data_2OJ7 # _entry.id 2OJ7 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 2OJ7 pdb_00002oj7 10.2210/pdb2oj7/pdb RCSB RCSB041202 ? ? WWPDB D_1000041202 ? ? # 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 2007-05-22 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-16 5 'Structure model' 1 4 2023-12-27 # _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' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 5 '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 4 'Structure model' database_2 2 4 'Structure model' pdbx_struct_assembly 3 4 'Structure model' pdbx_struct_oper_list 4 5 'Structure model' chem_comp_atom 5 5 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2OJ7 _pdbx_database_status.recvd_initial_deposition_date 2007-01-12 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _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 'Girard, F.C.' 1 'Ottink, O.M.' 2 'Ampt, K.A.M.' 3 'Tessari, M.' 4 'Wijmenga, S.S.' 5 # _citation.id primary _citation.title 'Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 35 _citation.page_first 2800 _citation.page_last 2811 _citation.year 2007 _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 17430968 _citation.pdbx_database_id_DOI 10.1093/nar/gkm131 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Girard, F.C.' 1 ? primary 'Ottink, O.M.' 2 ? primary 'Ampt, K.A.' 3 ? primary 'Tessari, M.' 4 ? primary 'Wijmenga, S.S.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-R(P*GP*CP*UP*GP*UP*UP*GP*U)-3'" _entity.formula_weight 2520.505 _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 GCUGUUGU _entity_poly.pdbx_seq_one_letter_code_can GCUGUUGU _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 C n 1 3 U n 1 4 G n 1 5 U n 1 6 U n 1 7 G n 1 8 U 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 'The Sequence of this RNA can be found in Duck Hepatitis B virus' # 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 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_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 11 11 G G A . n A 1 2 C 2 12 12 C C A . n A 1 3 U 3 13 13 U U A . n A 1 4 G 4 14 14 G G A . n A 1 5 U 5 15 15 U U A . n A 1 6 U 6 16 16 U U A . n A 1 7 G 7 17 17 G G A . n A 1 8 U 8 18 18 U U A . n # _exptl.entry_id 2OJ7 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _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 # _database_PDB_matrix.entry_id 2OJ7 _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 # _struct.entry_id 2OJ7 _struct.title 'NMR structure of the UGUU tetraloop of Duck Epsilon apical stem loop' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2OJ7 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'HBV, RNA, epsilon, Duck, UGUU, tetraloop' # _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_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2OJ7 _struct_ref.pdbx_db_accession 2OJ7 _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 2OJ7 _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 