data_1Z30 # _entry.id 1Z30 # _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 1Z30 pdb_00001z30 10.2210/pdb1z30/pdb RCSB RCSB032233 ? ? WWPDB D_1000032233 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1Z30 _pdbx_database_status.recvd_initial_deposition_date 2005-03-10 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _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 'Ihle, Y.' 1 'Ohlenschlager, O.' 2 'Duchardt, E.' 3 'Ramachandran, R.' 4 'Gorlach, M.' 5 # _citation.id primary _citation.title 'A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 33 _citation.page_first 2003 _citation.page_last 2011 _citation.year 2005 _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 15814817 _citation.pdbx_database_id_DOI 10.1093/nar/gki501 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ihle, Y.' 1 ? primary 'Ohlenschlager, O.' 2 ? primary 'Hafner, S.' 3 ? primary 'Duchardt, E.' 4 ? primary 'Zacharias, M.' 5 ? primary 'Seitz, S.' 6 ? primary 'Zell, R.' 7 ? primary 'Ramachandran, R.' 8 ? primary 'Gorlach, M.' 9 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-R(*GP*GP*CP*GP*UP*UP*CP*GP*UP*UP*AP*GP*AP*AP*CP*GP*UP*C)-3'" _entity.formula_weight 5765.451 _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 GGCGUUCGUUAGAACGUC _entity_poly.pdbx_seq_one_letter_code_can GGCGUUCGUUAGAACGUC _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 U n 1 6 U n 1 7 C n 1 8 G n 1 9 U n 1 10 U n 1 11 A n 1 12 G n 1 13 A n 1 14 A n 1 15 C n 1 16 G n 1 17 U n 1 18 C 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 naturally exist in bovine enterovirus 1 (Virus)' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1Z30 _struct_ref.pdbx_db_accession 1Z30 _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 1Z30 _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 18 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1Z30 _struct_ref_seq.db_align_beg 1 _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 1 _struct_ref_seq.pdbx_auth_seq_align_end 18 # 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_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 1 298 ambient 6.2 '10mM KH2PO4/K2HPO4, 40mM KCl, 0.2mM EDTA' ? K 2 283 ambient 6.2 '10mM KH2PO4/K2HPO4, 40mM KCl, 0.2mM EDTA' ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1.0mM U-[15N]-BEVSLDap RNA' '90% H2O/10% D2O' 2 '0.9mM U-[13C,15N]-BEVSLDap RNA' '90% H2O/10% D2O' 3 '0.9mM U-[13C,15N]-BEVSLDap RNA' '99.99% D2O' # 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 600 ? 2 INOVA Varian 750 ? # _pdbx_nmr_refine.entry_id 1Z30 _pdbx_nmr_refine.method 'distance geometry, simulated annealing, energy minimisation' _pdbx_nmr_refine.details ;518 upper limit distance constraints derived from NOE cross peaks, 184 torsion angle constraints defining 156 torsion angles, 36 hydrogen bond constraints ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1Z30 _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 15 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy, target function' _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 1Z30 _pdbx_nmr_representative.conformer_id 5 _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal collection VNMR '6.1, rev. c' 'Varian Inc.' 1 processing VNMR '6.1, rev. c' 'Varian Inc.' 2 'data analysis' XEASY 1.3.9 Bartels 3 'structure solution' CYANA 1.0.6 Herrmann 4 'structure solution' FOUND 'implemented in CYANA-1.0.6' Guntert 5 refinement OPAL 2.6 Luginbuhl 6 # _exptl.entry_id 1Z30 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1Z30 _struct.title 'NMR structure of the apical part of stemloop D from