data_1YLG # _entry.id 1YLG # _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 1YLG pdb_00001ylg 10.2210/pdb1ylg/pdb RCSB RCSB031652 ? ? WWPDB D_1000031652 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1YNC . unspecified PDB 1YNE . unspecified PDB 1YNG . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1YLG _pdbx_database_status.recvd_initial_deposition_date 2005-01-19 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Maris, C.' 1 'Masse, J.' 2 'Allain, F.H.' 3 'Chester, A.' 4 'Navaratnam, N.' 5 # _citation.id primary _citation.title 'NMR structure of the apoB mRNA stem-loop and its interaction with the C to U editing APOBEC1 complementary factor.' _citation.journal_abbrev Rna _citation.journal_volume 11 _citation.page_first 173 _citation.page_last 186 _citation.year 2005 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15659357 _citation.pdbx_database_id_DOI 10.1261/rna.7190705 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Maris, C.' 1 ? primary 'Masse, J.' 2 ? primary 'Chester, A.' 3 ? primary 'Navaratnam, N.' 4 ? primary 'Allain, F.H.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'apolipoprotein B mRNA' _entity.formula_weight 9890.887 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'Editing site of APOBEC-1 enzyme' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'apoB mRNA' # _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 GGAUAUAUGAUACAAUUUGAUCAGUAUAUCC _entity_poly.pdbx_seq_one_letter_code_can GGAUAUAUGAUACAAUUUGAUCAGUAUAUCC _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 A n 1 4 U n 1 5 A n 1 6 U n 1 7 A n 1 8 U n 1 9 G n 1 10 A n 1 11 U n 1 12 A n 1 13 C n 1 14 A n 1 15 A n 1 16 U n 1 17 U n 1 18 U n 1 19 G n 1 20 A n 1 21 U n 1 22 C n 1 23 A n 1 24 G n 1 25 U n 1 26 A n 1 27 U n 1 28 A n 1 29 U n 1 30 C n 1 31 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 'In vitro T7 polymerase transcription. The sequence of this RNA naturally exists in Homo sapiens (human)' # _struct_ref.id 1 _struct_ref.db_name GB _struct_ref.db_code NM_000384 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code AUAUAUGAUACAAUUUGAUCAGUAUAU _struct_ref.pdbx_align_begin 3 _struct_ref.pdbx_db_accession 4502152 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1YLG _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 3 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 29 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4502152 _struct_ref_seq.db_align_beg 6656 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 6682 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 3 _struct_ref_seq.pdbx_auth_seq_align_end 29 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 1YLG G A 1 ? GB 4502152 ? ? 'see remark 999' 1 1 1 1YLG G A 2 ? GB 4502152 ? ? 'see remark 999' 2 2 1 1YLG C A 30 ? GB 4502152 ? ? 'see remark 999' 30 3 1 1YLG C A 31 ? GB 4502152 ? ? 'see remark 999' 31 4 # 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.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D NOESY' 1 2 1 '2D TOCSY' 1 3 1 3D_13C-separated_NOESY 1 4 1 DQF-COSY 1 5 2 HNN_COSY 5 6 1 HCCH-TOCSY 1 # 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 1 313 1 5.8 '10 mM Na2HPO4' atm K 2 278 1 5.8 '10 mM Na2HPO4' atm K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '2 mM apoB RNA SL31;10 mM NaH2HPO4 adjusted at pH 5.8; Natural abundance labeling; 90% H2O, 10% D2O and only 99.98% D2O' '90% H2O, 10% D2O and only 99.98% D2O' 2 '1.2 mM apoB RNA SL31; 10 mM NaH2HPO4 adjusted at pH 5.8; Selective U 15N&13C labeling; 90% H2O, 10% D2O and only 99.98% D2O' ;90% H2O, 10% D2O and only 99.98% D2O ; 3 '1.0 mMapoB RNA SL31; 10 mM NaH2HPO4 adjusted at pH 5.8; Selective A 15N&13C labeling; 90% H2O, 10% D2O and only 99.98% D2O' ;90% H2O, 10% D2O and only 99.98% D2O ; 4 '1.0 mM apoB RNA SL31; 10 mM NaH2HPO4 adjusted at pH 5.8; Selective G&C 15N&13C labeling; 90% H2O, 10% D2O and only 99.98% D2O' ;90% H2O, 10% D2O and only 99.98% D2O ; 5 '1.5 mM apoB RNA SL31; 10 mM NaH2HPO4 adjusted at pH 5.8; full 15N&C13 labeling; 90% H2O, 10% D2O and only 99.98% D2O' '90% H2O/10% 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 DRX Bruker 500 ? 