data_2RO2 # _entry.id 2RO2 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2RO2 pdb_00002ro2 10.2210/pdb2ro2/pdb RCSB RCSB150080 ? ? WWPDB D_1000150080 ? ? # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2RO2 _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2008-03-05 _pdbx_database_status.SG_entry . _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Gallego, J.' 1 'Dufour, D.' 2 'Gago, S.' 3 'de la Pena, M.' 4 'Flores, R.' 5 # _citation.id primary _citation.title ;Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 37 _citation.page_first 368 _citation.page_last 381 _citation.year 2009 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19043070 _citation.pdbx_database_id_DOI 10.1093/nar/gkn918 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Dufour, D.' 1 ? primary 'de la Pena, M.' 2 ? primary 'Gago, S.' 3 ? primary 'Flores, R.' 4 ? primary 'Gallego, J.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3') ; _entity.formula_weight 7435.457 _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 GGGAGACCUGAAGUGGGUUUCCC _entity_poly.pdbx_seq_one_letter_code_can GGGAGACCUGAAGUGGGUUUCCC _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 G n 1 4 A n 1 5 G n 1 6 A n 1 7 C n 1 8 C n 1 9 U n 1 10 G n 1 11 A n 1 12 A n 1 13 G n 1 14 U n 1 15 G n 1 16 G n 1 17 G n 1 18 U n 1 19 U n 1 20 U n 1 21 C n 1 22 C n 1 23 C n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2RO2 _struct_ref.pdbx_db_accession 2RO2 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code GGGAGACCUGAAGUGGGUUUCCC _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2RO2 _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 2RO2 _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.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-1H NOESY' 1 2 1 '2D 1H-1H TOCSY' 1 3 1 '2D DQF-COSY' 2 4 2 '2D 1H-1H NOESY' 1 5 3 '2D 1H-15N HSQC' 1 6 3 '2D HNN COSY' 1 7 4 '2D 1H-13C HSQC' 1 8 4 '3D NOESY-HMQC' 1 9 4 '3D HCCH ECOSY' 1 10 4 '2D HCCH-TOCSY' 1 11 4 '3D HCP' 1 12 4 '3D 13C-ED-1H-31P HETCOR' 1 13 4 '3D HCP-CCH TOCSY' 1 14 4 '2D HCNCH' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.temperature_units 1 12.4 6 ambient ? 297 K 2 12.4 6 ambient ? 281 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;0.5mM RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA, 100% D2O ; 1 '100% D2O' ;0.5mM RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA, 90% H2O/10% D2O ; 2 '90% H2O/10% D2O' ;1mM [U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA, 90% H2O/10% D2O ; 3 '90% H2O/10% D2O' ;0.5mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA, 100% D2O ; 4 '100% D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 600 Bruker AVANCE 1 'Bruker Avance' 600 Bruker AVANCE 2 'Bruker Avance' 700 Bruker AVANCE 3 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2RO2 _pdbx_nmr_refine.method 'simulated annealing and restrained energy minimization' _pdbx_nmr_refine.details 'minimized average structure of 29 converged conformers with the least restraint violation energy and total energy' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'Structures with the least restraint violations and total energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2RO2 _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2RO2 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Bruker Biospin' collection TopSpin 1.3 1 'Bruker Biospin' processing TopSpin 1.3 2 Goddard 'data analysis' Sparky 3.110 3 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollm' refinement Amber 8.0 4 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2RO2 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2RO2 _struct.title 'Solution structure of domain I of the negative polarity CChMVd hammerhead ribozyme' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 2RO2 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'hammerhead ribozyme, viroid, CCHMVD, heptaloop, RNA' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 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 G 3 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 3 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 3 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 3 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 20 N3 ? ? A A 4 A U 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 A U 20 O4 ? ? A A 4 A U 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A U 19 O2 ? ? A G 5 A U 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog13 hydrog ? ? A G 5 O6 ? ? ? 