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2OJ7 _struct_ref_seq.db_align_beg 11 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 18 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 11 _struct_ref_seq.pdbx_auth_seq_align_end 18 # _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 # _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 U 8 O2 ? ? A G 11 A U 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog2 hydrog ? ? A G 1 O6 ? ? ? 1_555 A U 8 N3 ? ? A G 11 A U 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 7 N1 ? ? A C 12 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 7 O6 ? ? A C 12 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 7 N2 ? ? A C 12 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 3 O2 ? ? ? 1_555 A U 6 N3 ? ? A U 13 A U 16 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog7 hydrog ? ? A U 3 O2 ? ? ? 1_555 A G 7 N1 ? ? A U 13 A G 17 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 117.80 113.10 4.70 0.50 N 2 1 C8 A G 11 ? ? N9 A G 11 ? ? C4 A G 11 ? ? 103.21 106.40 -3.19 0.40 N 3 1 "C3'" A G 14 ? ? "C2'" A G 14 ? ? "C1'" A G 14 ? ? 106.39 101.50 4.89 0.80 N 4 1 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.65 113.10 4.55 0.50 N 5 1 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.35 106.40 -3.05 0.40 N 6 1 "C3'" A U 15 ? ? "C2'" A U 15 ? ? "C1'" A U 15 ? ? 106.46 101.50 4.96 0.80 N 7 1 "C3'" A U 16 ? ? "C2'" A U 16 ? ? "C1'" A U 16 ? ? 106.55 101.50 5.05 0.80 N 8 1 N7 A G 17 ? ? C8 A G 17 ? ? N9 A G 17 ? ? 117.40 113.10 4.30 0.50 N 9 1 C8 A G 17 ? ? N9 A G 17 ? ? C4 A G 17 ? ? 103.56 106.40 -2.84 0.40 N 10 2 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 117.76 113.10 4.66 0.50 N 11 2 C8 A G 11 ? ? N9 A G 11 ? ? C4 A G 11 ? ? 103.22 106.40 -3.18 0.40 N 12 2 "C3'" A U 13 ? ? "C2'" A U 13 ? ? "C1'" A U 13 ? ? 106.38 101.50 4.88 0.80 N 13 2 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.67 113.10 4.57 0.50 N 14 2 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.40 106.40 -3.00 0.40 N 15 2 "C3'" A U 15 ? ? "C2'" A U 15 ? ? "C1'" A U 15 ? ? 106.53 101.50 5.03 0.80 N 16 2 "C3'" A U 16 ? ? "C2'" A U 16 ? ? "C1'" A U 16 ? ? 106.78 101.50 5.28 0.80 N 17 2 N7 A G 17 ? ? C8 A G 17 ? ? N9 A G 17 ? ? 117.40 113.10 4.30 0.50 N 18 2 C8 A G 17 ? ? N9 A G 17 ? ? C4 A G 17 ? ? 103.48 106.40 -2.92 0.40 N 19 3 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 117.81 113.10 4.71 0.50 N 20 3 C8 A G 11 ? ? N9 A G 11 ? ? C4 A G 11 ? ? 103.20 106.40 -3.20 0.40 N 21 3 "C3'" A G 14 ? ? "C2'" A G 14 ? ? "C1'" A G 14 ? ? 106.48 101.50 4.98 0.80 N 22 3 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.70 113.10 4.60 0.50 N 23 3 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.39 106.40 -3.01 0.40 N 24 3 "C3'" A U 15 ? ? "C2'" A U 15 ? ? "C1'" A U 15 ? ? 106.50 101.50 5.00 0.80 N 25 3 "C3'" A U 16 ? ? "C2'" A U 16 ? ? "C1'" A U 16 ? ? 106.74 101.50 5.24 0.80 N 26 3 N7 A G 17 ? ? C8 A G 17 ? ? N9 A G 17 ? ? 