cloverleaf 1 of bovine enterovirus 1 RNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1Z30 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'cGUUAg RNA tetraloop, cUNCGg-type backbone conformation, A-form helix, 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 # 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 18 N3 ? ? A G 1 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 18 O2 ? ? A G 1 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 18 N4 ? ? A G 1 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 17 O2 ? ? A G 2 A U 17 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 17 N3 ? ? A G 2 A U 17 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog6 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 16 N1 ? ? A C 3 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 16 O6 ? ? A C 3 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 16 N2 ? ? A C 3 A G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 4 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 4 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 4 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 5 N3 ? ? ? 1_555 A A 14 N1 ? ? A U 5 A A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 5 O4 ? ? ? 1_555 A A 14 N6 ? ? A U 5 A A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 13 N1 ? ? A U 6 A A 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 13 N6 ? ? A U 6 A A 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 12 N1 ? ? A C 7 A G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 12 O6 ? ? A C 7 A G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 12 N2 ? ? A C 7 A G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1Z30 _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 # _atom_sites.entry_id 1Z30 _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 U 5 5 5 U U A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 G 8 8 8 G G A . n A 1 9 U 9 9 9 U U A . n A 1 10 U 10 10 10 U U 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 A 13 13 13 A A A . n A 1 14 A 14 14 14 A A A . n A 1 15 C 15 15 15 C C A . n A 1 16 G 16 16 16 G G A . n A 1 17 U 17 17 17 U U A . n A 1 18 C 18 18 18 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 2005-04-26 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-02 # _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' # 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 # 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' # 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 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.82 108.50 4.32 0.70 N 2 1 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.39 108.50 4.89 0.70 N 3 1 "O4'" A U 6 ? ? "C1'" A U 6 ? ? N1 A U 6 ? ? 112.82 108.50 4.32 0.70 N 4 1 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 113.44 108.50 4.94 0.70 N 5 2 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.19 108.50 4.69 0.70 N 6 2 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 112.93 108.50 4.43 0.70 N 7 3 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.84 108.50 4.34 0.70 N 8 3 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.23 108.50 4.73 0.70 N 9 3 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 112.95 108.50 4.45 0.70 N 10 3 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 112.74 108.50 4.24 0.70 N 11 3 "O4'" A U 17 ? ? "C1'" A U 17 ? ? N1 A U 17 ? ? 112.90 108.50 4.40 0.70 N 12 4 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.95 108.50 4.45 0.70 N 13 4 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.05 108.50 4.55 0.70 N 14 4 "O4'" A U 17 ? ? "C1'" A U 17 ? ? N1 A U 17 ? ? 