data_1LUU # _entry.id 1LUU # _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 1LUU pdb_00001luu 10.2210/pdb1luu/pdb RCSB RCSB016293 ? ? WWPDB D_1000016293 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1LUX _pdbx_database_related.details 'NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 3 MODIFICATIONS (OMC32 OMG34 M5C40)' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1LUU _pdbx_database_status.recvd_initial_deposition_date 2002-05-23 _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 'Stuart, J.W.' 1 'Koshlap, K.M.' 2 'Guenther, R.H.' 3 'Agris, P.F.' 4 # _citation.id primary _citation.title 'Naturally-occurring Modification Restricts the Anticodon Domain Conformational Space of tRNA(Phe).' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 334 _citation.page_first 901 _citation.page_last 918 _citation.year 2003 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 14643656 _citation.pdbx_database_id_DOI 10.1016/j.jmb.2003.09.058 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Stuart, J.W.' 1 ? primary 'Koshlap, K.M.' 2 ? primary 'Guenther, R.' 3 ? primary 'Agris, P.F.' 4 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-R(*CP*CP*AP*GP*AP*(OMC)P*UP*(OMG)P*AP*AP*(1MG)P*AP*UP*(5MC)P*UP*GP*G)-3'" _entity.formula_weight 5522.430 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ;ANTICODON (RESIDUES 27-43) OF TRNA-PHE WITH FOUR MODIFIED RESIDUES (OMC at position 32, OMG at 34, 1MG at 37, and 5MC at position 40) ; # _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 'CCAGA(OMC)U(OMG)AA(1MG)AU(5MC)UGG' _entity_poly.pdbx_seq_one_letter_code_can CCAGACUGAAGAUCUGG _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 C n 1 2 C n 1 3 A n 1 4 G n 1 5 A n 1 6 OMC n 1 7 U n 1 8 OMG n 1 9 A n 1 10 A n 1 11 1MG n 1 12 A n 1 13 U n 1 14 5MC n 1 15 U n 1 16 G n 1 17 G 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 'SEQUENCE WITH NATURALLY OCCURRING MODIFICATIONS SYNTHESIZED USING PHOSPHORAMIDITE CHEMISTRY.' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1LUU _struct_ref.pdbx_db_accession 1LUU _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 1LUU _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 1LUU _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 1MG 'RNA linking' n "1N-METHYLGUANOSINE-5'-MONOPHOSPHATE" ? 'C11 H16 N5 O8 P' 377.247 5MC 'RNA linking' n "5-METHYLCYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O8 P' 337.223 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 OMC 'RNA linking' n "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O8 P' 337.223 OMG 'RNA linking' n "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" ? 'C11 H16 N5 O8 P' 377.247 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 1 DQF-COSY 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 5.60 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '1.2 MM RNA, 10 MM CACODYLATE BUFFER, PH 5.6, 0.1 MM EDTA' _pdbx_nmr_sample_details.solvent_system ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 500 _pdbx_nmr_spectrometer.type ? # _pdbx_nmr_refine.entry_id 1LUU _pdbx_nmr_refine.method 'GLOBAL FOLD BY DISTANCE GEOMETRY. REFINEMENT BY SIMULATED ANNEALING USING THE AMBER FORCEFIELD' _pdbx_nmr_refine.details '269 RESTRAINTS (256 NOE-DERIVED, 13 H-BOND) 96 DIHEDRAL ANGLE.' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1LUU _pdbx_nmr_details.text 'THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES' # _pdbx_nmr_ensemble.entry_id 1LUU _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 11 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the least restraint violations,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 1LUU _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal collection XwinNMR ? Bruker 1 'data analysis' Felix 98 Accelrys 2 refinement Discover 98 Accelrys 3 # _exptl.entry_id 1LUU _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1LUU _struct.title 'NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 4 MODIFICATIONS (OMC32 OMG34 1MG37 5MC40)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 1LUU _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;TRNA, ANTICODON STEM LOOP, TRNA DOMAIN, RNA HAIRPIN, 1MG, 2'-O-METHYL, 5MC, 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 A 5 "O3'" ? ? ? 1_555 A OMC 6 P ? ? A A 31 A OMC 32 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale2 covale both ? A OMC 6 "O3'" ? ? ? 1_555 A U 7 P ? ? A OMC 32 A U 33 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale3 covale both ? A U 7 "O3'" ? ? ? 1_555 A OMG 8 P ? ? A U 33 A OMG 34 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale4 covale both ? A OMG 8 "O3'" ? ? ? 1_555 A A 9 P ? ? A OMG 34 A A 35 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale5 covale both ? A A 10 "O3'" ? ? ? 1_555 A 1MG 11 P ? ? A A 36 A 1MG 37 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale6 covale both ? A 1MG 11 "O3'" ? ? ? 1_555 A A 12 P ? ? A 1MG 37 A A 38 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale7 covale both ? A U 13 "O3'" ? ? ? 1_555 A 5MC 14 P ? ? A U 39 A 5MC 40 1_555 ? ? ? ? ? ? ? 1.618 ? ? covale8 covale both ? A 5MC 14 "O3'" ? ? ? 1_555 A U 15 P ? ? A 5MC 40 A U 41 1_555 ? ? ? ? ? ? ? 1.619 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 27 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 27 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 27 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 16 N1 ? ? A C 28 A G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 16 O6 ? ? A C 28 A G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 16 N2 ? ? A C 28 A G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 15 N3 ? ? A A 29 A U 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 15 O4 ? ? A A 29 A U 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A 5MC 14 N3 ? ? A G 30 A 5MC 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A 5MC 14 O2 ? ? A G 30 A 5MC 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A 5MC 14 N4 ? ? A G 30 A 5MC 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 13 N3 ? ? A A 31 A U 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 13 O4 ? ? A A 31 A U 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A OMC 6 O2 ? ? ? 