117.49 113.10 4.39 0.50 N 27 3 C8 A G 17 ? ? N9 A G 17 ? ? C4 A G 17 ? ? 103.43 106.40 -2.97 0.40 N 28 4 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 117.81 113.10 4.71 0.50 N 29 4 C8 A G 11 ? ? N9 A G 11 ? ? C4 A G 11 ? ? 103.20 106.40 -3.20 0.40 N 30 4 "C3'" A G 14 ? ? "C2'" A G 14 ? ? "C1'" A G 14 ? ? 106.47 101.50 4.97 0.80 N 31 4 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.71 113.10 4.61 0.50 N 32 4 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.34 106.40 -3.06 0.40 N 33 4 "C3'" A U 15 ? ? "C2'" A U 15 ? ? "C1'" A U 15 ? ? 106.51 101.50 5.01 0.80 N 34 4 "C3'" A U 16 ? ? "C2'" A U 16 ? ? "C1'" A U 16 ? ? 106.69 101.50 5.19 0.80 N 35 4 "O4'" A G 17 ? ? "C1'" A G 17 ? ? N9 A G 17 ? ? 112.72 108.50 4.22 0.70 N 36 4 N7 A G 17 ? ? C8 A G 17 ? ? N9 A G 17 ? ? 117.57 113.10 4.47 0.50 N 37 4 C8 A G 17 ? ? N9 A G 17 ? ? C4 A G 17 ? ? 103.39 106.40 -3.01 0.40 N 38 5 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 117.83 113.10 4.73 0.50 N 39 5 C8 A G 11 ? ? N9 A G 11 ? ? C4 A G 11 ? ? 103.21 106.40 -3.19 0.40 N 40 5 "C3'" A G 14 ? ? "C2'" A G 14 ? ? "C1'" A G 14 ? ? 106.49 101.50 4.99 0.80 N 41 5 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.69 113.10 4.59 0.50 N 42 5 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.40 106.40 -3.00 0.40 N 43 5 "C3'" A U 15 ? ? "C2'" A U 15 ? ? "C1'" A U 15 ? ? 106.35 101.50 4.85 0.80 N 44 5 "C3'" A U 16 ? ? "C2'" A U 16 ? ? "C1'" A U 16 ? ? 106.67 101.50 5.17 0.80 N 45 5 N7 A G 17 ? ? C8 A G 17 ? ? N9 A G 17 ? ? 117.40 113.10 4.30 0.50 N 46 5 C8 A G 17 ? ? N9 A G 17 ? ? C4 A G 17 ? ? 103.47 106.40 -2.93 0.40 N 47 6 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 117.80 113.10 4.70 0.50 N 48 6 C8 A G 11 ? ? N9 A G 11 ? ? C4 A G 11 ? ? 103.18 106.40 -3.22 0.40 N 49 6 "C3'" A G 14 ? ? "C2'" A G 14 ? ? "C1'" A G 14 ? ? 106.47 101.50 4.97 0.80 N 50 6 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.73 113.10 4.63 0.50 N 51 6 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.31 106.40 -3.09 0.40 N 52 6 "C3'" A U 15 ? ? "C2'" A U 15 ? ? "C1'" A U 15 ? ? 106.33 101.50 4.83 0.80 N 53 6 "C3'" A U 16 ? ? "C2'" A U 16 ? ? "C1'" A U 16 ? ? 106.74 101.50 5.24 0.80 N 54 6 "C3'" A G 17 ? ? "C2'" A G 17 ? ? "C1'" A G 17 ? ? 106.31 101.50 4.81 0.80 N 55 6 N7 A G 17 ? ? C8 A G 17 ? ? N9 A G 17 ? ? 117.50 113.10 4.40 0.50 N 56 6 C8 A G 17 ? ? N9 A G 17 ? ? C4 A G 17 ? ? 103.41 106.40 -2.99 0.40 N 57 7 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 117.77 113.10 4.67 0.50 N 58 7 C8 A G 11 ? ? N9 A G 11 ? ? C4 A G 11 ? ? 103.23 106.40 -3.17 0.40 N 59 7 "C3'" A G 14 ? ? "C2'" A G 14 ? ? "C1'" A G 14 ? ? 106.31 101.50 4.81 0.80 N 60 7 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.62 113.10 4.52 0.50 N 61 7 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.37 106.40 -3.03 0.40 N 62 7 "C3'" A U 15 ? ? "C2'" A U 15 ? ? "C1'" A U 15 ? ? 106.36 101.50 4.86 0.80 N 63 7 "C3'" A U 16 ? ? "C2'" A U 16 ? ? "C1'" A U 16 ? ? 