114.02 108.50 5.52 0.70 N 15 5 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.93 108.50 4.43 0.70 N 16 5 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.27 108.50 4.77 0.70 N 17 5 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 113.09 108.50 4.59 0.70 N 18 5 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 112.81 108.50 4.31 0.70 N 19 6 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.98 108.50 4.48 0.70 N 20 6 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.08 108.50 4.58 0.70 N 21 6 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 113.12 108.50 4.62 0.70 N 22 6 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 113.01 108.50 4.51 0.70 N 23 7 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.55 108.50 5.05 0.70 N 24 7 "O4'" A U 6 ? ? "C1'" A U 6 ? ? N1 A U 6 ? ? 113.28 108.50 4.78 0.70 N 25 8 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 113.02 108.50 4.52 0.70 N 26 8 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.35 108.50 4.85 0.70 N 27 8 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 113.73 108.50 5.23 0.70 N 28 8 "O4'" A U 17 ? ? "C1'" A U 17 ? ? N1 A U 17 ? ? 113.81 108.50 5.31 0.70 N 29 9 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.79 108.50 4.29 0.70 N 30 9 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.34 108.50 4.84 0.70 N 31 9 "O4'" A U 6 ? ? "C1'" A U 6 ? ? N1 A U 6 ? ? 112.90 108.50 4.40 0.70 N 32 9 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 112.94 108.50 4.44 0.70 N 33 10 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 113.10 108.50 4.60 0.70 N 34 10 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.11 108.50 4.61 0.70 N 35 10 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 113.53 108.50 5.03 0.70 N 36 10 "O4'" A U 17 ? ? "C1'" A U 17 ? ? N1 A U 17 ? ? 114.12 108.50 5.62 0.70 N 37 11 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 113.05 108.50 4.55 0.70 N 38 11 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.24 108.50 4.74 0.70 N 39 11 "O4'" A U 6 ? ? "C1'" A U 6 ? ? N1 A U 6 ? ? 112.75 108.50 4.25 0.70 N 40 11 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 113.79 108.50 5.29 0.70 N 41 11 "O4'" A U 17 ? ? "C1'" A U 17 ? ? N1 A U 17 ? ? 114.43 108.50 5.93 0.70 N 42 12 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.84 108.50 4.34 0.70 N 43 12 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.13 108.50 4.63 0.70 N 44 12 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 113.99 108.50 5.49 0.70 N 45 12 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 112.71 108.50 4.21 0.70 N 46 12 "O4'" A U 17 ? ? "C1'" A U 17 ? ? N1 A U 17 ? ? 112.71 108.50 4.21 0.70 N 47 13 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.88 108.50 4.38 0.70 N 48 13 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.23 108.50 4.73 0.70 N 49 13 "O4'" A U 6 ? ? "C1'" A U 6 ? ? N1 A U 6 ? ? 114.06 108.50 5.56 0.70 N 50 13 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 113.85 108.50 5.35 0.70 N 51 13 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 112.89 108.50 4.39 0.70 N 52 14 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 112.98 108.50 4.48 0.70 N 53 14 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 113.36 108.50 4.86 0.70 N 54 15 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 112.91 108.50 4.41 0.70 N 55 15 "O4'" A U 5 ? ? "C1'" A U 5 ? ? N1 A U 5 ? ? 113.63 108.50 5.13 0.70 N 56 15 "O4'" A U 6 ? ? "C1'" A U 6 ? ? N1 A U 6 ? ? 113.51 108.50 5.01 0.70 N 57 15 "O4'" A A 11 ? ? "C1'" A A 11 ? ? N9 A A 11 ? ? 