data_2RVO # _entry.id 2RVO # _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_code _database_2.database_id _database_2.pdbx_database_accession _database_2.pdbx_DOI RCSB150322 RCSB ? ? 2RVO PDB pdb_00002rvo 10.2210/pdb2rvo/pdb 11607 BMRB ? ? D_1000150322 WWPDB ? ? # _pdbx_database_related.db_id 11607 _pdbx_database_related.db_name BMRB _pdbx_database_related.content_type unspecified _pdbx_database_related.details . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2RVO _pdbx_database_status.methods_development_category ? _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2016-02-03 _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.status_code_cs REL _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Otsu, M.' 1 'Norose, N.' 2 'Arai, N.' 3 'Terao, R.' 4 'Kajikawa, M.' 5 'Okada, N.' 6 'Kawai, G.' 7 # _citation.id primary _citation.title 'Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish.' _citation.journal_abbrev 'J. Biochem.' _citation.journal_volume 162 _citation.page_first 279 _citation.page_last 285 _citation.year 2017 _citation.journal_id_ASTM ? _citation.country JP _citation.journal_id_ISSN 1756-2651 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 28431120 _citation.pdbx_database_id_DOI 10.1093/jb/mvx026 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Otsu, M.' 1 ? primary 'Kajikawa, M.' 2 ? primary 'Okada, N.' 3 ? primary 'Kawai, G.' 4 ? # _cell.entry_id 2RVO _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RVO _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'RNA (34-MER)' _entity.formula_weight 10859.503 _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 GGCGCUUUGACACAAUCUACAUUGUAAAAGCGCC _entity_poly.pdbx_seq_one_letter_code_can GGCGCUUUGACACAAUCUACAUUGUAAAAGCGCC _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 C n 1 4 G n 1 5 C n 1 6 U n 1 7 U n 1 8 U n 1 9 G n 1 10 A n 1 11 C n 1 12 A n 1 13 C n 1 14 A n 1 15 A n 1 16 U n 1 17 C n 1 18 U n 1 19 A n 1 20 C n 1 21 A n 1 22 U n 1 23 U n 1 24 G n 1 25 U n 1 26 A n 1 27 A n 1 28 A n 1 29 A n 1 30 G n 1 31 C n 1 32 G n 1 33 C n 1 34 C n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name zebrafish _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Danio rerio' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 7955 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'cell-free synthesis' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ? _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description 'RNA was prepared by in vitro transcription with the T7 RNA polymerase' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2RVO _struct_ref.pdbx_db_accession 2RVO _struct_ref.entity_id 1 _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 2RVO _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 2RVO _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.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 1H-13C HSQC' 1 4 1 '2D 1H-13C HSQC' 1 5 2 '2D 1H-13C HSQC' 1 6 1 '2D 1H-13C TROSY' 1 7 1 '2D 1H-13C TROSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 50 _pdbx_nmr_exptl_sample_conditions.pH 6.5 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 288 _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '0.3 mM RNA (34-MER)-1, 0.26 mM [U-100% 13C; U-100% 15N] RNA (34-MER)-2, 100% D2O' 1 '100% D2O' '0.18 mM [U-13C; U-15N]-Ade RNA (34-MER)-3, 0.19 mM [U-13C; U-15N]-Gua RNA (34-MER)-4, 95% H2O/5% D2O' 2 '95% H2O/5% 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 DRX 2 'Bruker DRX' 800 Bruker AVANCE 3 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2RVO _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _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 0 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 11 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2RVO _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation 0.5 _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation 30 _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation 0.5 _pdbx_nmr_ensemble.representative_conformer 1 _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2RVO _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.ordinal _pdbx_nmr_software.version 'Bruker Biospin' collection TopSpin 1 2.1 'Bruker Biospin' processing TopSpin 2 2.1 'Brunger, Adams, Clore, Gros, Nilges and Read' 'structure solution' CNSSOLVE 3 1.3 'Brunger, Adams, Clore, Gros, Nilges and Read' refinement CNSSOLVE 4 1.3 Goddard 'peak picking' Sparky 5 3.114 'Schwieters, Kuszewski, Tjandra and Clore' 'grid search' 'X-PLOR NIH' 6 2.32 # _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 2RVO _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2RVO _struct.title 'Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish' _struct.pdbx_model_details 'minimized average structure, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 2RVO _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, LINE, retrotransposon' # _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 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 C 3 N3 ? ? ? 1_555 A G 32 N1 ? ? A C 3 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 32 O6 ? ? A C 3 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 32 N2 ? ? A C 3 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 31 N3 ? ? A G 4 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 31 O2 ? ? A G 4 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 31 N4 ? ? A G 4 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 30 N1 ? ? A C 5 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 30 O6 ? ? A C 5 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 30 N2 ? ? A C 5 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 29 N1 ? ? A U 6 A A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 29 N6 ? ? A U 6 A A 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 28 N1 ? ? A U 7 A A 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 28 N6 ? ? A U 7 A A 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 8 N3 ? ? ? 1_555 A A 27 N1 ? ? A U 8 A A 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 8 O4 ? ? ? 1_555 A A 27 N6 ? ? A U 8 A A 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 9 N2 ? ? ? 1_555 A U 25 O4 ? ? A G 9 A U 25 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog23 hydrog ? ? A G 9 N2 ? ? ? 1_555 A A 26 N1 ? ? A G 9 A A 26 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog24 hydrog ? ? A A 10 N1 ? ? ? 1_555 A A 12 N6 ? ? A A 10 A A 12 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog25 hydrog ? ? A A 12 N1 ? ? ? 1_555 A U 25 N3 ? ? A A 12 A U 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A A 12 N6 ? ? ? 1_555 A U 25 O4 ? ? A A 12 A U 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 24 N1 ? ? A C 13 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 24 O6 ? ? A C 13 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 24 N2 ? ? A C 13 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 14 N1 ? ? ? 1_555 A U 23 N3 ? ? A A 14 A U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 14 N6 ? ? ? 1_555 A U 23 O4 ? ? A A 14 A U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A A 15 N1 ? ? ? 1_555 A U 22 N3 ? ? A A 15 A U 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A A 15 N6 ? ? ? 1_555 A U 22 O4 ? ? A A 15 A U 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A U 16 N3 ? ? ? 1_555 A A 21 N1 ? ? A U 16 A A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A U 16 O4 ? ? ? 1_555 A A 21 N6 ? ? A U 16 A A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2RVO _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 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 C 5 5 5 C C A . n A 1 6 U 6 6 6 U U A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 G 9 9 9 G G A . n A 1 10 A 10 10 10 A A A . n A 1 11 C 11 11 11 C C A . n A 1 12 A 12 12 12 A A A . n A 1 13 C 13 13 13 C C A . n A 1 14 A 14 14 14 A A A . n A 1 15 A 15 15 15 A A A . n A 1 16 U 16 16 16 U U A . n A 1 17 C 17 17 17 C C A . n A 1 18 U 18 18 18 U U A . n A 1 19 A 19 19 19 A A A . n A 1 20 C 20 20 20 C C A . n A 1 21 A 21 21 21 A A A . n A 1 22 U 22 22 22 U U A . n A 1 23 U 23 23 23 U U A . n A 1 24 G 24 24 24 G G A . n A 1 25 U 25 25 25 U U A . n