data_1R7Z # _entry.id 1R7Z # _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 1R7Z pdb_00001r7z 10.2210/pdb1r7z/pdb RCSB RCSB020549 ? ? WWPDB D_1000020549 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1R7W _pdbx_database_related.details 'NMR STRUCTURE OF THE R(GGAGGACAUCCCUCACGGGUGACCGUGGUCCUCC), DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES WITH AUCCCU BULGE' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1R7Z _pdbx_database_status.recvd_initial_deposition_date 2003-10-22 _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 'Du, Z.' 1 'Ulyanov, N.B.' 2 'Yu, J.' 3 'James, T.L.' 4 # _citation.id primary _citation.title ;NMR Structures of Loop B RNAs from the Stem-Loop IV Domain of the Enterovirus Internal Ribosome Entry Site: A Single C to U Substitution Drastically Changes the Shape and Flexibility of RNA(,). ; _citation.journal_abbrev Biochemistry _citation.journal_volume 43 _citation.page_first 5757 _citation.page_last 5771 _citation.year 2004 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15134450 _citation.pdbx_database_id_DOI 10.1021/bi0363228 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Du, Z.' 1 ? primary 'Ulyanov, N.B.' 2 ? primary 'Yu, J.' 3 ? primary 'Andino, R.' 4 ? primary 'James, T.L.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 34-MER _entity.formula_weight 10898.495 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation 'SEQUENCE VARIANT WITH THE AUUCCU BULGE' _entity.pdbx_fragment 'DOMAIN IV, LOOP B' _entity.details 'RNA FRAGMENT OF ENTEROVIRAL IRES' # _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 GGAGGACAUUCCUCACGGGUGACCGUGGUCCUCC _entity_poly.pdbx_seq_one_letter_code_can GGAGGACAUUCCUCACGGGUGACCGUGGUCCUCC _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 C n 1 8 A n 1 9 U n 1 10 U n 1 11 C n 1 12 C n 1 13 U n 1 14 C n 1 15 A n 1 16 C n 1 17 G n 1 18 G n 1 19 G n 1 20 U n 1 21 G n 1 22 A n 1 23 C n 1 24 C n 1 25 G n 1 26 U n 1 27 G n 1 28 G n 1 29 U n 1 30 C n 1 31 C n 1 32 U 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 'RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1R7Z _struct_ref.pdbx_db_accession 1R7Z _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 1R7Z _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 1R7Z _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.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D NOESY' 1 2 2 '2D NOESY' 2 3 2 DQF-COSY 2 4 2 '1H-13C CONSTANT TIME HSQC' 3 # 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 1 278 ambient 6.5 '50 mM Na+ ions' ? K 2 298 ambient 6.5 '50 mM Na+ ions' ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1mM unlabeled RNA, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), 90% H2O; 10% D2O' '90% H2O/10% D2O' 2 '1mM unlabeled RNA, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), D2O' D2O 3 ;1mM of RNA labeled in residues A and U with 13C, 15N, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), 5% (weight/volume) of C12E6/n-hexanol mixture (molar ratio 0.64), D2O ; D2O # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.type ? # _pdbx_nmr_refine.entry_id 1R7Z _pdbx_nmr_refine.method 'FULL MATRIX RELAXATION ANALYSIS OF NOE, RANDOM ERROR ANALYSIS OF NOE, SIMULATED ANNEALING USING RESTRAINED MOLECULAR DYNAMICS' _pdbx_nmr_refine.details 'STRUCTURES ARE REFINED BASED ON 614 NOE-DERIVED DISTANCES AND 26 RESIDUAL DIPOLAR COUPLINGS' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1R7Z _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'LOWEST TOTAL ENERGY (A WEIGHTED SUM OF CONFORMATIONAL ENERGY AND RESTRAINT 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 1R7Z _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal collection VNMR 6.1 'Varian Associates, Inc.' 1 processing NMRPipe 2.1 F.Delaglio 2 'iterative matrix relaxation' MARDIGRAS 3.2 T.L.James 3 refinement DYANA 1.5 P.Guntert 4 refinement Amber 7 D.A.Case 5 # _exptl.entry_id 1R7Z _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol ? _exptl_crystal.density_Matthews ? _exptl_crystal.description ? # _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.