1_555 A U 19 N3 ? ? A G 5 A U 19 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog14 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 18 N3 ? ? A A 6 A U 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 18 O4 ? ? A A 6 A U 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 7 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 7 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 7 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 8 N3 ? ? ? 1_555 A G 16 N1 ? ? A C 8 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 N4 ? ? ? 1_555 A G 16 O6 ? ? A C 8 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 8 O2 ? ? ? 1_555 A G 16 N2 ? ? A C 8 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 9 N3 ? ? ? 1_555 A G 15 O6 ? ? A U 9 A G 15 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog23 hydrog ? ? A U 9 O2 ? ? ? 1_555 A G 15 N1 ? ? A U 9 A G 15 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog24 hydrog ? ? A G 10 N2 ? ? ? 1_555 A G 13 N7 ? ? A G 10 A G 13 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2RO2 _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 G 3 3 3 G G A . n A 1 4 A 4 4 4 A A 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 C 8 8 8 C C A . n A 1 9 U 9 9 9 U U 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 G 13 13 13 G G A . n A 1 14 U 14 14 14 U U A . n A 1 15 G 15 15 15 G G A . n A 1 16 G 16 16 16 G G A . n A 1 17 G 17 17 17 G G A . n A 1 18 U 18 18 18 U U A . n A 1 19 U 19 19 19 U U A . n A 1 20 U 20 20 20 U U A . n A 1 21 C 21 21 21 C C 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 # _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 2008-12-30 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2022-03-16 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 '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 3 'Structure model' database_2 2 3 'Structure model' pdbx_nmr_software 3 3 'Structure model' pdbx_nmr_spectrometer 4 3 'Structure model' pdbx_struct_assembly 5 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_nmr_software.name' 4 3 'Structure model' '_pdbx_nmr_spectrometer.model' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id ;RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3') ; 1 mM ? 1 'sodium phosphate' 10 mM ? 1 EDTA 0.1 mM ? 1 ;RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3') ; 1 mM ? 2 'sodium phosphate' 10 mM ? 2 EDTA 0.1 mM ? 2 ;RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3') ; 1 mM '[U-100% 15N]' 3 'sodium phosphate' 10 mM ? 3 EDTA 0.1 mM ? 3 ;RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3') ; 1 mM '[U-100% 13C; U-100% 15N]' 4 'sodium phosphate' 10 mM ? 4 EDTA 0.1 mM ? 4 # 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 C4 A A 4 ? ? C5 A A 4 ? ? C6 A A 4 ? ? 113.98 117.00 -3.02 0.50 N 2 1 C5 A A 4 ? ? C6 A A 4 ? ? N1 A A 4 ? ? 121.10 117.70 3.40 0.50 N 3 1 N1 A A 4 ? ? C6 A A 4 ? ? N6 A A 4 ? ? 114.14 118.60 -4.46 0.60 N 4 1 C5 A A 6 ? ? C6 A A 6 ? ? N1 A A 6 ? ? 121.09 117.70 3.39 0.50 N 5 1 N1 A A 6 ? ? C6 A A 6 ? ? N6 A A 6 ? ? 113.86 118.60 -4.74 0.60 N 6 1 N3 A C 7 ? ? C2 A C 7 ? ? O2 A C 7 ? ? 117.09 121.90 -4.81 0.70 N 7 1 "O4'" A C 8 ? ? "C1'" A C 8 ? ? N1 A C 8 ? ? 113.03 108.50 4.53 0.70 N 8 1 N3 A C 8 ? ? C2 A C 8 ? ? O2 A C 8 ? ? 116.69 121.90 -5.21 0.70 N 9 1 "O4'" A G 10 ? ? "C1'" A G 10 ? ? N9 A G 10 ? ? 