data_2RQJ # _entry.id 2RQJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 2RQJ pdb_00002rqj 10.2210/pdb2rqj/pdb RCSB RCSB150165 ? ? WWPDB D_1000150165 ? ? # 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 2009-11-17 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2022-03-16 4 'Structure model' 1 3 2024-05-29 # _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' 5 4 'Structure model' 'Data collection' # 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_struct_assembly 4 3 'Structure model' pdbx_struct_oper_list 5 4 'Structure model' chem_comp_atom 6 4 'Structure model' chem_comp_bond # 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' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2RQJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2009-07-18 _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 'Katahira, M.' 1 'Mashima, T.' 2 'Matsugami, A.' 3 'Nishikawa, F.' 4 'Nishikawa, S.' 5 # _citation.id primary _citation.title 'Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 37 _citation.page_first 6249 _citation.page_last 6258 _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 19666719 _citation.pdbx_database_id_DOI 10.1093/nar/gkp647 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mashima, T.' 1 ? primary 'Matsugami, A.' 2 ? primary 'Nishikawa, F.' 3 ? primary 'Nishikawa, S.' 4 ? primary 'Katahira, M.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') ; _entity.formula_weight 4033.512 _entity.pdbx_number_of_molecules 2 _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 GGAGGAGGAGGA _entity_poly.pdbx_seq_one_letter_code_can GGAGGAGGAGGA _entity_poly.pdbx_strand_id A,B _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 G n 1 8 G n 1 9 A n 1 10 G n 1 11 G n 1 12 A n # 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 # 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 G 7 7 7 G G A . n A 1 8 G 8 8 8 G G A . n A 1 9 A 9 9 9 A A A . n A 1 10 G 10 10 10 G G A . n A 1 11 G 11 11 11 G G A . n A 1 12 A 12 12 12 A A A . n B 1 1 G 1 13 13 G G B . n B 1 2 G 2 14 14 G G B . n B 1 3 A 3 15 15 A A B . n B 1 4 G 4 16 16 G G B . n B 1 5 G 5 17 17 G G B . n B 1 6 A 6 18 18 A A B . n B 1 7 G 7 19 19 G G B . n B 1 8 G 8 20 20 G G B . n B 1 9 A 9 21 21 A A B . n B 1 10 G 10 22 22 G G B . n B 1 11 G 11 23 23 G G B . n B 1 12 A 12 24 24 A A B . n # _cell.entry_id 2RQJ _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 2RQJ _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _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 'refined structure' _exptl.entry_id 2RQJ _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2RQJ _struct.title 'Quadruplex structure of an RNA aptamer against bovine prion protein' _struct.pdbx_model_details 'lowest energy, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2RQJ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Aptamer, Prion, Quadruplex, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2RQJ _struct_ref.pdbx_db_accession 2RQJ _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2RQJ A 1 ? 12 ? 2RQJ 1 ? 12 ? 1 12 2 1 2RQJ B 1 ? 12 ? 2RQJ 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 # _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 N2 ? ? ? 1_555 A A 3 N7 ? ? A G 1 A A 3 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog2 hydrog ? ? A G 1 N3 ? ? ? 1_555 A A 3 N6 ? ? A G 1 A A 3 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog3 hydrog ? ? A G 1 N1 ? ? ? 1_555 A G 4 O6 ? ? A G 1 A G 4 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog4 hydrog ? ? A G 1 N2 ? ? ? 