2 DRX Bruker 600 ? 3 AVANCE Bruker 900 ? # _pdbx_nmr_refine.entry_id 1YLG _pdbx_nmr_refine.method 'CYANA & AMBER7' _pdbx_nmr_refine.details 'calculation in vacuum condition' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1YLG _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria ;back calculated data agree with experimental NOESY spectrum,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 1YLG _pdbx_nmr_representative.conformer_id 12 _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 'structure solution' CYANA 2.0 'Guentert, P.' 1 collection XwinNMR 2004 Bruker 2 'data analysis' Sparky 2002 'Goddard, T. D. and Kneller, D. G.' 3 'data analysis' X-EASY 2001 'Bartels, C.' 4 refinement AMBER7 7 'Ponder, J.W. and Case, D.A.' 5 # _exptl.entry_id 1YLG _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol ? _exptl_crystal.density_Matthews ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1YLG _struct.title 'NMR structure of the apoB mRNA stem-loop and its interaction with the C to U editing APOBEC1 complementary factor' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YLG _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA editing, apoB mRNA, APOBEC1, ACF, 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 31 N3 ? ? A G 1 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 31 O2 ? ? A G 1 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 31 N4 ? ? A G 1 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 30 N3 ? ? A G 2 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 30 O2 ? ? A G 2 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 30 N4 ? ? A G 2 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 29 N3 ? ? A A 3 A U 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 29 O4 ? ? A A 3 A U 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 28 N1 ? ? A U 4 A A 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 28 N6 ? ? A U 4 A A 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 27 N3 ? ? A A 5 A U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 27 O4 ? ? A A 5 A U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 26 N1 ? ? A U 6 A A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 26 N6 ? ? A U 6 A A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 7 N1 ? ? ? 1_555 A G 24 N1 ? ? A A 7 A G 24 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog16 hydrog ? ? A A 7 N6 ? ? ? 1_555 A G 24 O6 ? ? A A 7 A G 24 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog17 hydrog ? ? A U 8 N3 ? ? ? 1_555 A A 23 N1 ? ? A U 8 A A 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 8 O4 ? ? ? 1_555 A A 23 N6 ? ? A U 8 A A 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 22 N3 ? ? A G 9 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 22 O2 ? ? A G 9 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 22 N4 ? ? A G 9 A C 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 10 N1 ? ? ? 1_555 A U 21 N3 ? ? A A 10 A U 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A A 10 N6 ? ? ? 1_555 A U 21 O4 ? ? A A 10 A U 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A U 11 N3 ? ? ? 1_555 A A 20 N1 ? ? A U 11 A A 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 11 O4 ? ? ? 1_555 A A 20 N6 ? ? A U 11 A A 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A A 12 N1 ? ? ? 1_555 A G 19 N1 ? ? A A 12 A G 19 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog27 hydrog ? ? A A 12 N6 ? ? ? 