data_1FL8 # _entry.id 1FL8 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1FL8 pdb_00001fl8 10.2210/pdb1fl8/pdb RCSB RCSB011684 ? ? WWPDB D_1000011684 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1BZU 'the same anticodon loop sequence but without modified nucleosides at position 34 and 37. Pseudouridine is present at postion 39' unspecified PDB 1BZ2 'the same anticodon loop sequence but without modified nucleosides at position 34, 37 or 39' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1FL8 _pdbx_database_status.recvd_initial_deposition_date 2000-08-11 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _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 'Sundaram, M.' 1 'Durant, P.C.' 2 'Davis, D.R.' 3 # _citation.id primary _citation.title 'Hypermodified nucleosides in the anticodon of tRNALys stabilize a canonical U-turn structure.' _citation.journal_abbrev Biochemistry _citation.journal_volume 39 _citation.page_first 12575 _citation.page_last 12584 _citation.year 2000 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 11027137 _citation.pdbx_database_id_DOI 10.1021/bi0014655 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sundaram, M.' 1 ? primary 'Durant, P.C.' 2 ? primary 'Davis, D.R.' 3 ? # _cell.entry_id 1FL8 _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 1FL8 _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 'ANTICODON DOMAIN OF TRNA(LYS)' _entity.formula_weight 5554.438 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation 'G27U, U28C, U29A, A41U, A42G, U43A' _entity.pdbx_fragment '17-MER TRNA(LYS) ANTICODON DOMAIN' _entity.details ;RESIDUES 30-40 (TRNA NUMBERING) ARE IDENTICAL TO THOSE FOUND IN THE ANTICODON DOMAIN OF E. COLI TRNA(LYS) INCLUDING MODIFIED NUCLEOSIDES ; # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'UCAGACU(U8U)UU(T6A)A(PSU)CUGA' _entity_poly.pdbx_seq_one_letter_code_can UCAGACUUUUAAUCUGA _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 U n 1 2 C n 1 3 A n 1 4 G n 1 5 A n 1 6 C n 1 7 U n 1 8 U8U n 1 9 U n 1 10 U n 1 11 T6A n 1 12 A n 1 13 PSU n 1 14 C n 1 15 U n 1 16 G n 1 17 A n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1FL8 _struct_ref.pdbx_db_accession 1FL8 _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 1FL8 _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 17 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1FL8 _struct_ref_seq.db_align_beg 27 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 43 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 27 _struct_ref_seq.pdbx_auth_seq_align_end 43 # 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 PSU 'RNA linking' n "PSEUDOURIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 T6A 'RNA linking' n "N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL)CARBAMOYL]THREONINE-5'-MONOPHOSPHATE" "N-(NEBULARIN-6-YLCARBAMOYL)-L-THREONINE-5'-MONOPHOSPHATE" 'C15 H21 N6 O11 P' 492.335 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 U8U 'RNA linking' n "5-METHYLAMINOMETHYL-2-THIOURIDINE-5'-MONOPHOSPHATE" ? 'C11 H18 N3 O8 P S' 383.315 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 2 1 '2D NOESY' 3 2 1 DQF-COSY 4 2 1 1H-31P-COSY 5 2 1 1H-31P-hetero-TOCSY-TOCSY # 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 1 285 ambient 7 120mM ? K 2 303 ambient 7 120mM ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1.5mM natural abundance RNA; 10mM phosphate buffer; 50mM KCl; 50mM NaCl; 10mM MgCl2' '90% H2O/10% D2O' 2 '1.5mM natural abundance RNA; 10mM phosphate buffer; 50mM KCl; 50mM NaCl; 10mM MgCl2' '99.99% D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.field_strength 1 ? Varian UNITYPLUS 600 2 ? Varian UNITY 500 # _pdbx_nmr_refine.entry_id 1FL8 _pdbx_nmr_refine.method ;used H5-H6 distances for distance calculations then simulated annealing/molecular dynamics in vacuo then restrained minimization in vacuo ; _pdbx_nmr_refine.details ;123 NOE-derived restraints, 15 hydrogen bond restraints, 102 