106.71 101.50 5.21 0.80 N 64 7 N7 A G 17 ? ? C8 A G 17 ? ? N9 A G 17 ? ? 117.51 113.10 4.41 0.50 N 65 7 C8 A G 17 ? ? N9 A G 17 ? ? C4 A G 17 ? ? 103.47 106.40 -2.93 0.40 N 66 8 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 117.78 113.10 4.68 0.50 N 67 8 C8 A G 11 ? ? N9 A G 11 ? ? C4 A G 11 ? ? 103.28 106.40 -3.12 0.40 N 68 8 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.70 113.10 4.60 0.50 N 69 8 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.27 106.40 -3.13 0.40 N 70 8 "C3'" A U 15 ? ? "C2'" A U 15 ? ? "C1'" A U 15 ? ? 106.34 101.50 4.84 0.80 N 71 8 "C3'" A U 16 ? ? "C2'" A U 16 ? ? "C1'" A U 16 ? ? 106.48 101.50 4.98 0.80 N 72 8 "C3'" A G 17 ? ? "C2'" A G 17 ? ? "C1'" A G 17 ? ? 106.33 101.50 4.83 0.80 N 73 8 N7 A G 17 ? ? C8 A G 17 ? ? N9 A G 17 ? ? 117.57 113.10 4.47 0.50 N 74 8 C8 A G 17 ? ? N9 A G 17 ? ? C4 A G 17 ? ? 103.39 106.40 -3.01 0.40 N 75 9 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 117.79 113.10 4.69 0.50 N 76 9 C8 A G 11 ? ? N9 A G 11 ? ? C4 A G 11 ? ? 103.25 106.40 -3.15 0.40 N 77 9 "C3'" A G 14 ? ? "C2'" A G 14 ? ? "C1'" A G 14 ? ? 106.33 101.50 4.83 0.80 N 78 9 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.70 113.10 4.60 0.50 N 79 9 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.44 106.40 -2.96 0.40 N 80 9 "C3'" A U 15 ? ? "C2'" A U 15 ? ? "C1'" A U 15 ? ? 106.50 101.50 5.00 0.80 N 81 9 "C3'" A U 16 ? ? "C2'" A U 16 ? ? "C1'" A U 16 ? ? 106.51 101.50 5.01 0.80 N 82 9 N7 A G 17 ? ? C8 A G 17 ? ? N9 A G 17 ? ? 117.58 113.10 4.48 0.50 N 83 9 C8 A G 17 ? ? N9 A G 17 ? ? C4 A G 17 ? ? 103.42 106.40 -2.98 0.40 N 84 10 N7 A G 11 ? ? C8 A G 11 ? ? N9 A G 11 ? ? 117.84 113.10 4.74 0.50 N 85 10 C8 A G 11 ? ? N9 A G 11 ? ? C4 A G 11 ? ? 103.19 106.40 -3.21 0.40 N 86 10 N7 A G 14 ? ? C8 A G 14 ? ? N9 A G 14 ? ? 117.73 113.10 4.63 0.50 N 87 10 C8 A G 14 ? ? N9 A G 14 ? ? C4 A G 14 ? ? 103.32 106.40 -3.08 0.40 N 88 10 "C3'" A U 15 ? ? "C2'" A U 15 ? ? "C1'" A U 15 ? ? 106.48 101.50 4.98 0.80 N 89 10 "C3'" A U 16 ? ? "C2'" A U 16 ? ? "C1'" A U 16 ? ? 106.85 101.50 5.35 0.80 N 90 10 N7 A G 17 ? ? C8 A G 17 ? ? N9 A G 17 ? ? 117.43 113.10 4.33 0.50 N 91 10 C8 A G 17 ? ? N9 A G 17 ? ? C4 A G 17 ? ? 103.39 106.40 -3.01 0.40 N # _pdbx_nmr_ensemble.entry_id 2OJ7 _pdbx_nmr_ensemble.conformers_calculated_total_number 800 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest 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 2OJ7 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1.2 mM RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, 95% H2O, 5% D2O' ? 2 '1.0 mM 13C/15N/2H-U labeled RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, 95% H2O, 5% D2O' ? 3 '1.2 mM RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, D2O' ? 