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _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 1R7Z _struct.title 'NMR STRUCTURE OF THE R(GGAGGACAUUCCUCACGGGUGACCGUGGUCCUCC), DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES WITH AUUCCU BULGE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1R7Z _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'STEM-AND-LOOP STRUCTURE, SIX-NUCLEOTIDE BULGE, GUGA TETRALOOP, 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 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 33 O2 ? ? A G 2 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 33 N4 ? ? A G 2 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 32 N3 ? ? A A 3 A U 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 32 O4 ? ? A A 3 A U 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 31 N3 ? ? A G 4 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 31 O2 ? ? A G 4 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 31 N4 ? ? A G 4 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 30 N3 ? ? A G 5 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 30 O2 ? ? A G 5 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 30 N4 ? ? A G 5 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 29 N3 ? ? A A 6 A U 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 29 O4 ? ? A A 6 A U 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 28 N1 ? ? A C 7 A G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 28 O6 ? ? A C 7 A G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 28 N2 ? ? A C 7 A G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 7 O2 ? ? ? 1_555 A U 29 N3 ? ? A C 7 A U 29 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog21 hydrog ? ? A C 11 O2 ? ? ? 1_555 A G 27 N1 ? ? A C 11 A G 27 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog22 hydrog ? ? A C 14 N3 ? ? ? 1_555 A G 27 N1 ? ? A C 14 A G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 14 N4 ? ? ? 1_555 A G 27 O6 ? ? A C 14 A G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 14 O2 ? ? ? 1_555 A G 27 N2 ? ? A C 14 A G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A A 15 N1 ? ? ? 1_555 A U 26 N3 ? ? A A 15 A U 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A A 15 N6 ? ? ? 1_555 A U 26 O4 ? ? A A 15 A U 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 16 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 16 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 16 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 16 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 16 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 16 A G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 17 N1 ? ? ? 1_555 A C 24 N3 ? ? A G 17 A C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 17 N2 ? ? ? 1_555 A C 24 O2 ? ? A G 17 A C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 17 O6 ? ? ? 1_555 A C 24 N4 ? ? A G 17 A C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 18 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 18 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 18 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 18 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 18 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 18 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 19 N2 ? ? ? 1_555 A A 22 N7 ? ? A G 19 A A 22 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1R7Z _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 1R7Z _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 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 A 6 6 6 A A A . n A 1 7 C 7 7 7 C C A . n A 1 8 A 8 8 8 A A A . n A 1 9 U 9 9 9 U U A . n A 1 10 U 10 10 10 U U A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 U 13 13 13 U U A . n A 1 14 C 14 14 14 C C A . n A 1 15 A 15 15 15 A A A . n A 1 16 C 16 16 16 C C A . n A 1 17 G 17 17 17 G G A . n A 1 18 G 18 18 18 G G A . n A 1 19 G 19 19 19 G G A . n A 1 20 U 20 20 20 U U A . n A 1 21 G 21 21 21 G G A . n A 1 22 A 22 22 22 A A A . n A 1 23 C 23 23 23 C C A . n A 1 24 C 24 24 24 C C A . n A 1 25 G 25 25 25 G G A . n A 1 26 U 26 26 26 U U A . n A 1 27 G 27 27 27 G G A . n A 1 28 G 28 28 28 G G A . n A 1 29 U 29 29 29 U U A . n A 1 30 C 30 30 30 C C A . n A 1 31 C 31 31 31 C C A . n A 1 32 U 32 32 32 U U A . n A 1 33 C 33 