data_2JYM # _entry.id 2JYM # _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 2JYM pdb_00002jym 10.2210/pdb2jym/pdb RCSB RCSB100453 ? ? WWPDB D_1000100453 ? ? # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2JYM _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2007-12-14 _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 'Ohlenschlager, O.' 1 'Gorlach, M.' 2 'Schwalbe, M.' 3 # _citation.id primary _citation.title 'Solution structure of stem-loop alpha of the hepatitis B virus post-transcriptional regulatory element' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 36 _citation.page_first 1681 _citation.page_last 1689 _citation.year 2008 _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 18263618 _citation.pdbx_database_id_DOI 10.1093/nar/gkn006 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Schwalbe, M.' 1 ? primary 'Ohlenschlager, O.' 2 ? primary 'Marchanka, A.' 3 ? primary 'Ramachandran, R.' 4 ? primary 'Hafner, S.' 5 ? primary 'Heise, T.' 6 ? primary 'Gorlach, M.' 7 ? # _cell.entry_id 2JYM _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 2JYM _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 syn _entity.pdbx_description ;RNA (5'-R(*GP*GP*CP*UP*CP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*UP*GP*GP*AP*GP*UP*C)-3') ; _entity.formula_weight 7105.267 _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 GGCUCGCAGCAGGUCUGGAGUC _entity_poly.pdbx_seq_one_letter_code_can GGCUCGCAGCAGGUCUGGAGUC _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 U n 1 5 C n 1 6 G n 1 7 C n 1 8 A n 1 9 G n 1 10 C n 1 11 A n 1 12 G n 1 13 G n 1 14 U n 1 15 C n 1 16 U n 1 17 G n 1 18 G n 1 19 A n 1 20 G n 1 21 U n 1 22 C n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2JYM _struct_ref.pdbx_db_accession 2JYM _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GGCUCGCAGCAGGUCUGGAGUC _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2JYM _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 22 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2JYM _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 22 _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 22 # 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-15N HSQC' 2 2 1 '2D 1H-13C HSQC' 2 3 2 '2D 1H-13C HSQC' 1 4 1 '2D 1H-1H NOESY' 2 5 2 '3D 1H-13C NOESY' 2 6 2 '3D HCCH-TOCSY' # 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 50 6.2 ambient atm 283 K 2 50 6.2 ambient atm 293 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '1mM [U-100% 13C; U-100% 15N] RNA, 10mM potassium phosphate, 40mM potassium chloride, 0. mM EDTA, 90% H2O/10% D2O' 1 '90% H2O/10% D2O' '1mM [U-100% 13C; U-100% 15N] RNA, 10mM potassium phosphate, 40mM potassium chloride, 0.2mM EDTA, 99% D2O' 2 '99% 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 Varian INOVA 1 'Varian INOVA' 750 Varian INOVA 2 'Varian INOVA' # _pdbx_nmr_refine.entry_id 2JYM _pdbx_nmr_refine.method 'DGSA-distance geometry simulated annealing, force field-based em' _pdbx_nmr_refine.details 'structure calculation, energy minimisation' _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 'target function' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 15 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2JYM _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 2JYM _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Guntert, Mumenthaler and Wuthrich' 'structure solution' CYANA 2.0 1 'Bartels et al.' 