1_555 A G 4 N7 ? ? A G 1 A G 4 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog5 hydrog ? ? A G 1 N7 ? ? ? 1_555 A G 10 N2 ? ? A G 1 A G 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog6 hydrog ? ? A G 1 O6 ? ? ? 1_555 A G 10 N1 ? ? A G 1 A G 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog7 hydrog ? ? A G 2 N1 ? ? ? 1_555 A G 5 O6 ? ? A G 2 A G 5 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog8 hydrog ? ? A G 2 N2 ? ? ? 1_555 A G 5 N7 ? ? A G 2 A G 5 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog9 hydrog ? ? A G 2 N7 ? ? ? 1_555 A G 11 N2 ? ? A G 2 A G 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog10 hydrog ? ? A G 2 O6 ? ? ? 1_555 A G 11 N1 ? ? A G 2 A G 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog11 hydrog ? ? A G 4 N1 ? ? ? 1_555 A G 7 O6 ? ? A G 4 A G 7 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog12 hydrog ? ? A G 4 N2 ? ? ? 1_555 A G 7 N7 ? ? A G 4 A G 7 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog13 hydrog ? ? A G 5 N1 ? ? ? 1_555 A G 8 O6 ? ? A G 5 A G 8 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog14 hydrog ? ? A G 5 N2 ? ? ? 1_555 A G 8 N7 ? ? A G 5 A G 8 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog15 hydrog ? ? A G 7 N2 ? ? ? 1_555 A A 9 N7 ? ? A G 7 A A 9 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog16 hydrog ? ? A G 7 N3 ? ? ? 1_555 A A 9 N6 ? ? A G 7 A A 9 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog17 hydrog ? ? A G 7 N1 ? ? ? 1_555 A G 10 O6 ? ? A G 7 A G 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog18 hydrog ? ? A G 7 N2 ? ? ? 1_555 A G 10 N7 ? ? A G 7 A G 10 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog19 hydrog ? ? A G 8 N1 ? ? ? 1_555 A G 11 O6 ? ? A G 8 A G 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog20 hydrog ? ? A G 8 N2 ? ? ? 1_555 A G 11 N7 ? ? A G 8 A G 11 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog21 hydrog ? ? B G 1 N2 ? ? ? 1_555 B A 3 N7 ? ? B G 13 B A 15 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog22 hydrog ? ? B G 1 N3 ? ? ? 1_555 B A 3 N6 ? ? B G 13 B A 15 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog23 hydrog ? ? B G 1 N1 ? ? ? 1_555 B G 4 O6 ? ? B G 13 B G 16 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog24 hydrog ? ? B G 1 N2 ? ? ? 1_555 B G 4 N7 ? ? B G 13 B G 16 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog25 hydrog ? ? B G 1 N7 ? ? ? 1_555 B G 10 N2 ? ? B G 13 B G 22 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog26 hydrog ? ? B G 1 O6 ? ? ? 1_555 B G 10 N1 ? ? B G 13 B G 22 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog27 hydrog ? ? B G 2 N1 ? ? ? 1_555 B G 5 O6 ? ? B G 14 B G 17 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog28 hydrog ? ? B G 2 N2 ? ? ? 1_555 B G 5 N7 ? ? B G 14 B G 17 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog29 hydrog ? ? B G 2 N7 ? ? ? 1_555 B G 11 N2 ? ? B G 14 B G 23 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog30 hydrog ? ? B G 2 O6 ? ? ? 1_555 B G 11 N1 ? ? B G 14 B G 23 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog31 hydrog ? ? B G 4 N1 ? ? ? 1_555 B G 7 O6 ? ? B G 16 B G 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog32 hydrog ? ? B G 4 N2 ? ? ? 1_555 B G 7 N7 ? ? B G 16 B G 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog33 hydrog ? ? B G 5 N1 ? ? ? 1_555 B G 8 O6 ? ? B G 17 B G 20 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog34 hydrog ? ? B G 5 N2 ? ? ? 1_555 B G 8 N7 ? ? B G 17 B G 20 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog35 hydrog ? ? B G 7 N2 ? ? ? 