lower/upper bound restraints, 161 dihedral restraints, 68 chiral restraints ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1FL8 _pdbx_nmr_details.text 'This structure was determined using standard 2D homonuclear techniques and standard 1H-31P 2D correlation experiments.' # _pdbx_nmr_ensemble.entry_id 1FL8 _pdbx_nmr_ensemble.conformers_calculated_total_number 35 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _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 1FL8 _pdbx_nmr_representative.conformer_id 4 _pdbx_nmr_representative.selection_criteria 'closest to the average,lowest energy' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal VNMR 6.1B collection Varian 1 VNMR 6.1B processing Varian 2 VNMR 6.1B 'data analysis' Varian 3 Felix ? processing MSI 4 Felix ? 'data analysis' MSI 5 Discover ? 'structure solution' MSI 6 Discover ? refinement MSI 7 # _exptl.entry_id 1FL8 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1FL8 _struct.title 'HYPERMODIFIED NUCLEOSIDES IN THE ANTICODON OF TRNALYS STABILIZE A CANONICAL U-TURN STRUCTURE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1FL8 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'tRNA, anticodon, pseudouridine, mnm5s2U, t6a, 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 covale1 covale both ? A U 7 "O3'" ? ? ? 1_555 A U8U 8 P ? ? A U 33 A U8U 34 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale2 covale both ? A U8U 8 "O3'" ? ? ? 1_555 A U 9 P ? ? A U8U 34 A U 35 1_555 ? ? ? ? ? ? ? 1.621 ? ? covale3 covale both ? A U 10 "O3'" ? ? ? 1_555 A T6A 11 P ? ? A U 36 A T6A 37 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale4 covale both ? A T6A 11 "O3'" ? ? ? 1_555 A A 12 P ? ? A T6A 37 A A 38 1_555 ? ? ? ? ? ? ? 1.624 ? ? covale5 covale both ? A A 12 "O3'" ? ? ? 1_555 A PSU 13 P ? ? A A 38 A PSU 39 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale6 covale both ? A PSU 13 "O3'" ? ? ? 1_555 A C 14 P ? ? A PSU 39 A C 40 1_555 ? ? ? ? ? ? ? 1.622 ? ? hydrog1 hydrog ? ? A U 1 N3 ? ? ? 1_555 A A 17 N1 ? ? A U 27 A A 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A U 1 O4 ? ? ? 1_555 A A 17 N6 ? ? A U 27 A A 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 16 N1 ? ? A C 28 A G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 16 O6 ? ? A C 28 A G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 16 N2 ? ? A C 28 A G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 15 N3 ? ? A A 29 A U 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 15 O4 ? ? A A 29 A U 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 14 N3 ? ? A G 30 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 14 O2 ? ? A G 30 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 14 N4 ? ? A G 30 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 5 N1 ? ? ? 1_555 A PSU 13 N3 ? ? A A 31 A PSU 39 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog12 hydrog ? ? A A 5 N6 ? ? ? 1_555 A PSU 13 O2 ? ? A A 31 A PSU 39 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1FL8 _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 1FL8 _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 S # 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 U 1 27 27 U U A . n A 1 2 C 2 28 28 C C A . n A 1 3 A 3 29 29 A A A . n A 1 4 G 4 30 30 G G A . n A 1 5 A 5 31 31 A A A . n A 1 6 C 6 32 32 C C A . n A 1 7 U 7 33 33 U U A . n A 1 8 U8U 8 34 34 U8U U8U A . n A 1 9 U 9 35 35 U U A . n A 1 10 U 10 36 36 U U A . n A 1 11 T6A 11 37 37 T6A T6A A . n A 1 12 A 12 38 38 A A A . n A 1 13 PSU 13 39 39 PSU PSU A . n A 1 14 C 14 40 40 C C A . n A 1 15 U 15 41 41 U U A . n A 1 16 G 16 42 42 G G A . n A 1 17 A 17 43 43 A A A . n # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A U8U 8 A U8U 34 ? U ? 2 A T6A 11 A T6A 37 ? A ? 