'peak picking' XEASY ? 2 'Bartels et al.' 'chemical shift assignment' XEASY ? 3 Varian processing VNMR ? 4 Varian collection VNMR ? 5 'Luginbuhl, Guntert, Billeter and Wuthrich' refinement OPAL ? 6 'Luginbuhl, Guntert, Billeter and Wuthrich' collection OPAL ? 7 # _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 2JYM _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2JYM _struct.title 'Solution structure of stem-loop alpha of the hepatitis B virus post-transcriptional regulatory element' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2JYM _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'hepatitis B virus, post-transcriptional regulatory element, stem-loop alpha, NMR solution structure, 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 22 N3 ? ? A G 1 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 22 O2 ? ? A G 1 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 22 N4 ? ? A G 1 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 21 O2 ? ? A G 2 A U 21 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 21 N3 ? ? A G 2 A U 21 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog6 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 3 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 3 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 3 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 19 N1 ? ? A U 4 A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 19 N6 ? ? A U 4 A A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 18 N1 ? ? A C 5 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 18 O6 ? ? A C 5 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 18 N2 ? ? A C 5 A G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 7 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 7 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 7 A G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 16 N3 ? ? A A 8 A U 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 16 O4 ? ? A A 8 A U 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 9 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 9 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 9 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 13 N1 ? ? A C 10 A G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 13 O6 ? ? A C 10 A G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 13 N2 ? ? A C 10 A G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2JYM _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 U 4 4 4 U U A . n A 1 5 C 5 5 5 C C A . n A 1 6 G 6 6 6 G G A . n A 1 7 C 7 7 7 C C A . n A 1 8 A 8 8 8 A A A . n A 1 9 G 9 9 9 G G A . n A 1 10 C 10 10 10 C C A . n A 1 11 A 11 11 11 A A A . n A 1 12 G 12 12 12 G G 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 C 15 15 15 C C A . n A 1 16 U 16 16 16 U U A . n A 1 17 G 17 17 17 G G A . n A 1 18 G 18 18 18 G G A . n A 1 19 A 19 19 19 A A A . n A 1 20 G 20 20 20 G G A . n A 1 21 U 21 21 21 U U A . n A 1 22 C 22 22 22 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 2008-04-29 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' 'Database references' 3 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_struct_assembly 3 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' # 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 1 mM '[U-100% 13C; U-100% 15N]' 1 'potassium phosphate' 10 mM ? 