1_555 B A 9 N7 ? ? B G 19 B A 21 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog36 hydrog ? ? B G 7 N3 ? ? ? 1_555 B A 9 N6 ? ? B G 19 B A 21 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog37 hydrog ? ? B G 7 N1 ? ? ? 1_555 B G 10 O6 ? ? B G 19 B G 22 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog38 hydrog ? ? B G 7 N2 ? ? ? 1_555 B G 10 N7 ? ? B G 19 B G 22 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog39 hydrog ? ? B G 8 N1 ? ? ? 1_555 B G 11 O6 ? ? B G 20 B G 23 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog40 hydrog ? ? B G 8 N2 ? ? ? 1_555 B G 11 N7 ? ? B G 20 B G 23 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 1 "HO2'" A G 1 ? ? "O5'" A G 2 ? ? 1.54 2 1 N7 A G 1 ? ? H21 A G 10 ? ? 1.59 3 1 N7 B G 13 ? ? H21 B G 22 ? ? 1.60 4 2 "HO2'" A G 1 ? ? OP2 A G 2 ? ? 1.49 5 2 N7 A G 1 ? ? H21 A G 10 ? ? 1.60 6 3 "HO2'" A G 10 ? ? "O2'" B A 18 ? ? 1.39 7 3 "HO2'" A G 1 ? ? OP2 A G 2 ? ? 1.50 8 3 "HO2'" A G 4 ? ? N1 A A 6 ? ? 1.51 9 3 N7 B G 13 ? ? H21 B G 22 ? ? 1.58 10 3 "HO2'" A G 7 ? ? "O5'" A G 8 ? ? 1.58 11 3 N7 A G 1 ? ? H21 A G 10 ? ? 1.59 12 4 "O2'" A A 6 ? ? "HO2'" B G 22 ? ? 1.41 13 4 N7 A G 1 ? ? H21 A G 10 ? ? 1.58 14 4 N7 B G 13 ? ? H21 B G 22 ? ? 1.59 15 5 "HO2'" B G 16 ? ? N1 B A 18 ? ? 1.41 16 5 N7 A G 1 ? ? H21 A G 10 ? ? 1.59 17 6 "HO2'" B G 13 ? ? OP2 B G 14 ? ? 1.48 18 6 "HO2'" B G 23 ? ? "O5'" B A 24 ? ? 1.52 19 6 "O2'" B G 16 ? ? "H5'" B G 17 ? ? 1.56 20 6 "O2'" A G 10 ? ? "HO2'" B A 18 ? ? 1.58 21 6 N7 A G 1 ? ? H21 A G 10 ? ? 1.59 22 6 "O2'" A A 6 ? ? "O2'" B G 22 ? ? 2.14 23 7 "HO2'" A G 4 ? ? N1 A A 6 ? ? 1.39 24 7 "HO2'" A G 1 ? ? OP2 A G 2 ? ? 1.39 25 7 N7 B G 13 ? ? H21 B G 22 ? ? 1.59 26 7 N7 A G 1 ? ? H21 A G 10 ? ? 1.60 27 8 OP1 A G 2 ? ? H61 A A 3 ? ? 1.49 28 8 N7 B G 13 ? ? H21 B G 22 ? ? 1.58 29 9 "HO2'" A A 6 ? ? "O2'" B G 22 ? ? 1.36 30 9 "HO2'" B G 19 ? ? "O5'" B G 20 ? ? 1.50 31 9 "HO2'" A G 7 ? ? OP2 A G 8 ? ? 1.57 32 9 "O2'" A A 6 ? ? "O2'" B G 22 ? ? 2.12 # _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 lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 9 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2RQJ _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.representative_conformer 1 _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2RQJ _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '1mM RNA-1, 10mM potassium phosphate-2, 100mM potassium chloride-3, 0.01mM DSS-4, 3mM sodium azide-5, 95% H2O/5% D2O' 1 '95% H2O/5% D2O' '1mM RNA-6, 10mM potassium phosphate-7, 100mM potassium chloride-8, 0.01mM DSS-9, 3mM sodium azide-10, 95% H2O/5% D2O' 2 '100% D2O' # 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-1 1 ? mM ? 1 'potassium phosphate-2' 10 ? mM ? 1 'potassium chloride-3' 100 ? mM ? 1 DSS-4 0.01 ? mM ? 1 'sodium azide-5' 3 ? mM ? 1 RNA-6 1 ? mM ? 2 'potassium phosphate-7' 10 ? mM ? 2 'potassium chloride-8' 100 ? mM ? 2 DSS-9 0.01 ? mM ? 2 'sodium azide-10' 3 ? mM ? 2 # 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 0.1 6.2 ambient atm 278 K 2 0.1 6.2 ambient atm 303 K # 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' 2 2 1 '2D 1H-1H NOESY' 2 3 2 '2D 1H-1H NOESY' 2 4 1 '2D 1H-1H TOCSY' 2 5 2 '2D 1H-1H TOCSY' 2 6 2 '2D DQF-COSY' 2 7 2 '2D 1H-13C HSQC' 2 8 1 JRHMBC # _pdbx_nmr_refine.entry_id 2RQJ _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Schwieters, Kuszewski, Tjandra and Clore' 'structure solution' 'X-PLOR NIH' 2.20 1 'Bruker Biospin' collection XwinNMR ? 2 'Bruker Biospin' collection TopSpin ? 3 Goddard 'chemical shift assignment' Sparky ? 4 Goddard 'peak picking' Sparky ? 5 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRPipe ? 