A 1 26 A 26 26 26 A A A . n A 1 27 A 27 27 27 A A A . n A 1 28 A 28 28 28 A A A . n A 1 29 A 29 29 29 A A A . n A 1 30 G 30 30 30 G G A . n A 1 31 C 31 31 31 C C A . n A 1 32 G 32 32 32 G G 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 2017-02-08 2 'Structure model' 1 1 2017-11-15 3 'Structure model' 1 2 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 ? # 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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' Other # 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 2 'Structure model' citation_author 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_database_status 5 3 'Structure model' pdbx_nmr_software 6 3 'Structure model' pdbx_nmr_spectrometer # 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_abbrev' 3 2 'Structure model' '_citation.journal_id_CSD' 4 2 'Structure model' '_citation.journal_id_ISSN' 5 2 'Structure model' '_citation.journal_volume' 6 2 'Structure model' '_citation.page_first' 7 2 'Structure model' '_citation.page_last' 8 2 'Structure model' '_citation.pdbx_database_id_DOI' 9 2 'Structure model' '_citation.pdbx_database_id_PubMed' 10 2 'Structure model' '_citation.title' 11 2 'Structure model' '_citation.year' 12 3 'Structure model' '_database_2.pdbx_DOI' 13 3 'Structure model' '_database_2.pdbx_database_accession' 14 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' 15 3 'Structure model' '_pdbx_nmr_software.name' 16 3 'Structure model' '_pdbx_nmr_spectrometer.model' # _pdbx_nmr_ensemble_rms.atom_type ? _pdbx_nmr_ensemble_rms.bond_angle_rms_dev ? _pdbx_nmr_ensemble_rms.bond_angle_rms_dev_error ? _pdbx_nmr_ensemble_rms.chain_range_begin ? _pdbx_nmr_ensemble_rms.chain_range_end ? _pdbx_nmr_ensemble_rms.coord_average_rmsd_method ? _pdbx_nmr_ensemble_rms.covalent_bond_rms_dev ? _pdbx_nmr_ensemble_rms.covalent_bond_rms_dev_error ? _pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev ? _pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev_error ? _pdbx_nmr_ensemble_rms.distance_rms_dev 0.0880 _pdbx_nmr_ensemble_rms.distance_rms_dev_error 0.0011 _pdbx_nmr_ensemble_rms.entry_id 2RVO _pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev ? _pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev_error ? _pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev ? _pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev_error ? _pdbx_nmr_ensemble_rms.residue_range_begin ? _pdbx_nmr_ensemble_rms.residue_range_end ? # loop_ _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 _pdbx_nmr_exptl_sample.solution_id 'RNA (34-MER)-1' 0.3 ? mM ? 1 'RNA (34-MER)-2' 0.26 ? mM '[U-100% 13C; U-100% 15N]' 1 'RNA (34-MER)-3' 0.18 ? mM '[U-13C; U-15N]-Ade' 2 'RNA (34-MER)-4' 0.19 ? mM '[U-13C; U-15N]-Gua' 2 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2RVO _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count 32 _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count 22 _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count 22 _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count 24 _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count 32 _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count 22 _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count 22 _pdbx_nmr_constraints.NA_other-angle_constraints_total_count 22 _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count 128 _pdbx_nmr_constraints.NOE_constraints_total 358 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count 74 _pdbx_nmr_constraints.NOE_long_range_total_count 11 _pdbx_nmr_constraints.NOE_medium_range_total_count 12 _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count 135 _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 2 H3 A U 7 ? ? H62 A A 28 ? ? 1.26 2 2 "HO2'" A C 20 ? ? "H5''" A A 21 ? ? 1.29 3 3 H3 A U 7 ? ? H62 A A 28 ? ? 1.26 4 3 H3 A U 16 ? ? H62 A A 21 ? ? 1.32 5 5 "H2'" A U 16 ? ? "H2'" A C 17 ? ? 1.20 6 5 "HO2'" A A 12 ? ? "H5'" A C 13 ? ? 1.30 7 6 H3 A U 7 ? ? H62 A A 28 ? ? 1.26 8 8 H3 A U 7 ? ? H62 A A 28 ? ? 1.26 9 9 H3 A U 7 ? ? H62 A A 28 ? ? 1.26 10 9 H3 A U 16 ? ? H62 A A 21 ? ? 