1 'potassium chloride' 40 mM ? 1 EDTA 0.2 mM ? 1 RNA 1 mM '[U-100% 13C; U-100% 15N]' 2 'potassium phosphate' 10 mM ? 2 'potassium chloride' 40 mM ? 2 EDTA 0.2 mM ? 2 # 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 "O4'" A C 10 ? ? "C1'" A C 10 ? ? N1 A C 10 ? ? 113.66 108.50 5.16 0.70 N 2 1 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 113.96 108.50 5.46 0.70 N 3 1 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 114.21 108.50 5.71 0.70 N 4 1 "O4'" A G 18 ? ? "C1'" A G 18 ? ? N9 A G 18 ? ? 112.91 108.50 4.41 0.70 N 5 2 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 113.49 108.50 4.99 0.70 N 6 2 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 112.92 108.50 4.42 0.70 N 7 2 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.60 108.50 5.10 0.70 N 8 3 "O4'" A G 6 ? ? "C1'" A G 6 ? ? N9 A G 6 ? ? 112.99 108.50 4.49 0.70 N 9 3 "O4'" A C 10 ? ? "C1'" A C 10 ? ? N1 A C 10 ? ? 112.89 108.50 4.39 0.70 N 10 3 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 112.86 108.50 4.36 0.70 N 11 3 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 113.35 108.50 4.85 0.70 N 12 3 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.34 108.50 4.84 0.70 N 13 4 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 113.34 108.50 4.84 0.70 N 14 4 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.15 108.50 4.65 0.70 N 15 4 "O4'" A U 21 ? ? "C1'" A U 21 ? ? N1 A U 21 ? ? 113.36 108.50 4.86 0.70 N 16 5 "O4'" A C 10 ? ? "C1'" A C 10 ? ? N1 A C 10 ? ? 112.92 108.50 4.42 0.70 N 17 5 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 114.64 108.50 6.14 0.70 N 18 5 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.77 108.50 5.27 0.70 N 19 6 "O4'" A C 10 ? ? "C1'" A C 10 ? ? N1 A C 10 ? ? 112.77 108.50 4.27 0.70 N 20 6 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 113.48 108.50 4.98 0.70 N 21 6 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.71 108.50 5.21 0.70 N 22 7 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 114.72 108.50 6.22 0.70 N 23 7 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 113.45 108.50 4.95 0.70 N 24 7 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.39 108.50 4.89 0.70 N 25 7 "O4'" A U 21 ? ? "C1'" A U 21 ? ? N1 A U 21 ? ? 113.79 108.50 5.29 0.70 N 26 8 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 112.98 108.50 4.48 0.70 N 27 8 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 113.42 108.50 4.92 0.70 N 28 8 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.70 108.50 5.20 0.70 N 29 8 "O4'" A U 21 ? ? "C1'" A U 21 ? ? N1 A U 21 ? ? 113.94 108.50 5.44 0.70 N 30 9 "O4'" A C 10 ? ? "C1'" A C 10 ? ? N1 A C 10 ? ? 