3 A PSU 13 A PSU 39 ? U "PSEUDOURIDINE-5'-MONOPHOSPHATE" # _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 2000-10-16 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _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' 'Data collection' 4 4 'Structure model' 'Database references' 5 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_nmr_software 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list 5 4 'Structure model' struct_conn # 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' 3 4 'Structure model' '_pdbx_nmr_software.name' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # 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 32 ? ? "C1'" A C 32 ? ? N1 A C 32 ? ? 112.71 108.50 4.21 0.70 N 2 1 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.15 119.70 -7.55 1.20 Y 3 2 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.06 119.70 -7.64 1.20 Y 4 3 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.21 119.70 -7.49 1.20 Y 5 4 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.19 119.70 -7.51 1.20 Y 6 5 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.38 119.70 -7.32 1.20 Y 7 6 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.17 119.70 -7.53 1.20 Y 8 7 "O4'" A C 32 ? ? "C1'" A C 32 ? ? N1 A C 32 ? ? 112.75 108.50 4.25 0.70 N 9 7 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.37 119.70 -7.33 1.20 Y 10 8 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.29 119.70 -7.41 1.20 Y 11 9 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.19 119.70 -7.51 1.20 Y 12 10 "O4'" A C 32 ? ? "C1'" A C 32 ? ? N1 A C 32 ? ? 112.73 108.50 4.23 0.70 N 13 10 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.30 119.70 -7.40 1.20 Y 14 10 "C3'" A PSU 39 ? ? "O3'" A PSU 39 ? ? P A C 40 ? ? 112.49 119.70 -7.21 1.20 Y 15 11 "O4'" A C 32 ? ? "C1'" A C 32 ? ? N1 A C 32 ? ? 112.75 108.50 4.25 0.70 N 16 11 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.04 119.70 -7.66 1.20 Y 17 12 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.29 119.70 -7.41 1.20 Y 18 13 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.09 119.70 -7.61 1.20 Y 19 14 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.14 119.70 -7.56 1.20 Y 20 15 "O4'" A U 33 ? ? "C1'" A U 33 ? ? N1 A U 33 ? ? 112.70 108.50 4.20 0.70 N 21 16 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.18 119.70 -7.52 1.20 Y 22 17 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.20 119.70 -7.50 1.20 Y 23 18 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.28 119.70 -7.42 1.20 Y 24 19 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.19 119.70 -7.51 1.20 Y 25 20 "C3'" A U8U 34 ? ? "O3'" A U8U 34 ? ? P A U 35 ? ? 112.16 119.70 -7.54 1.20 Y # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1FL8 'a-form double helix' 1FL8 'hairpin loop' 1FL8 '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 U 1 1_555 A A 17 1_555 0.651 0.183 -0.767 -1.839 -11.710 3.402 1 A_U27:A43_A A 27 ? A 43 ? 20 1 1 A C 2 1_555 A G 16 1_555 -0.727 -0.170 0.228 -2.299 -21.698 -3.618 2 A_C28:G42_A A 28 ? A 42 ? 19 1 1 A A 3 1_555 A U 15 1_555 0.820 -0.092 0.187 0.130 -18.295 -3.002 3 A_A29:U41_A A 29 ? A 41 ? 20 1 1 A G 4 1_555 A C 14 1_555 0.640 -0.168 -0.447 -12.282 -25.398 -1.543 4 A_G30:C40_A A 30 ? A 40 ? 19 1 1 A A 5 1_555 A PSU 13 1_555 1.408 -0.158 0.206 -20.718 -25.768 -18.979 5 A_A31:PSU39_A A 31 ? A 39 ? 21 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 U 1 1_555 A A 17 1_555 A C 2 1_555 A G 16 1_555 -0.562 -1.536 3.758 -4.150 9.682 23.384 -6.411 0.004 2.953 22.482 9.636 25.617 1 AA_U27C28:G42A43_AA A 27 ? A 43 ? A 28 ? A 42 ? 1 A C 2 1_555 A G 16 1_555 A A 3 1_555 A U 15 1_555 0.113 -1.188 3.401 -0.219 12.740 36.164 -3.385 -0.199 2.837 19.782 0.339 38.272 2 AA_C28A29:U41G42_AA A 28 ? A 42 ? A 29 ? A 41 ? 1 A A 3 1_555 A U 15 1_555 A G 4 1_555 A C 14 1_555 0.128 -1.479 4.189 5.364 10.119 29.787 -4.935 0.955 3.484 18.831 -9.983 31.866 3 AA_A29G30:C40U41_AA A 29 ? A 41 ? A 30 ? A 40 ? 1 A G 4 1_555 A C 14 1_555 A A 5 1_555 A PSU 13 1_555 -0.863 -1.433 3.919 -2.248 12.526 35.835 -4.024 1.001 3.300 19.612 3.520 37.958 4 AA_G30A31:PSU39C40_AA A 30 ? A 40 ? A 31 ? A 39 ? #