? ? 1_555 A U 17 N3 ? ? A A 7 A U 17 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? hydrog17 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 16 N3 ? ? A G 9 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 9 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 9 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 10 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 10 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 10 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 5UF3 _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 C 4 4 4 C C A . n A 1 5 A 5 5 5 A A A . n A 1 6 U 6 6 6 U U A . n A 1 7 A 7 7 7 A A A . n A 1 8 A 8 8 8 A A A . n A 1 9 G 9 9 9 G G A . n A 1 10 G 10 10 10 G G A . n A 1 11 A 11 11 11 A A A . n A 1 12 A 12 12 12 A A A . n A 1 13 A 13 13 13 A A A . n A 1 14 A 14 14 14 A A A . n A 1 15 C 15 15 15 C C A . n A 1 16 C 16 16 16 C C A . n A 1 17 U 17 17 17 U U A . n A 1 18 A 18 18 18 A A A . n A 1 19 U 19 19 19 U U A . n A 1 20 G 20 20 20 G G A . n A 1 21 U 21 21 21 U U A . n A 1 22 C 22 22 22 C C A . n A 1 23 C 23 23 23 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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 4740 ? # _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 2017-05-31 2 'Structure model' 1 1 2017-06-14 3 'Structure model' 1 2 2017-07-26 # _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 ? # 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' 'Database references' 2 3 'Structure model' 'Database references' # 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 2 'Structure model' citation 2 3 'Structure model' pdbx_database_related # 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 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_id_ASTM' 3 2 'Structure model' '_citation.journal_id_CSD' 4 2 'Structure model' '_citation.journal_volume' 5 2 'Structure model' '_citation.page_first' 6 2 'Structure model' '_citation.page_last' # 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 'phage GA operator RNA hairpin' 1 ? mM '[U-13C; U-15N]' 1 'potassium phosphate' 10 ? mM 'natural abundance' 1 'potassium chloride' 10 ? mM 'natural abundance' 1 EDTA 0.02 ? mM 'natural abundance' 2 'phage GA operator RNA hairpin' 1.5 ? mM 'natural abundance' 2 'potassium phosphate' 10 ? mM 'natural abundance' 2 'potassium chloride' 10 ? mM 'natural abundance' 2 EDTA 0.02 ? mM 'natural abundance' 3 'phage GA operator RNA hairpin' 1 ? mM '[U-13C; U-15N]' 3 'potassium chloride' 10 ? mM 'natural abundance' 3 'potassium phosphate' 10 ? mM 'natural abundance' 3 EDTA 0.02 ? mM 'natural abundance' 4 'phage GA operator RNA hairpin' 0.3 ? mM '[U-13C; U-15N]' 4 'potassium chloride' 10 ? mM 'natural abundance' 4 'potassium phosphate' 10 ? mM 'natural abundance' 4 'Pf1 phage' 15 ? mg/mL 'natural abundance' 5 'phage GA operator RNA hairpin' 1.2 ? mM '2H, 40%-85%' 5 'potassium chloride' 10 ? mM 'natural abundance' 5 'potassium phosphate' 10 ? mM 'natural abundance' 5 EDTA 0.02 ? mM 'natural abundance' 6 'phage GA operator RNA hairpin' 1.1 ? mM '13C, 4%-20%' 6 'potassium chloride' 10 ? mM 'natural abundance' 6 'potassium phosphate' 10 ? mM 'natural abundance' 6 EDTA 0.02 ? mM na # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5UF3 'double helix' 5UF3 'a-form double helix' 5UF3 'hairpin loop' 5UF3 'bulge loop' # 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 23 1_555 -1.450 -0.277 -0.016 5.049 -5.834 9.621 1 A_G1:C23_A A 1 ? A 23 ? 19 1 1 A G 2 1_555 A C 22 1_555 -0.858 0.145 0.154 -9.430 -2.134 6.412 2 A_G2:C22_A A 2 ? A 22 ? 19 1 1 A A 3 1_555 A U 21 1_555 1.040 -0.186 0.531 7.994 14.265 -2.972 3 A_A3:U21_A A 3 ? A 21 ? 20 1 1 A C 4 1_555 A G 20 1_555 0.690 -0.022 -0.666 3.267 -3.955 7.121 4 A_C4:G20_A A 4 ? A 20 ? 19 1 1 A A 5 1_555 A U 19 1_555 0.561 -0.039 -0.570 -1.510 4.976 7.152 5 A_A5:U19_A A 5 ? A 19 ? 20 1 1 A U 6 1_555 A A 18 1_555 0.195 -0.012 -0.697 -5.657 17.902 4.185 6 A_U6:A18_A A 6 ? A 18 ? 20 1 1 A A 7 1_555 A U 17 1_555 2.646 0.062 -0.130 -8.208 18.887 -1.856 7 A_A7:U17_A A 7 ? A 17 ? ? 1 1 A G 9 1_555 A C 16 1_555 -0.845 0.093 -0.274 -17.112 -8.451 1.019 8 A_G9:C16_A A 9 ? A 16 ? 19 1 1 A G 10 1_555 A C 15 1_555 0.739 0.238 0.411 -4.096 9.827 -5.452 9 A_G10:C15_A A 10 ? A 15 ? 19 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 23 1_555 A G 2 1_555 A C 22 1_555 -0.208 -1.650 3.897 -4.138 13.784 31.743 -5.072 -0.347 2.953 23.735 7.125 34.777 1 AA_G1G2:C22C23_AA A 1 ? A 23 ? A 2 ? A 22 ? 1 A G 2 1_555 A C 22 1_555 A A 3 1_555 A U 21 1_555 -0.736 -1.438 2.931 -3.561 -1.956 35.992 -2.061 0.725 3.059 -3.152 5.740 36.213 2 AA_G2A3:U21C22_AA A 2 ? A 22 ? A 3 ? A 21 ? 1 A A 3 1_555 A U 21 1_555 A C 4 1_555 A G 20 1_555 0.476 -1.977 3.646 12.394 18.080 27.421 -5.970 1.045 2.039 32.375 -22.193 34.974 3 AA_A3C4:G20U21_AA A 3 ? A 21 ? A 4 ? A 20 ? 1 A C 4 1_555 A G 20 1_555 A A 5 1_555 A U 19 1_555 0.431 -1.645 3.747 -2.898 7.888 24.135 -6.107 -1.851 2.996 18.175 6.677 25.536 4 AA_C4A5:U19G20_AA A 4 ? A 20 ? A 5 ? A 19 ? 1 A A 5 1_555 A U 19 1_555 A U 6 1_555 A A 18 1_555 -0.241 -2.124 4.259 -0.863 -0.587 27.284 -4.308 0.229 4.308 -1.243 1.829 27.304 5 AA_A5U6:A18U19_AA A 5 ? A 19 ? A 6 ? A 18 ? 1 A U 6 1_555 A A 18 1_555 A A 7 1_555 A U 17 1_555 -0.463 -1.659 3.800 3.116 4.593 35.805 -3.394 1.237 3.516 7.415 -5.031 36.219 6 AA_U6A7:U17A18_AA A 6 ? A 18 ? A 7 ? A 17 ? 1 A A 7 1_555 A U 17 1_555 A G 9 1_555 A C 16 1_555 -1.988 -2.608 5.281 22.211 23.005 31.344 -6.074 5.164 1.486 33.589 -32.428 44.489 7 AA_A7G9:C16U17_AA A 7 ? A 17 ? A 9 ? A 16 ? 1 A G 9 1_555 A C 16 1_555 A G 10 1_555 A C 15 1_555 -0.707 -1.417 3.316 -7.542 9.242 30.697 -4.053 -0.014 2.871 16.688 13.619 32.881 8 AA_G9G10:C15C16_AA A 9 ? A 16 ? A 10 ? A 15 ? #