1.30 11 10 H3 A U 7 ? ? H62 A A 28 ? ? 1.26 12 10 "HO2'" A C 20 ? ? OP2 A A 21 ? ? 1.56 13 11 "H2'" A C 17 ? ? H6 A U 18 ? ? 1.15 14 11 H3 A U 7 ? ? H62 A A 28 ? ? 1.26 15 11 H3 A U 16 ? ? H62 A A 21 ? ? 1.29 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2RVO 'double helix' 2RVO 'a-form double helix' 2RVO 'hairpin loop' 2RVO '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 0.540 -0.030 -0.064 6.745 -1.053 1.026 1 A_G1:C34_A A 1 ? A 34 ? 19 1 1 A G 2 1_555 A C 33 1_555 -1.181 -0.571 0.020 -6.474 2.117 -3.341 2 A_G2:C33_A A 2 ? A 33 ? 19 1 1 A C 3 1_555 A G 32 1_555 -1.009 -0.214 0.040 9.336 -2.539 -5.972 3 A_C3:G32_A A 3 ? A 32 ? 19 1 1 A G 4 1_555 A C 31 1_555 -1.355 -0.654 0.227 8.386 1.372 -1.111 4 A_G4:C31_A A 4 ? A 31 ? 19 1 1 A C 5 1_555 A G 30 1_555 1.166 -0.561 -0.097 4.021 -0.813 -4.961 5 A_C5:G30_A A 5 ? A 30 ? 19 1 1 A U 6 1_555 A A 29 1_555 0.967 -0.330 0.186 -11.151 -6.004 3.489 6 A_U6:A29_A A 6 ? A 29 ? 20 1 1 A U 7 1_555 A A 28 1_555 0.930 -0.401 0.322 -8.243 0.173 4.658 7 A_U7:A28_A A 7 ? A 28 ? 20 1 1 A U 8 1_555 A A 27 1_555 -1.261 -0.207 0.140 -3.886 -8.238 -2.651 8 A_U8:A27_A A 8 ? A 27 ? 20 1 1 A G 9 1_555 A A 26 1_555 3.376 0.536 2.073 -50.550 5.808 -2.094 9 A_G9:A26_A A 9 ? A 26 ? ? ? 1 A A 12 1_555 A U 25 1_555 -1.095 -0.488 0.223 4.003 -10.713 0.631 10 A_A12:U25_A A 12 ? A 25 ? 20 1 1 A C 13 1_555 A G 24 1_555 0.967 -0.456 0.047 9.467 -5.615 -5.510 11 A_C13:G24_A A 13 ? A 24 ? 19 1 1 A A 14 1_555 A U 23 1_555 -0.900 -0.271 0.112 0.034 0.801 -1.762 12 A_A14:U23_A A 14 ? A 23 ? 20 1 1 A A 15 1_555 A U 22 1_555 1.309 -0.238 -0.064 2.149 -2.548 -9.676 13 A_A15:U22_A A 15 ? A 22 ? 20 1 1 A U 16 1_555 A A 21 1_555 1.036 -0.357 0.301 -11.882 -4.704 -2.034 14 A_U16:A21_A A 16 ? A 21 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 34 1_555 A G 2 1_555 A C 33 1_555 -0.097 -0.919 4.074 -13.728 41.640 12.684 -5.238 -1.211 0.355 70.898 23.374 45.556 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 C 3 1_555 A G 32 1_555 -1.033 -0.692 3.053 -5.409 -0.986 36.591 -0.964 0.931 3.185 -1.559 8.556 36.988 2 AA_G2C3:G32C33_AA A 2 ? A 33 ? A 3 ? A 32 ? 1 A C 3 1_555 A G 32 1_555 A G 4 1_555 A C 31 1_555 1.154 -1.138 2.786 -4.867 18.357 39.367 -2.888 -1.914 1.946 25.527 6.768 43.544 3 AA_C3G4:C31G32_AA A 3 ? A 32 ? A 4 ? A 31 ? 1 A G 4 1_555 A C 31 1_555 A C 5 1_555 A G 30 1_555 -0.132 -1.063 3.140 0.677 4.761 40.673 -2.010 0.259 3.000 6.821 -0.969 40.944 4 AA_G4C5:G30C31_AA A 4 ? A 31 ? A 5 ? A 30 ? 1 A C 5 1_555 A G 30 1_555 A U 6 1_555 A A 29 1_555 0.348 -1.921 3.229 2.051 13.141 33.050 -4.841 -0.305 2.337 22.023 -3.438 35.556 5 AA_C5U6:A29G30_AA A 5 ? A 30 ? A 6 ? A 29 ? 1 A U 6 1_555 A A 29 1_555 A U 7 1_555 A A 28 1_555 0.886 -1.496 2.931 0.550 0.258 34.392 -2.566 -1.422 2.933 0.437 -0.931 34.397 6 AA_U6U7:A28A29_AA A 6 ? A 29 ? A 7 ? A 28 ? 1 A U 7 1_555 A A 28 1_555 A U 8 1_555 A A 27 1_555 -1.203 -1.726 2.764 1.948 2.222 24.110 -4.668 3.356 2.493 5.295 -4.642 24.288 7 AA_U7U8:A27A28_AA A 7 ? A 28 ? A 8 ? A 27 ? 1 A U 8 1_555 A A 27 1_555 A G 9 1_555 A A 26 1_555 0.564 -0.909 5.194 -8.863 11.304 50.804 -2.167 -1.531 4.752 12.883 10.101 52.666 8 AA_U8G9:A26A27_AA A 8 ? A 27 ? A 9 ? A 26 ? 1 A G 9 1_555 A A 26 1_555 A A 12 1_555 A U 25 1_555 -4.407 -1.519 2.357 37.116 5.778 55.186 -1.474 4.553 -0.400 5.582 -35.853 65.916 9 AA_G9A12:U25A26_AA A 9 ? A 26 ? A 12 ? A 25 ? 1 A A 12 1_555 A U 25 1_555 A C 13 1_555 A G 24 1_555 -0.479 -0.661 3.059 0.379 2.203 42.722 -1.111 0.691 3.019 3.021 -0.520 42.778 10 AA_A12C13:G24U25_AA A 12 ? A 25 ? A 13 ? A 24 ? 1 A C 13 1_555 A G 24 1_555 A A 14 1_555 A U 23 1_555 0.391 -1.939 3.012 -0.973 21.832 22.401 -6.467 -0.855 0.824 44.779 1.995 31.198 11 AA_C13A14:U23G24_AA A 13 ? A 24 ? A 14 ? A 23 ? 1 A A 14 1_555 A U 23 1_555 A A 15 1_555 A U 22 1_555 -0.756 -1.826 3.012 -2.421 8.113 38.512 -3.546 0.871 2.630 12.122 3.617 39.397 12 AA_A14A15:U22U23_AA A 14 ? A 23 ? A 15 ? A 22 ? 1 A A 15 1_555 A U 22 1_555 A U 16 1_555 A A 21 1_555 0.655 -2.376 3.317 0.308 3.619 25.965 -6.184 -1.365 2.971 8.004 -0.682 26.213 13 AA_A15U16:A21U22_AA A 15 ? A 22 ? A 16 ? A 21 ? #