6 Garrett 'chemical shift assignment' PIPP ? 7 Garrett 'peak picking' PIPP ? 8 'Schwieters, Kuszewski, Tjandra and Clore' refinement 'X-PLOR NIH' 2.20 9 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 G OP3 O N N 38 G P P N N 39 G OP1 O N N 40 G OP2 O N N 41 G "O5'" O N N 42 G "C5'" C N N 43 G "C4'" C N R 44 G "O4'" O N N 45 G "C3'" C N S 46 G "O3'" O N N 47 G "C2'" C N R 48 G "O2'" O N N 49 G "C1'" C N R 50 G N9 N Y N 51 G C8 C Y N 52 G N7 N Y N 53 G C5 C Y N 54 G C6 C N N 55 G O6 O N N 56 G N1 N N N 57 G C2 C N N 58 G N2 N N N 59 G N3 N N N 60 G C4 C Y N 61 G HOP3 H N N 62 G HOP2 H N N 63 G "H5'" H N N 64 G "H5''" H N N 65 G "H4'" H N N 66 G "H3'" H N N 67 G "HO3'" H N N 68 G "H2'" H N N 69 G "HO2'" H N N 70 G "H1'" H N N 71 G H8 H N N 72 G H1 H N N 73 G H21 H N N 74 G H22 H N N 75 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 G OP3 P sing N N 40 G OP3 HOP3 sing N N 41 G P OP1 doub N N 42 G P OP2 sing N N 43 G P "O5'" sing N N 44 G OP2 HOP2 sing N N 45 G "O5'" "C5'" sing N N 46 G "C5'" "C4'" sing N N 47 G "C5'" "H5'" sing N N 48 G "C5'" "H5''" sing N N 49 G "C4'" "O4'" sing N N 50 G "C4'" "C3'" sing N N 51 G "C4'" "H4'" sing N N 52 G "O4'" "C1'" sing N N 53 G "C3'" "O3'" sing N N 54 G "C3'" "C2'" sing N N 55 G "C3'" "H3'" sing N N 56 G "O3'" "HO3'" sing N N 57 G "C2'" "O2'" sing N N 58 G "C2'" "C1'" sing N N 59 G "C2'" "H2'" sing N N 60 G "O2'" "HO2'" sing N N 61 G "C1'" N9 sing N N 62 G "C1'" "H1'" sing N N 63 G N9 C8 sing Y N 64 G N9 C4 sing Y N 65 G C8 N7 doub Y N 66 G C8 H8 sing N N 67 G N7 C5 sing Y N 68 G C5 C6 sing N N 69 G C5 C4 doub Y N 70 G C6 O6 doub N N 71 G C6 N1 sing N N 72 G N1 C2 sing N N 73 G N1 H1 sing N N 74 G C2 N2 sing N N 75 G C2 N3 doub N N 76 G N2 H21 sing N N 77 G N2 H22 sing N N 78 G N3 C4 sing N N 79 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2RQJ 'double helix' 2RQJ 'quadruple helix' # 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 2 1_555 A G 11 1_555 -0.643 -3.514 0.170 0.376 -0.973 97.799 1 A_G2:G11_A A 2 ? A 11 ? 6 3 1 A G 5 1_555 A G 8 1_555 0.339 3.799 -0.349 3.148 0.249 -88.943 2 A_G5:G8_A A 5 ? A 8 ? 6 3 1 A G 1 1_555 A G 4 1_555 0.528 3.864 0.007 0.765 -1.248 -86.907 3 A_G1:G4_A A 1 ? A 4 ? 6 3 1 A G 7 1_555 A G 10 1_555 1.300 3.493 -0.207 5.387 5.868 -98.276 4 A_G7:G10_A A 7 ? A 10 ? 6 ? 1 B G 11 1_555 B G 8 1_555 -0.510 -3.857 -0.014 2.138 -0.033 90.662 5 B_G23:G20_B B 23 ? B 20 ? 6 3 1 B G 7 1_555 B G 10 1_555 1.116 3.607 -0.291 5.077 8.231 -98.053 6 B_G19:G22_B B 19 ? B 22 ? 6 ? 1 B G 4 1_555 B G 1 1_555 -0.423 -3.841 -0.009 -1.580 0.798 88.183 7 B_G16:G13_B B 16 ? B 13 ? 6 3 # 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 2 1_555 A G 11 1_555 A G 5 1_555 A G 8 1_555 -1.158 -3.923 -0.084 3.346 2.885 176.431 -1.962 0.579 -0.088 1.443 -1.674 176.433 1 AA_G2G5:G8G11_AA A 2 ? A 11 ? A 5 ? A 8 ? 1 A G 5 1_555 A G 8 1_555 A G 1 1_555 A G 4 1_555 -0.096 3.744 -3.162 -2.703 3.245 -126.510 -2.070 -0.032 -3.216 -1.817 -1.513 -126.549 2 AA_G5G1:G4G8_AA A 5 ? A 8 ? A 1 ? A 4 ? 1 B G 11 1_555 B G 8 1_555 B G 7 1_555 B G 10 1_555 0.760 1.435 -3.201 5.513 -2.185 -30.963 -3.043 0.388 -3.179 4.046 10.210 -31.513 3 BB_G23G19:G22G20_BB B 23 ? B 20 ? B 19 ? B 22 ? 1 B G 7 1_555 B G 10 1_555 B G 4 1_555 B G 1 1_555 -0.832 -3.833 -0.050 -0.668 2.759 174.976 -1.918 0.417 -0.054 1.381 0.334 174.977 4 BB_G19G16:G13G22_BB B 19 ? B 22 ? B 16 ? B 13 ? # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 800 Bruker DRX 1 'Bruker DRX' 600 Bruker DRX 2 'Bruker DRX' # _atom_sites.entry_id 2RQJ _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_