113.60 108.50 5.10 0.70 N 31 9 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 113.78 108.50 5.28 0.70 N 32 9 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.42 108.50 4.92 0.70 N 33 10 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 113.09 108.50 4.59 0.70 N 34 10 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 114.40 108.50 5.90 0.70 N 35 11 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 113.24 108.50 4.74 0.70 N 36 11 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 112.84 108.50 4.34 0.70 N 37 11 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 114.00 108.50 5.50 0.70 N 38 12 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 114.03 108.50 5.53 0.70 N 39 12 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.22 108.50 4.72 0.70 N 40 13 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 114.23 108.50 5.73 0.70 N 41 13 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.35 108.50 4.85 0.70 N 42 13 "O4'" A U 21 ? ? "C1'" A U 21 ? ? N1 A U 21 ? ? 113.80 108.50 5.30 0.70 N 43 14 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.74 108.50 4.24 0.70 N 44 14 "O4'" A C 10 ? ? "C1'" A C 10 ? ? N1 A C 10 ? ? 113.03 108.50 4.53 0.70 N 45 14 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 113.38 108.50 4.88 0.70 N 46 14 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.24 108.50 4.74 0.70 N 47 15 "O4'" A C 10 ? ? "C1'" A C 10 ? ? N1 A C 10 ? ? 113.51 108.50 5.01 0.70 N 48 15 "O4'" A G 13 ? ? "C1'" A G 13 ? ? N9 A G 13 ? ? 113.40 108.50 4.90 0.70 N 49 15 "O4'" A U 16 ? ? "C1'" A U 16 ? ? N1 A U 16 ? ? 113.22 108.50 4.72 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 G A 2 ? ? 0.062 'SIDE CHAIN' 2 1 C A 7 ? ? 0.068 'SIDE CHAIN' 3 1 A A 8 ? ? 0.083 'SIDE CHAIN' 4 1 G A 9 ? ? 0.082 'SIDE CHAIN' 5 1 G A 13 ? ? 0.076 'SIDE CHAIN' 6 1 U A 16 ? ? 0.068 'SIDE CHAIN' 7 1 G A 17 ? ? 0.053 'SIDE CHAIN' 8 1 C A 22 ? ? 0.070 'SIDE CHAIN' 9 2 G A 2 ? ? 0.072 'SIDE CHAIN' 10 2 C A 7 ? ? 0.062 'SIDE CHAIN' 11 2 A A 8 ? ? 0.077 'SIDE CHAIN' 12 2 G A 9 ? ? 0.083 'SIDE CHAIN' 13 2 G A 12 ? ? 0.068 'SIDE CHAIN' 14 2 G A 13 ? ? 0.063 'SIDE CHAIN' 15 2 U A 16 ? ? 0.091 'SIDE CHAIN' 16 2 G A 17 ? ? 0.053 'SIDE CHAIN' 17 3 G A 2 ? ? 0.079 'SIDE CHAIN' 18 3 A A 8 ? ? 0.056 'SIDE CHAIN' 19 3 A A 11 ? ? 0.064 'SIDE CHAIN' 20 3 G A 13 ? ? 0.054 'SIDE CHAIN' 21 3 U A 16 ? ? 0.073 'SIDE CHAIN' 22 3 G A 17 ? ? 0.072 'SIDE CHAIN' 23 4 A A 8 ? ? 0.097 'SIDE CHAIN' 24 4 G A 9 ? ? 0.076 'SIDE CHAIN' 25 4 A A 11 ? ? 0.078 'SIDE CHAIN' 26 4 G A 12 ? ? 0.084 'SIDE CHAIN' 27 4 G A 13 ? ? 0.064 'SIDE CHAIN' 28 4 G A 17 ? ? 0.058 'SIDE CHAIN' 29 5 G A 2 ? ? 0.059 'SIDE CHAIN' 30 5 C A 7 ? ? 0.065 'SIDE CHAIN' 31 5 A A 8 ? ? 0.075 'SIDE CHAIN' 32 5 G A 13 ? ? 0.067 'SIDE CHAIN' 33 5 C A 22 ? ? 0.063 'SIDE CHAIN' 34 6 G A 2 ? ? 0.059 'SIDE CHAIN' 35 6 C A 7 ? ? 0.082 'SIDE CHAIN' 36 6 A A 8 ? ? 0.078 'SIDE CHAIN' 37 6 A A 11 ? ? 0.065 'SIDE CHAIN' 38 6 G A 13 ? ? 0.077 'SIDE CHAIN' 39 7 A A 8 ? ? 0.076 'SIDE CHAIN' 40 7 G A 13 ? ? 0.080 'SIDE CHAIN' 41 7 U A 16 ? ? 0.063 'SIDE CHAIN' 42 8 C A 7 ? ? 0.071 'SIDE CHAIN' 43 8 A A 8 ? ? 0.088 'SIDE CHAIN' 44 8 C A 10 ? ? 0.062 'SIDE CHAIN' 45 8 U A 16 ? ? 0.067 'SIDE CHAIN' 46 8 G A 17 ? ? 0.047 'SIDE CHAIN' 47 9 A A 8 ? ? 0.062 'SIDE CHAIN' 48 9 G A 9 ? ? 0.074 'SIDE CHAIN' 49 9 G A 12 ? ? 0.059 'SIDE CHAIN' 50 9 G A 13 ? ? 0.051 'SIDE CHAIN' 51 9 U A 16 ? ? 0.096 'SIDE CHAIN' 52 9 G A 17 ? ? 0.069 'SIDE CHAIN' 53 10 G A 2 ? ? 0.065 'SIDE CHAIN' 54 10 C A 7 ? ? 0.079 'SIDE CHAIN' 55 10 A A 8 ? ? 0.082 'SIDE CHAIN' 56 10 G A 9 ? ? 0.065 'SIDE CHAIN' 57 10 C A 15 ? ? 0.067 'SIDE CHAIN' 58 10 G A 17 ? ? 0.049 'SIDE CHAIN' 59 10 C A 22 ? ? 0.067 'SIDE CHAIN' 60 11 G A 2 ? ? 