4 '1.0 mM 13C/15N/2H-U labeled RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, D2O' ? # 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 5 ambient 6.7 '10 mM' . K 2 15 ambient 6.7 '10 mM' . K 3 25 ambient 6.7 '10 mM' . K # 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' 1 3 1 HMQC-15N/1H 2 4 3 DQF-COSY 3 5 3 HMQC-13C/1H 4 6 3 '2D NOESY' 3 # _pdbx_nmr_details.entry_id 2OJ7 _pdbx_nmr_details.text 'In addition TOCSY spectra and 31P 1D and 31P HMBC spectra were recorded.' # _pdbx_nmr_refine.entry_id 2OJ7 _pdbx_nmr_refine.method 'Torsion angle dynamics using XPLOR 3.851' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal 'structure solution' X-PLOR 3.851 'Stein, E.G. Rice L.M. and Brunger A.T.' 1 refinement X-PLOR 3.851 'Stein, E.G. Rice L.M. and Brunger A.T.' 2 # 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 C OP3 O N N 1 C P P N N 2 C OP1 O N N 3 C OP2 O N N 4 C "O5'" O N N 5 C "C5'" C N N 6 C "C4'" C N R 7 C "O4'" O N N 8 C "C3'" C N S 9 C "O3'" O N N 10 C "C2'" C N R 11 C "O2'" O N N 12 C "C1'" C N R 13 C N1 N N N 14 C C2 C N N 15 C O2 O N N 16 C N3 N N N 17 C C4 C N N 18 C N4 N N N 19 C C5 C N N 20 C C6 C N N 21 C HOP3 H N N 22 C HOP2 H N N 23 C "H5'" H N N 24 C "H5''" H N N 25 C "H4'" H N N 26 C "H3'" H N N 27 C "HO3'" H N N 28 C "H2'" H N N 29 C "HO2'" H N N 30 C "H1'" H N N 31 C H41 H N N 32 C H42 H N N 33 C H5 H N N 34 C H6 H N N 35 G OP3 O N N 36 G P P N N 37 G OP1 O N N 38 G OP2 O N N 39 G "O5'" O N N 40 G "C5'" C N N 41 G "C4'" C N R 42 G "O4'" O N N 43 G "C3'" C N S 44 G "O3'" O N N 45 G "C2'" C N R 46 G "O2'" O N N 47 G "C1'" C N R 48 G N9 N Y N 49 G C8 C Y N 50 G N7 N Y N 51 G C5 C Y N 52 G C6 C N N 53 G O6 O N N 54 G N1 N N N 55 G C2 C N N 56 G N2 N N N 57 G N3 N N N 58 G C4 C Y N 59 G HOP3 H N N 60 G HOP2 H N N 61 G "H5'" H N N 62 G "H5''" H N N 63 G "H4'" H N N 64 G "H3'" H N N 65 G "HO3'" H N N 66 G "H2'" H N N 67 G "HO2'" H N N 68 G "H1'" H N N 69 G H8 H N N 70 G H1 H N N 71 G H21 H N N 72 G H22 H N N 73 U OP3 O N N 74 U P P N N 75 U OP1 O N N 76 U OP2 O N N 77 U "O5'" O N N 78 U "C5'" C N N 79 U "C4'" C N R 80 U "O4'" O N N 81 U "C3'" C N S 82 U "O3'" O N N 83 U "C2'" C N R 84 U "O2'" O N N 85 U "C1'" C N R 86 U N1 N N N 87 U C2 C N N 88 U O2 O N N 89 U N3 N N N 90 U C4 C N N 91 U O4 O N N 92 U C5 C N N 93 U C6 C N N 94 U HOP3 H N N 95 U HOP2 H N N 96 U "H5'" H N N 97 U "H5''" H N N 98 U "H4'" H N N 99 U "H3'" H N N 100 U "HO3'" H N N 101 U "H2'" H N N 102 U "HO2'" H N N 103 U "H1'" H N N 104 U H3 H N N 105 U H5 H N N 106 U H6 H N N 107 # 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 C OP3 P sing N N 1 C OP3 HOP3 sing N N 2 C P OP1 doub N N 3 C P OP2 sing N N 4 C P "O5'" sing N N 5 C OP2 HOP2 sing N N 6 C "O5'" "C5'" sing N N 7 C "C5'" "C4'" sing N N 8 C "C5'" "H5'" sing N N 9 C "C5'" "H5''" sing N N 10 C "C4'" "O4'" sing N N 11 C "C4'" "C3'" sing N N 12 C "C4'" "H4'" sing N N 13 C "O4'" "C1'" sing N N 14 C "C3'" "O3'" sing N N 15 C "C3'" "C2'" sing N N 16 C "C3'" "H3'" sing N N 17 C "O3'" "HO3'" sing N N 18 C "C2'" "O2'" sing N N 19 C "C2'" "C1'" sing N N 20 C "C2'" "H2'" sing N N 21 C "O2'" "HO2'" sing N N 22 C "C1'" N1 sing N N 23 C "C1'" "H1'" sing N N 24 C N1 C2 sing N N 25 C N1 