33 33 C C A . n A 1 34 C 34 34 34 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 2004-05-25 2 'Structure model' 1 1 2008-04-29 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' # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 13 _pdbx_validate_rmsd_bond.auth_atom_id_1 P _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 U _pdbx_validate_rmsd_bond.auth_seq_id_1 13 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "O5'" _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 U _pdbx_validate_rmsd_bond.auth_seq_id_2 13 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.653 _pdbx_validate_rmsd_bond.bond_target_value 1.593 _pdbx_validate_rmsd_bond.bond_deviation 0.060 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.010 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1R7Z 'double helix' 1R7Z 'a-form double helix' 1R7Z tetraloop 1R7Z 'bulge loop' 1R7Z '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 -0.480 -0.082 -0.167 -1.248 -8.935 -0.542 1 A_G1:C34_A A 1 ? A 34 ? 19 1 1 A G 2 1_555 A C 33 1_555 -0.584 -0.124 -0.048 -0.002 -6.242 -1.165 2 A_G2:C33_A A 2 ? A 33 ? 19 1 1 A A 3 1_555 A U 32 1_555 -0.870 -0.249 0.575 12.612 -5.385 8.223 3 A_A3:U32_A A 3 ? A 32 ? 20 1 1 A G 4 1_555 A C 31 1_555 -0.324 -0.231 -0.422 -4.915 -22.856 2.355 4 A_G4:C31_A A 4 ? A 31 ? 19 1 1 A G 5 1_555 A C 30 1_555 0.401 -0.021 -0.100 -8.950 1.983 -5.253 5 A_G5:C30_A A 5 ? A 30 ? 19 1 1 A A 6 1_555 A U 29 1_555 0.863 0.044 -1.131 -2.326 9.111 -24.893 6 A_A6:U29_A A 6 ? A 29 ? 20 1 1 A C 7 1_555 A G 28 1_555 0.363 -0.179 -0.849 12.956 -4.308 -2.357 7 A_C7:G28_A A 7 ? A 28 ? 19 1 1 A C 14 1_555 A G 27 1_555 -0.743 -0.110 0.201 28.823 -33.277 -12.827 8 A_C14:G27_A A 14 ? A 27 ? 19 1 1 A A 15 1_555 A U 26 1_555 0.515 -0.246 -0.509 24.019 -33.541 18.884 9 A_A15:U26_A A 15 ? A 26 ? 20 1 1 A C 16 1_555 A G 25 1_555 1.118 -0.397 -0.442 2.021 -18.237 7.737 10 A_C16:G25_A A 16 ? A 25 ? 19 1 1 A G 17 1_555 A C 24 1_555 0.135 0.005 -0.255 -18.288 -13.747 -1.631 11 A_G17:C24_A A 17 ? A 24 ? 19 1 1 A G 18 1_555 A C 23 1_555 -0.151 -0.018 0.549 3.139 -1.747 -1.182 12 A_G18:C23_A A 18 ? A 23 ? 19 1 1 A G 19 1_555 A A 22 1_555 7.932 -4.732 0.154 46.036 -18.285 -52.839 13 A_G19:A22_A A 19 ? A 22 ? ? ? # 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 -0.080 -1.723 3.193 -2.805 5.156 28.734 -4.442 -0.407 2.842 10.255 5.579 29.316 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 A 3 1_555 A U 32 1_555 0.099 -1.531 2.708 -5.972 4.187 31.216 -3.374 -1.037 2.427 7.651 10.912 32.036 2 AA_G2A3:U32C33_AA A 2 ? A 33 ? A 3 ? A 32 ? 1 A A 3 1_555 A U 32 1_555 A G 4 1_555 A C 31 1_555 -0.361 -1.605 3.598 4.994 14.556 38.335 -3.872 1.059 2.770 21.156 -7.259 41.200 3 AA_A3G4:C31U32_AA A 3 ? A 32 ? A 4 ? A 31 ? 1 A G 4 1_555 A C 31 1_555 A G 5 1_555 A C 30 1_555 -0.443 -1.605 3.370 -2.243 2.347 38.596 -2.714 0.388 3.291 3.543 3.386 38.727 4 AA_G4G5:C30C31_AA A 4 ? A 31 ? A 5 ? A 30 ? 1 A G 5 1_555 A C 30 1_555 A A 6 1_555 A U 29 1_555 -1.485 -1.829 3.611 8.405 -11.012 28.789 -1.032 4.457 3.503 -20.702 -15.801 31.885 5 AA_G5A6:U29C30_AA A 5 ? A 30 ? A 6 ? A 29 ? 1 A A 6 1_555 A U 29 1_555 A C 7 1_555 A G 28 1_555 1.600 -1.679 2.900 -1.602 -0.964 26.781 -3.398 -3.811 2.859 -2.077 3.454 26.845 6 AA_A6C7:G28U29_AA A 6 ? A 29 ? A 7 ? A 28 ? 1 A C 14 1_555 A G 27 1_555 A A 15 1_555 A U 26 1_555 2.131 -0.499 4.515 4.073 -12.390 49.046 0.665 -2.081 4.657 -14.628 -4.808 50.647 7 AA_C14A15:U26G27_AA A 14 ? A 27 ? A 15 ? A 26 ? 1 A A 15 1_555 A U 26 1_555 A C 16 1_555 A G 25 1_555 -0.663 -1.210 4.023 -1.570 11.988 32.318 -4.231 0.834 3.400 20.657 2.705 34.449 8 AA_A15C16:G25U26_AA A 15 ? A 26 ? A 16 ? A 25 ? 1 A C 16 1_555 A G 25 1_555 A G 17 1_555 A C 24 1_555 -0.835 -1.194 4.166 0.641 7.890 29.817 -4.132 1.725 3.717 15.003 -1.219 30.827 9 AA_C16G17:C24G25_AA A 16 ? A 25 ? A 17 ? A 24 ? 1 A G 17 1_555 A C 24 1_555 A G 18 1_555 A C 23 1_555 0.062 -1.452 2.702 -4.583 3.110 25.905 -3.828 -1.105 2.466 6.839 10.076 26.480 10 AA_G17G18:C23C24_AA A 17 ? A 24 ? A 18 ? A 23 ? 1 A G 18 1_555 A C 23 1_555 A G 19 1_555 A A 22 1_555 -2.976 -1.342 2.577 6.158 -2.545 52.205 -1.390 3.658 2.295 -2.879 -6.965 52.599 11 AA_G18G19:A22C23_AA A 18 ? A 23 ? A 19 ? A 22 ? #