0.057 'SIDE CHAIN' 61 11 C A 7 ? ? 0.083 'SIDE CHAIN' 62 11 A A 8 ? ? 0.056 'SIDE CHAIN' 63 11 G A 9 ? ? 0.066 'SIDE CHAIN' 64 11 G A 12 ? ? 0.065 'SIDE CHAIN' 65 11 G A 13 ? ? 0.058 'SIDE CHAIN' 66 11 U A 16 ? ? 0.070 'SIDE CHAIN' 67 12 G A 12 ? ? 0.065 'SIDE CHAIN' 68 12 G A 13 ? ? 0.062 'SIDE CHAIN' 69 12 U A 16 ? ? 0.083 'SIDE CHAIN' 70 12 G A 17 ? ? 0.062 'SIDE CHAIN' 71 12 C A 22 ? ? 0.068 'SIDE CHAIN' 72 13 A A 8 ? ? 0.077 'SIDE CHAIN' 73 13 U A 16 ? ? 0.076 'SIDE CHAIN' 74 13 G A 17 ? ? 0.062 'SIDE CHAIN' 75 14 G A 12 ? ? 0.068 'SIDE CHAIN' 76 14 G A 13 ? ? 0.064 'SIDE CHAIN' 77 14 U A 16 ? ? 0.092 'SIDE CHAIN' 78 14 G A 17 ? ? 0.067 'SIDE CHAIN' 79 14 C A 22 ? ? 0.059 'SIDE CHAIN' 80 15 A A 8 ? ? 0.050 'SIDE CHAIN' 81 15 A A 11 ? ? 0.057 'SIDE CHAIN' 82 15 G A 13 ? ? 0.069 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2JYM 'a-form double helix' 2JYM 'hairpin loop' 2JYM 'bulge loop' 2JYM '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 22 1_555 -0.540 -0.149 -0.129 3.708 -4.733 -0.906 1 A_G1:C22_A A 1 ? A 22 ? 19 1 1 A G 2 1_555 A U 21 1_555 -2.077 -0.110 0.410 5.936 -15.345 9.282 2 A_G2:U21_A A 2 ? A 21 ? 28 1 1 A C 3 1_555 A G 20 1_555 0.598 -0.179 0.023 4.142 -19.983 -0.143 3 A_C3:G20_A A 3 ? A 20 ? 19 1 1 A U 4 1_555 A A 19 1_555 -0.023 0.007 0.062 -0.806 -10.191 -2.198 4 A_U4:A19_A A 4 ? A 19 ? 20 1 1 A C 5 1_555 A G 18 1_555 0.110 -0.018 -0.373 18.562 -9.834 -0.303 5 A_C5:G18_A A 5 ? A 18 ? 19 1 1 A C 7 1_555 A G 17 1_555 0.387 0.067 -0.447 32.545 -26.996 1.689 6 A_C7:G17_A A 7 ? A 17 ? 19 1 1 A A 8 1_555 A U 16 1_555 -0.237 0.096 -0.040 -7.933 -11.110 10.588 7 A_A8:U16_A A 8 ? A 16 ? 20 1 1 A G 9 1_555 A C 15 1_555 -0.246 -0.094 0.121 -6.420 -7.908 -3.647 8 A_G9:C15_A A 9 ? A 15 ? 19 1 1 A C 10 1_555 A G 13 1_555 0.315 -0.135 -0.493 -2.933 9.185 -3.293 9 A_C10:G13_A A 10 ? A 13 ? 19 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 22 1_555 A G 2 1_555 A U 21 1_555 0.375 -2.122 2.860 -8.284 9.683 26.626 -5.723 -2.064 1.801 19.658 16.818 29.469 1 AA_G1G2:U21C22_AA A 1 ? A 22 ? A 2 ? A 21 ? 1 A G 2 1_555 A U 21 1_555 A C 3 1_555 A G 20 1_555 -0.893 -1.136 3.265 0.037 3.301 45.536 -1.749 1.154 3.179 4.258 -0.048 45.649 2 AA_G2C3:G20U21_AA A 2 ? A 21 ? A 3 ? A 20 ? 1 A C 3 1_555 A G 20 1_555 A U 4 1_555 A A 19 1_555 -0.162 -1.513 3.281 1.657 10.552 29.422 -4.657 0.591 2.584 19.966 -3.136 31.260 3 AA_C3U4:A19G20_AA A 3 ? A 20 ? A 4 ? A 19 ? 1 A U 4 1_555 A A 19 1_555 A C 5 1_555 A G 18 1_555 0.299 -1.002 2.873 3.118 2.383 28.503 -2.482 0.007 2.798 4.810 -6.294 28.767 4 AA_U4C5:G18A19_AA A 4 ? A 19 ? A 5 ? A 18 ? 1 A C 5 1_555 A G 18 1_555 A C 7 1_555 A G 17 1_555 -0.844 0.531 3.546 4.405 -11.467 48.748 1.500 1.331 3.268 -13.642 -5.241 50.180 5 AA_C5C7:G17G18_AA A 5 ? A 18 ? A 7 ? A 17 ? 1 A C 7 1_555 A G 17 1_555 A A 8 1_555 A U 16 1_555 -0.106 -1.349 4.185 -5.751 11.115 39.283 -3.400 -0.616 3.667 16.046 8.303 41.153 6 AA_C7A8:U16G17_AA A 7 ? A 17 ? A 8 ? A 16 ? 1 A A 8 1_555 A U 16 1_555 A G 9 1_555 A C 15 1_555 -1.271 -1.617 3.340 -3.726 -4.008 33.884 -2.068 1.530 3.617 -6.821 6.341 34.310 7 AA_A8G9:C15U16_AA A 8 ? A 16 ? A 9 ? A 15 ? 1 A G 9 1_555 A C 15 1_555 A C 10 1_555 A G 13 1_555 -0.504 -2.556 3.309 7.128 0.439 19.045 -7.436 4.567 2.873 1.271 -20.628 20.329 8 AA_G9C10:G13C15_AA A 9 ? A 15 ? A 10 ? A 13 ? #