C6 sing N N 26 C C2 O2 doub N N 27 C C2 N3 sing N N 28 C N3 C4 doub N N 29 C C4 N4 sing N N 30 C C4 C5 sing N N 31 C N4 H41 sing N N 32 C N4 H42 sing N N 33 C C5 C6 doub N N 34 C C5 H5 sing N N 35 C C6 H6 sing N N 36 G OP3 P sing N N 37 G OP3 HOP3 sing N N 38 G P OP1 doub N N 39 G P OP2 sing N N 40 G P "O5'" sing N N 41 G OP2 HOP2 sing N N 42 G "O5'" "C5'" sing N N 43 G "C5'" "C4'" sing N N 44 G "C5'" "H5'" sing N N 45 G "C5'" "H5''" sing N N 46 G "C4'" "O4'" sing N N 47 G "C4'" "C3'" sing N N 48 G "C4'" "H4'" sing N N 49 G "O4'" "C1'" sing N N 50 G "C3'" "O3'" sing N N 51 G "C3'" "C2'" sing N N 52 G "C3'" "H3'" sing N N 53 G "O3'" "HO3'" sing N N 54 G "C2'" "O2'" sing N N 55 G "C2'" "C1'" sing N N 56 G "C2'" "H2'" sing N N 57 G "O2'" "HO2'" sing N N 58 G "C1'" N9 sing N N 59 G "C1'" "H1'" sing N N 60 G N9 C8 sing Y N 61 G N9 C4 sing Y N 62 G C8 N7 doub Y N 63 G C8 H8 sing N N 64 G N7 C5 sing Y N 65 G C5 C6 sing N N 66 G C5 C4 doub Y N 67 G C6 O6 doub N N 68 G C6 N1 sing N N 69 G N1 C2 sing N N 70 G N1 H1 sing N N 71 G C2 N2 sing N N 72 G C2 N3 doub N N 73 G N2 H21 sing N N 74 G N2 H22 sing N N 75 G N3 C4 sing N N 76 U OP3 P sing N N 77 U OP3 HOP3 sing N N 78 U P OP1 doub N N 79 U P OP2 sing N N 80 U P "O5'" sing N N 81 U OP2 HOP2 sing N N 82 U "O5'" "C5'" sing N N 83 U "C5'" "C4'" sing N N 84 U "C5'" "H5'" sing N N 85 U "C5'" "H5''" sing N N 86 U "C4'" "O4'" sing N N 87 U "C4'" "C3'" sing N N 88 U "C4'" "H4'" sing N N 89 U "O4'" "C1'" sing N N 90 U "C3'" "O3'" sing N N 91 U "C3'" "C2'" sing N N 92 U "C3'" "H3'" sing N N 93 U "O3'" "HO3'" sing N N 94 U "C2'" "O2'" sing N N 95 U "C2'" "C1'" sing N N 96 U "C2'" "H2'" sing N N 97 U "O2'" "HO2'" sing N N 98 U "C1'" N1 sing N N 99 U "C1'" "H1'" sing N N 100 U N1 C2 sing N N 101 U N1 C6 sing N N 102 U C2 O2 doub N N 103 U C2 N3 sing N N 104 U N3 C4 sing N N 105 U N3 H3 sing N N 106 U C4 O4 doub N N 107 U C4 C5 sing N N 108 U C5 C6 doub N N 109 U C5 H5 sing N N 110 U C6 H6 sing N N 111 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2OJ7 'double helix' 2OJ7 'hairpin loop' 2OJ7 '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 U 8 1_555 -2.253 -0.360 -0.055 1.417 3.723 -3.022 1 A_G11:U18_A A 11 ? A 18 ? 28 ? 1 A C 2 1_555 A G 7 1_555 0.167 0.024 -0.319 7.339 -0.320 5.549 2 A_C12:G17_A A 12 ? A 17 ? 19 1 1 A U 3 1_555 A U 6 1_555 2.696 -1.595 -2.057 33.250 1.019 29.128 3 A_U13:U16_A A 13 ? A 16 ? ? ? # 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 U 8 1_555 A C 2 1_555 A G 7 1_555 0.976 -0.303 4.195 1.699 2.990 37.997 -0.950 -1.218 4.198 4.580 -2.602 38.147 1 AA_G11C12:G17U18_AA A 11 ? A 18 ? A 12 ? A 17 ? 1 A C 2 1_555 A G 7 1_555 A U 3 1_555 A U 6 1_555 1.499 -0.404 3.318 5.224 0.931 37.713 -0.743 -1.606 3.476 1.431 -8.032 38.071 2 AA_C12U13:U16G17_AA A 12 ? A 17 ? A 13 ? A 16 ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 INOVA Varian 500 ? 2 INOVA Varian 800 ? # _atom_sites.entry_id 2OJ7 _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_