1_555 A A 12 N6 ? ? A OMC 32 A A 38 1_555 ? ? ? ? ? ? 'OMC-A MISPAIR' ? ? ? hydrog15 hydrog ? ? A OMG 8 O6 ? ? ? 1_555 A A 10 N6 ? ? A OMG 34 A A 36 1_555 ? ? ? ? ? ? 'OMG-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1LUU _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 1LUU _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 C 1 27 27 C C 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 OMC 6 32 32 OMC OMC A . n A 1 7 U 7 33 33 U U A . n A 1 8 OMG 8 34 34 OMG OMG A . n A 1 9 A 9 35 35 A A A . n A 1 10 A 10 36 36 A A A . n A 1 11 1MG 11 37 37 1MG 1MG A . n A 1 12 A 12 38 38 A A A . n A 1 13 U 13 39 39 U U A . n A 1 14 5MC 14 40 40 5MC 5MC 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 G 17 43 43 G G 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 OMC 6 A OMC 32 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 2 A OMG 8 A OMG 34 ? G "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" 3 A 1MG 11 A 1MG 37 ? G "1N-METHYLGUANOSINE-5'-MONOPHOSPHATE" 4 A 5MC 14 A 5MC 40 ? C "5-METHYLCYTIDINE-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 2003-09-09 2 'Structure model' 1 1 2008-04-28 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_nmr_spectrometer 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list 6 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' '_pdbx_nmr_spectrometer.model' 5 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 5 C6 A A 38 ? ? N1 A A 38 ? ? 1.393 1.351 0.042 0.007 N 2 8 N1 A A 38 ? ? C2 A A 38 ? ? 1.394 1.339 0.055 0.009 N 3 8 C6 A A 38 ? ? N1 A A 38 ? ? 1.394 1.351 0.043 0.007 N # 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 U 33 ? ? "C1'" A U 33 ? ? N1 A U 33 ? ? 112.85 108.50 4.35 0.70 N 2 1 "O4'" A A 36 ? ? "C1'" A A 36 ? ? N9 A A 36 ? ? 114.92 108.50 6.42 0.70 N 3 1 N1 A A 38 ? ? C2 A A 38 ? ? N3 A A 38 ? ? 123.71 129.30 -5.59 0.50 N 4 1 C2 A A 38 ? ? N3 A A 38 ? ? C4 A A 38 ? ? 114.85 110.60 4.25 0.50 N 5 2 N9 A A 35 ? ? "C1'" A A 35 ? ? "C2'" A A 35 ? ? 123.93 114.00 9.93 1.30 N 6 2 "O4'" A A 35 ? ? "C1'" A A 35 ? ? N9 A A 35 ? ? 112.84 108.50 4.34 0.70 N 7 2 "O4'" A A 36 ? ? "C1'" A A 36 ? ? N9 A A 36 ? ? 113.74 108.50 5.24 0.70 N 8 2 N1 A A 38 ? ? C2 A A 38 ? ? N3 A A 38 ? ? 123.94 129.30 -5.36 0.50 N 9 2 C2 A A 38 ? ? N3 A A 38 ? ? C4 A A 38 ? ? 114.41 110.60 3.81 0.50 N 10 3 N9 A A 35 ? ? "C1'" A A 35 ? ? "C2'" A A 35 ? ? 123.87 114.00 9.87 1.30 N 11 3 N1 A A 38 ? ? C2 A A 38 ? ? N3 A A 38 ? ? 123.80 129.30 -5.50 0.50 N 12 3 C2 A A 38 ? ? N3 A A 38 ? ? C4 A A 38 ? ? 114.40 110.60 3.80 0.50 N 13 4 "O4'" A U 33 ? ? "C1'" A U 33 ? ? N1 A U 33 ? ? 114.89 108.50 6.39 0.70 N 14 4 N9 A A 35 ? ? "C1'" A A 35 ? ? "C2'" A A 35 ? ? 124.62 114.00 10.62 1.30 N 15 4 "O4'" A A 35 ? ? "C1'" A A 35 ? ? N9 A A 35 ? ? 115.27 108.50 6.77 0.70 N 16 4 C8 A A 35 ? ? N9 A A 35 ? ? C4 A A 35 ? ? 102.81 105.80 -2.99 0.40 N 17 4 "C1'" A A 38 ? ? "O4'" A A 38 ? ? "C4'" A A 38 ? ? 103.57 109.70 -6.13 0.70 N 18 4 "O4'" A A 38 ? ? "C1'" A A 38 ? ? N9 A A 38 ? ? 114.23 108.50 5.73 0.70 N 19 4 N1 A A 38 ? ? C2 A A 38 ? ? N3 A A 38 ? ? 