113.11 108.50 4.61 0.70 N 10 1 "C3'" A A 11 ? ? "C2'" A A 11 ? ? "C1'" A A 11 ? ? 95.59 101.30 -5.71 0.70 N 11 1 C4 A A 11 ? ? C5 A A 11 ? ? C6 A A 11 ? ? 113.95 117.00 -3.05 0.50 N 12 1 C5 A A 11 ? ? C6 A A 11 ? ? N1 A A 11 ? ? 121.34 117.70 3.64 0.50 N 13 1 N1 A A 11 ? ? C6 A A 11 ? ? N6 A A 11 ? ? 113.27 118.60 -5.33 0.60 N 14 1 C5 A A 12 ? ? C6 A A 12 ? ? N1 A A 12 ? ? 121.00 117.70 3.30 0.50 N 15 1 N1 A A 12 ? ? C6 A A 12 ? ? N6 A A 12 ? ? 113.43 118.60 -5.17 0.60 N 16 1 "C5'" A G 13 ? ? "C4'" A G 13 ? ? "O4'" A G 13 ? ? 101.26 109.10 -7.84 1.20 N 17 1 "C1'" A G 13 ? ? "O4'" A G 13 ? ? "C4'" A G 13 ? ? 104.88 109.70 -4.82 0.70 N 18 1 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 114.73 108.50 6.23 0.70 N 19 1 N1 A G 15 ? ? C6 A G 15 ? ? O6 A G 15 ? ? 115.93 119.90 -3.97 0.60 N 20 1 "O4'" A U 18 ? ? "C1'" A U 18 ? ? N1 A U 18 ? ? 113.18 108.50 4.68 0.70 N 21 1 N3 A C 21 ? ? C2 A C 21 ? ? O2 A C 21 ? ? 116.97 121.90 -4.93 0.70 N 22 1 N3 A C 22 ? ? C2 A C 22 ? ? O2 A C 22 ? ? 116.91 121.90 -4.99 0.70 N 23 1 N3 A C 23 ? ? C2 A C 23 ? ? O2 A C 23 ? ? 116.90 121.90 -5.00 0.70 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 U A 9 ? ? 0.057 'SIDE CHAIN' 2 1 G A 10 ? ? 0.122 'SIDE CHAIN' 3 1 A A 12 ? ? 0.096 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2RO2 'a-form double helix' 2RO2 'hairpin loop' 2RO2 '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 23 1_555 -0.498 -0.104 -0.215 -7.500 -7.255 -0.044 1 A_G1:C23_A A 1 ? A 23 ? 19 1 1 A G 2 1_555 A C 22 1_555 -0.419 -0.105 -0.142 -7.233 -10.090 -0.056 2 A_G2:C22_A A 2 ? A 22 ? 19 1 1 A G 3 1_555 A C 21 1_555 -0.378 -0.092 -0.141 -8.540 -12.130 -0.315 3 A_G3:C21_A A 3 ? A 21 ? 19 1 1 A A 4 1_555 A U 20 1_555 0.047 -0.004 -0.026 -5.173 -11.287 -0.798 4 A_A4:U20_A A 4 ? A 20 ? 20 1 1 A G 5 1_555 A U 19 1_555 -2.243 -0.341 0.243 4.444 -9.537 1.861 5 A_G5:U19_A A 5 ? A 19 ? 28 1 1 A A 6 1_555 A U 18 1_555 0.142 0.016 -0.076 8.104 -13.120 -0.877 6 A_A6:U18_A A 6 ? A 18 ? 20 1 1 A C 7 1_555 A G 17 1_555 0.446 -0.104 -0.171 9.393 -12.206 0.410 7 A_C7:G17_A A 7 ? A 17 ? 19 1 1 A C 8 1_555 A G 16 1_555 0.601 -0.177 -0.194 2.633 -12.972 0.959 8 A_C8:G16_A A 8 ? A 16 ? 19 1 1 A U 9 1_555 A G 15 1_555 2.086 -0.225 -0.134 -7.040 -4.271 7.930 9 A_U9:G15_A A 9 ? A 15 ? 28 1 1 A G 10 1_555 A G 13 1_555 7.849 -4.354 1.281 28.289 3.956 -33.177 10 A_G10:G13_A A 10 ? A 13 ? ? ? # 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 -0.061 -1.877 3.313 -0.561 6.649 31.104 -4.588 0.014 2.861 12.224 1.031 31.795 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 G 3 1_555 A C 21 1_555 -0.074 -1.808 3.332 -0.137 7.378 31.097 -4.566 0.111 2.839 13.525 0.251 31.939 2 AA_G2G3:C21C22_AA A 2 ? A 22 ? A 3 ? A 21 ? 1 A G 3 1_555 A C 21 1_555 A A 4 1_555 A U 20 1_555 -0.077 -1.527 3.228 -0.609 5.118 31.827 -3.618 0.036 2.954 9.256 1.101 32.230 3 AA_G3A4:U20C21_AA A 3 ? A 21 ? A 4 ? A 20 ? 1 A A 4 1_555 A U 20 1_555 A G 5 1_555 A U 19 1_555 0.130 -1.887 2.858 -4.324 7.349 23.074 -6.206 -1.348 2.107 17.618 10.366 24.579 4 AA_A4G5:U19U20_AA A 4 ? A 20 ? A 5 ? A 19 ? 1 A G 5 1_555 A U 19 1_555 A A 6 1_555 A U 18 1_555 -0.472 -1.729 3.269 -0.740 4.184 38.196 -3.133 0.627 3.078 6.370 1.126 38.423 5 AA_G5A6:U18U19_AA A 5 ? A 19 ? A 6 ? A 18 ? 1 A A 6 1_555 A U 18 1_555 A C 7 1_555 A G 17 1_555 -0.055 -1.795 3.298 -0.651 3.465 32.144 -3.824 -0.014 3.093 6.234 1.171 32.331 6 AA_A6C7:G17U18_AA A 6 ? A 18 ? A 7 ? A 17 ? 1 A C 7 1_555 A G 17 1_555 A C 8 1_555 A G 16 1_555 0.113 -1.853 3.401 1.044 8.322 31.927 -4.637 -0.027 2.843 14.811 -1.858 32.982 7 AA_C7C8:G16G17_AA A 7 ? A 17 ? A 8 ? A 16 ? 1 A C 8 1_555 A G 16 1_555 A U 9 1_555 A G 15 1_555 1.048 -1.424 3.509 4.257 6.238 42.224 -2.605 -0.986 3.361 8.577 -5.853 42.864 8 AA_C8U9:G15G16_AA A 8 ? A 16 ? A 9 ? A 15 ? 1 A U 9 1_555 A G 15 1_555 A G 10 1_555 A G 13 1_555 -2.604 -0.318 2.625 -3.674 7.134 48.171 -0.833 2.921 2.735 8.670 4.465 48.795 9 AA_U9G10:G13G15_AA A 9 ? A 15 ? A 10 ? A 13 ? #