113.07 108.50 4.57 0.70 N 58 15 "O4'" A C 15 ? ? "C1'" A C 15 ? ? N1 A C 15 ? ? 113.00 108.50 4.50 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 8 ? ? 0.066 'SIDE CHAIN' 2 1 A A 11 ? ? 0.101 'SIDE CHAIN' 3 1 G A 12 ? ? 0.052 'SIDE CHAIN' 4 1 G A 16 ? ? 0.074 'SIDE CHAIN' 5 2 G A 4 ? ? 0.065 'SIDE CHAIN' 6 2 G A 8 ? ? 0.060 'SIDE CHAIN' 7 2 A A 11 ? ? 0.088 'SIDE CHAIN' 8 2 G A 16 ? ? 0.068 'SIDE CHAIN' 9 3 G A 4 ? ? 0.069 'SIDE CHAIN' 10 3 G A 8 ? ? 0.060 'SIDE CHAIN' 11 3 A A 11 ? ? 0.064 'SIDE CHAIN' 12 3 G A 16 ? ? 0.074 'SIDE CHAIN' 13 4 G A 8 ? ? 0.070 'SIDE CHAIN' 14 5 G A 8 ? ? 0.075 'SIDE CHAIN' 15 5 A A 11 ? ? 0.063 'SIDE CHAIN' 16 5 G A 16 ? ? 0.079 'SIDE CHAIN' 17 6 G A 4 ? ? 0.066 'SIDE CHAIN' 18 6 U A 5 ? ? 0.063 'SIDE CHAIN' 19 6 A A 11 ? ? 0.088 'SIDE CHAIN' 20 6 G A 12 ? ? 0.062 'SIDE CHAIN' 21 6 G A 16 ? ? 0.077 'SIDE CHAIN' 22 7 G A 8 ? ? 0.062 'SIDE CHAIN' 23 7 A A 11 ? ? 0.081 'SIDE CHAIN' 24 7 G A 12 ? ? 0.058 'SIDE CHAIN' 25 7 G A 16 ? ? 0.058 'SIDE CHAIN' 26 8 G A 8 ? ? 0.058 'SIDE CHAIN' 27 8 A A 11 ? ? 0.079 'SIDE CHAIN' 28 9 G A 8 ? ? 0.056 'SIDE CHAIN' 29 9 A A 11 ? ? 0.090 'SIDE CHAIN' 30 9 G A 16 ? ? 0.080 'SIDE CHAIN' 31 10 G A 8 ? ? 0.050 'SIDE CHAIN' 32 11 G A 12 ? ? 0.065 'SIDE CHAIN' 33 12 G A 4 ? ? 0.064 'SIDE CHAIN' 34 12 A A 11 ? ? 0.069 'SIDE CHAIN' 35 12 G A 12 ? ? 0.070 'SIDE CHAIN' 36 12 G A 16 ? ? 0.074 'SIDE CHAIN' 37 13 A A 11 ? ? 0.084 'SIDE CHAIN' 38 13 G A 16 ? ? 0.058 'SIDE CHAIN' 39 14 G A 4 ? ? 0.063 'SIDE CHAIN' 40 14 A A 11 ? ? 0.082 'SIDE CHAIN' 41 14 G A 12 ? ? 0.055 'SIDE CHAIN' 42 15 G A 8 ? ? 0.066 'SIDE CHAIN' 43 15 G A 12 ? ? 0.065 'SIDE CHAIN' 44 15 G A 16 ? ? 0.061 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1Z30 'a-form double helix' 1Z30 'hairpin loop' 1Z30 '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 18 1_555 -0.462 -0.138 -0.586 -13.381 -9.569 -0.187 1 A_G1:C18_A A 1 ? A 18 ? 19 1 1 A G 2 1_555 A U 17 1_555 -1.972 -0.266 0.019 -1.525 -13.478 5.243 2 A_G2:U17_A A 2 ? A 17 ? 28 1 1 A C 3 1_555 A G 16 1_555 0.481 -0.133 -0.080 0.433 -14.218 0.308 3 A_C3:G16_A A 3 ? A 16 ? 19 1 1 A G 4 1_555 A C 15 1_555 -0.054 -0.038 -0.038 -12.677 -20.395 -0.550 4 A_G4:C15_A A 4 ? A 15 ? 19 1 1 A U 5 1_555 A A 14 1_555 -0.106 0.021 0.408 -7.263 -7.535 -5.018 5 A_U5:A14_A A 5 ? A 14 ? 20 1 1 A U 6 1_555 A A 13 1_555 -0.272 0.094 -0.034 12.019 -9.695 -5.178 6 A_U6:A13_A A 6 ? A 13 ? 20 1 1 A C 7 1_555 A G 12 1_555 0.679 -0.107 -0.408 22.480 -16.559 0.614 7 A_C7:G12_A A 7 ? A 12 ? 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 18 1_555 A G 2 1_555 A U 17 1_555 0.585 -1.401 2.883 -7.408 11.445 24.363 -5.008 -2.573 1.806 24.792 16.048 27.868 1 AA_G1G2:U17C18_AA A 1 ? A 18 ? A 2 ? A 17 ? 1 A G 2 1_555 A U 17 1_555 A C 3 1_555 A G 16 1_555 -0.514 -0.854 3.212 0.052 4.174 43.220 -1.547 0.699 3.119 5.651 -0.071 43.411 2 AA_G2C3:G16U17_AA A 2 ? A 17 ? A 3 ? A 16 ? 1 A C 3 1_555 A G 16 1_555 A G 4 1_555 A C 15 1_555 0.265 -1.378 3.462 2.327 15.191 30.902 -4.625 -0.095 2.541 26.550 -4.068 34.429 3 AA_C3G4:C15G16_AA A 3 ? A 16 ? A 4 ? A 15 ? 1 A G 4 1_555 A C 15 1_555 A U 5 1_555 A A 14 1_555 -0.266 -1.438 3.218 -4.607 -0.407 31.484 -2.549 -0.350 3.241 -0.745 8.433 31.814 4 AA_G4U5:A14C15_AA A 4 ? A 15 ? A 5 ? A 14 ? 1 A U 5 1_555 A A 14 1_555 A U 6 1_555 A A 13 1_555 -0.048 -1.371 2.933 2.739 -7.440 29.751 -1.205 0.599 3.158 -14.176 -5.220 30.766 5 AA_U5U6:A13A14_AA A 5 ? A 14 ? A 6 ? A 13 ? 1 A U 6 1_555 A A 13 1_555 A C 7 1_555 A G 12 1_555 0.392 -0.794 3.158 3.885 -0.670 33.864 -1.251 -0.068 3.196 -1.146 -6.641 34.086 6 AA_U6C7:G12A13_AA A 6 ? A 13 ? A 7 ? A 12 ? #