123.86 129.30 -5.44 0.50 N 20 4 C2 A A 38 ? ? N3 A A 38 ? ? C4 A A 38 ? ? 114.32 110.60 3.72 0.50 N 21 5 "O4'" A A 36 ? ? "C1'" A A 36 ? ? N9 A A 36 ? ? 112.78 108.50 4.28 0.70 N 22 5 N1 A A 38 ? ? C2 A A 38 ? ? N3 A A 38 ? ? 123.89 129.30 -5.41 0.50 N 23 5 C2 A A 38 ? ? N3 A A 38 ? ? C4 A A 38 ? ? 114.54 110.60 3.94 0.50 N 24 6 "O4'" A U 33 ? ? "C1'" A U 33 ? ? N1 A U 33 ? ? 115.38 108.50 6.88 0.70 N 25 6 N9 A A 35 ? ? "C1'" A A 35 ? ? "C2'" A A 35 ? ? 125.00 114.00 11.00 1.30 N 26 6 "O4'" A A 35 ? ? "C1'" A A 35 ? ? N9 A A 35 ? ? 115.30 108.50 6.80 0.70 N 27 6 C8 A A 35 ? ? N9 A A 35 ? ? C4 A A 35 ? ? 102.84 105.80 -2.96 0.40 N 28 6 "C1'" A A 38 ? ? "O4'" A A 38 ? ? "C4'" A A 38 ? ? 105.28 109.70 -4.42 0.70 N 29 6 N1 A A 38 ? ? C2 A A 38 ? ? N3 A A 38 ? ? 123.64 129.30 -5.66 0.50 N 30 6 C2 A A 38 ? ? N3 A A 38 ? ? C4 A A 38 ? ? 114.27 110.60 3.67 0.50 N 31 6 "O4'" A U 41 ? ? "C1'" A U 41 ? ? N1 A U 41 ? ? 112.71 108.50 4.21 0.70 N 32 7 "O4'" A A 36 ? ? "C1'" A A 36 ? ? N9 A A 36 ? ? 114.98 108.50 6.48 0.70 N 33 7 N1 A A 38 ? ? C2 A A 38 ? ? N3 A A 38 ? ? 123.79 129.30 -5.51 0.50 N 34 7 C2 A A 38 ? ? N3 A A 38 ? ? C4 A A 38 ? ? 114.46 110.60 3.86 0.50 N 35 8 "O4'" A U 33 ? ? "C1'" A U 33 ? ? N1 A U 33 ? ? 112.82 108.50 4.32 0.70 N 36 8 "O4'" A A 36 ? ? "C1'" A A 36 ? ? N9 A A 36 ? ? 112.77 108.50 4.27 0.70 N 37 8 N1 A A 38 ? ? C2 A A 38 ? ? N3 A A 38 ? ? 124.03 129.30 -5.27 0.50 N 38 8 C2 A A 38 ? ? N3 A A 38 ? ? C4 A A 38 ? ? 114.43 110.60 3.83 0.50 N 39 8 "O4'" A U 41 ? ? "C1'" A U 41 ? ? N1 A U 41 ? ? 112.73 108.50 4.23 0.70 N 40 9 "O4'" A A 36 ? ? "C1'" A A 36 ? ? N9 A A 36 ? ? 114.87 108.50 6.37 0.70 N 41 9 N1 A A 38 ? ? C2 A A 38 ? ? N3 A A 38 ? ? 123.86 129.30 -5.44 0.50 N 42 9 C2 A A 38 ? ? N3 A A 38 ? ? C4 A A 38 ? ? 114.38 110.60 3.78 0.50 N 43 10 "O4'" A A 36 ? ? "C1'" A A 36 ? ? N9 A A 36 ? ? 113.09 108.50 4.59 0.70 N 44 10 N1 A A 38 ? ? C2 A A 38 ? ? N3 A A 38 ? ? 123.93 129.30 -5.37 0.50 N 45 10 C2 A A 38 ? ? N3 A A 38 ? ? C4 A A 38 ? ? 114.46 110.60 3.86 0.50 N 46 11 "O4'" A U 33 ? ? "C1'" A U 33 ? ? N1 A U 33 ? ? 113.32 108.50 4.82 0.70 N 47 11 "O4'" A A 36 ? ? "C1'" A A 36 ? ? N9 A A 36 ? ? 115.88 108.50 7.38 0.70 N 48 11 N1 A A 38 ? ? C2 A A 38 ? ? N3 A A 38 ? ? 123.73 129.30 -5.57 0.50 N 49 11 C2 A A 38 ? ? N3 A A 38 ? ? C4 A A 38 ? ? 114.27 110.60 3.67 0.50 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 C A 27 ? ? 0.088 'SIDE CHAIN' 2 1 C A 28 ? ? 0.075 'SIDE CHAIN' 3 1 A A 29 ? ? 0.079 'SIDE CHAIN' 4 1 G A 42 ? ? 0.076 'SIDE CHAIN' 5 2 C A 27 ? ? 0.086 'SIDE CHAIN' 6 2 C A 28 ? ? 0.057 'SIDE CHAIN' 7 2 A A 29 ? ? 0.073 'SIDE CHAIN' 8 2 U A 33 ? ? 0.059 'SIDE CHAIN' 9 2 A A 35 ? ? 0.071 'SIDE CHAIN' 10 2 U A 41 ? ? 0.069 'SIDE CHAIN' 11 2 G A 42 ? ? 0.073 'SIDE CHAIN' 12 3 C A 27 ? ? 0.070 'SIDE CHAIN' 13 3 C A 28 ? ? 0.062 'SIDE CHAIN' 14 3 G A 30 ? ? 0.073 'SIDE CHAIN' 15 3 U A 33 ? ? 0.098 'SIDE CHAIN' 16 3 A A 35 ? ? 0.073 'SIDE CHAIN' 17 3 G A 42 ? ? 0.074 'SIDE CHAIN' 18 4 C A 27 ? ? 0.096 'SIDE CHAIN' 19 4 G A 30 ? ? 0.085 'SIDE CHAIN' 20 4 A A 35 ? ? 0.090 'SIDE CHAIN' 21 4 G A 42 ? ? 0.081 'SIDE CHAIN' 22 5 C A 27 ? ? 0.063 'SIDE CHAIN' 23 5 C A 28 ? ? 0.105 'SIDE CHAIN' 24 5 A A 29 ? ? 0.104 'SIDE CHAIN' 25 5 G A 30 ? ? 0.082 'SIDE CHAIN' 26 5 U A 33 ? ? 0.057 'SIDE CHAIN' 27 5 U A 41 ? ? 0.076 'SIDE CHAIN' 28 5 G A 42 ? ? 0.075 'SIDE CHAIN' 29 6 C A 27 ? ? 0.077 'SIDE CHAIN' 30 6 C A 28 ? ? 0.092 'SIDE CHAIN' 31 6 G A 30 ? ? 0.078 'SIDE CHAIN' 32 6 A A 35 ? ? 0.094 'SIDE CHAIN' 33 6 G A 42 ? ? 0.065 'SIDE CHAIN' 34 7 C A 27 ? ? 0.103 'SIDE CHAIN' 35 7 A A 29 ? ? 0.064 'SIDE CHAIN' 36 7 G A 42 ? ? 0.078 'SIDE CHAIN' 37 8 C A 27 ? ? 0.082 'SIDE CHAIN' 38 8 C A 28 ? ? 0.112 'SIDE CHAIN' 39 8 A A 29 ? ? 0.087 'SIDE CHAIN' 40 8 G A 30 ? ? 0.061 'SIDE CHAIN' 41 8 U A 33 ? ? 0.056 'SIDE CHAIN' 42 8 A A 38 ? ? 0.060 'SIDE CHAIN' 43 8 U A 41 ? ? 0.065 'SIDE CHAIN' 44 8 G A 42 ? ? 0.077 'SIDE CHAIN' 45 9 C A 27 ? ? 0.072 'SIDE CHAIN' 46 9 C A 28 ? ? 0.096 'SIDE CHAIN' 47 9 A A 29 ? ? 0.061 'SIDE CHAIN' 48 9 G A 30 ? ? 0.078 'SIDE CHAIN' 49 9 G A 42 ? ? 0.075 'SIDE CHAIN' 50 10 C A 27 ? ? 0.086 'SIDE CHAIN' 51 10 C A 28 ? ? 0.115 'SIDE CHAIN' 52 10 G A 30 ? ? 0.066 'SIDE CHAIN' 53 10 U A 41 ? ? 0.067 'SIDE CHAIN' 54 10 G A 42 ? ? 0.083 'SIDE CHAIN' 55 11 C A 27 ? ? 0.068 'SIDE CHAIN' 56 11 C A 28 ? ? 0.070 'SIDE CHAIN' 57 11 G A 30 ? ? 0.059 'SIDE CHAIN' 58 11 G A 42 ? ? 0.068 'SIDE CHAIN' 59 11 G A 43 ? ? 0.064 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1LUU 'double helix' 1LUU 'a-form double helix' 1LUU 'hairpin loop' 1LUU '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 C 1 1_555 A G 17 1_555 -0.211 -0.035 -0.033 8.735 -6.496 -3.183 1 A_C27:G43_A A 27 ? A 43 ? 19 1 1 A C 2 1_555 A G 16 1_555 -0.428 -0.008 -0.114 15.331 -11.798 -0.803 2 A_C28:G42_A A 28 ? A 42 ? 19 1 1 A A 3 1_555 A U 15 1_555 -0.535 -0.210 -0.594 -3.519 -11.069 2.525 3 A_A29:U41_A A 29 ? A 41 ? 20 1 1 A G 4 1_555 A 5MC 14 1_555 0.311 -0.177 -1.102 -16.975 -6.340 -4.456 4 A_G30:5MC40_A A 30 ? A 40 ? 19 1 1 A A 5 1_555 A U 13 1_555 0.035 0.043 -0.216 -16.861 3.104 -0.102 5 A_A31:U39_A A 31 ? A 39 ? 20 1 1 A OMC 6 1_555 A A 12 1_555 3.709 -0.805 0.143 -8.413 -0.272 7.868 6 A_OMC32:A38_A A 32 ? A 38 ? ? 1 1 A OMG 8 1_555 A A 10 1_555 -1.622 -5.162 -0.685 -47.808 1.244 165.804 7 A_OMG34:A36_A A 34 ? A 36 ? ? ? # 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 C 1 1_555 A G 17 1_555 A C 2 1_555 A G 16 1_555 0.289 -1.014 3.090 -0.651 13.417 28.704 -4.044 -0.637 2.383 25.382 1.231 31.631 1 AA_C27C28:G42G43_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 0.245 -1.432 4.021 5.345 33.620 33.055 -4.791 0.170 1.896 46.517 -7.395 47.106 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 5MC 14 1_555 -0.686 -1.266 3.846 1.407 13.985 34.090 -4.104 1.298 3.079 22.695 -2.283 36.794 3 AA_A29G30:5MC40U41_AA A 29 ? A 41 ? A 30 ? A 40 ? 1 A G 4 1_555 A 5MC 14 1_555 A A 5 1_555 A U 13 1_555 0.886 -1.378 3.400 -7.026 6.286 33.684 -3.223 -2.512 2.867 10.592 11.839 34.941 4 AA_G30A31:U395MC40_AA A 30 ? A 40 ? A 31 ? A 39 ? 1 A A 5 1_555 A U 13 1_555 A OMC 6 1_555 A A 12 1_555 -0.054 -1.339 3.184 2.599 12.950 42.054 -2.910 0.298 2.671 17.533 -3.518 43.990 5 AA_A31OMC32:A38U39_AA A 31 ? A 39 ? A 32 ? A 38 ? #