1_555 A G 19 O6 ? ? A A 12 A G 19 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog28 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 19 N2 ? ? A C 13 A G 19 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1YLG _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 1YLG _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 A 3 3 3 A A A . n A 1 4 U 4 4 4 U U A . n A 1 5 A 5 5 5 A A A . n A 1 6 U 6 6 6 U U A . n A 1 7 A 7 7 7 A A A . n A 1 8 U 8 8 8 U U A . n A 1 9 G 9 9 9 G G A . n A 1 10 A 10 10 10 A A A . n A 1 11 U 11 11 11 U U A . n A 1 12 A 12 12 12 A A A . n A 1 13 C 13 13 13 C C A . n A 1 14 A 14 14 14 A A A . n A 1 15 A 15 15 15 A A A . n A 1 16 U 16 16 16 U U A . n A 1 17 U 17 17 17 U U A . n A 1 18 U 18 18 18 U U A . n A 1 19 G 19 19 19 G G A . n A 1 20 A 20 20 20 A A A . n A 1 21 U 21 21 21 U U A . n A 1 22 C 22 22 22 C C A . n A 1 23 A 23 23 23 A A A . n A 1 24 G 24 24 24 G G A . n A 1 25 U 25 25 25 U U A . n A 1 26 A 26 26 26 A A A . n A 1 27 U 27 27 27 U U A . n A 1 28 A 28 28 28 A A A . n A 1 29 U 29 29 29 U U A . n A 1 30 C 30 30 30 C C A . n A 1 31 C 31 31 31 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 2005-02-01 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' '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 # 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' # _pdbx_entry_details.entry_id 1YLG _pdbx_entry_details.sequence_details ;THE EDITED APOB MRNA SEQUENCE LEADING TO THE TRUNCATED PROTEIN HAS THE SAME ACCESSION NUMBER SINCE IT COMES FROM THE SAME GENE. THE NUMBERING STARTS AT 6656 ON THE APOB MRNA SEQUENCE BUT FOR EXPERIMENTAL REASON THE FIRST AND LAST TWO NUCLEOTIDES GG AND CC WERE ADDED, WHICH DO NOT BELONG TO THE NATIVE SEQUENCE, THE NUMBER STARTS AT 6654. ; _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.has_ligand_of_interest ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 "HO2'" A G 9 ? ? OP1 A A 10 ? ? 1.57 2 1 "HO2'" A U 21 ? ? OP1 A C 22 ? ? 1.58 3 2 "HO2'" A G 9 ? ? OP1 A A 10 ? ? 1.52 4 2 "HO2'" A U 16 ? ? OP2 A U 17 ? ? 1.60 5 3 "HO2'" A U 16 ? ? OP2 A U 17 ? ? 1.54 6 3 "HO2'" A G 19 ? ? OP1 A A 20 ? ? 1.55 7 3 "HO2'" A A 14 ? ? "O5'" A A 15 ? ? 1.59 8 5 "HO2'" A A 23 ? ? OP1 A G 24 ? ? 1.54 9 6 "HO2'" A A 14 ? ? "O5'" A A 15 ? ? 1.59 10 8 "HO2'" A A 14 ? ? "O5'" A A 15 ? ? 1.52 11 8 "HO2'" A A 7 ? ? OP1 A U 8 ? ? 1.53 12 8 "HO2'" A A 12 ? ? OP1 A C 13 ? ? 1.56 13 8 "HO2'" A A 23 ? ? OP1 A G 24 ? ? 1.58 14 9 "HO2'" A A 23 ? ? OP1 A G 24 ? ? 1.55 15 10 "HO2'" A A 23 ? ? OP1 A G 24 ? ? 1.52 16 10 "HO2'" A A 14 ? ? OP1 A A 15 ? ? 1.54 17 10 "HO2'" A U 8 ? ? OP1 A G 9 ? ? 1.54 18 11 "HO2'" A A 23 ? ? OP1 A G 24 ? ? 1.52 19 11 "HO2'" A U 16 ? ? OP1 A U 17 ? ? 1.54 20 11 "HO2'" A U 21 ? ? OP1 A C 22 ? ? 1.56 21 11 "HO2'" A G 24 ? ? OP2 A U 25 ? ? 1.59 22 12 "HO2'" A A 23 ? ? OP1 A G 24 ? ? 1.52 23 12 "HO2'" A G 19 ? ? OP1 A A 20 ? ? 1.52 24 12 "HO2'" A U 16 ? ? OP1 A U 17 ? ? 1.59 25 13 "HO2'" A U 16 ? ? OP2 A U 17 ? ? 1.56 26 15 "HO2'" A A 23 ? ? OP1 A G 24 ? ? 1.56 27 16 "HO2'" A A 14 ? ? OP1 A A 15 ? ? 1.53 28 16 "HO2'" A A 23 ? ? OP1 A G 24 ? ? 1.53 29 16 "HO2'" A A 12 ? ? OP1 A C 13 ? ? 1.56 30 17 "HO2'" A U 8 ? ? OP1 A G 9 ? ? 1.57 31 17 "HO2'" A U 16 ? ? OP1 A U 17 ? ? 1.58 32 18 "HO2'" A U 16 ? ? OP1 A U 17 ? ? 1.49 33 18 "HO2'" A A 12 ? ? OP1 A C 13 ? ? 1.57 34 18 "HO2'" A U 21 ? ? OP1 A C 22 ? ? 1.57 35 19 "HO2'" A U 16 ? ? OP2 A U 17 ? ? 1.58 36 20 "HO2'" A U 21 ? ? OP1 A C 22 ? ? 1.52 37 20 "HO2'" A A 23 ? ? OP1 A G 24 ? ? 1.54 38 20 "HO2'" A U 17 ? ? OP1 A U 18 ? ? 1.56 # 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 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 113.11 108.50 4.61 0.70 N 2 1 "O4'" A U 6 ? ? "C1'" A U 6 ? ? N1 A U 6 ? ? 113.30 108.50 4.80 0.70 N 3 1 "O4'" A U 11 ? ? "C1'" A U 11 ? ? N1 A U 11 ? ? 113.78 108.50 5.28 0.70 N 4 1 C4 A A 14 ? ? C5 A A 14 ? ? C6 A A 14 ? ? 113.74 117.00 -3.26 0.50 N 5 1 C5 A A 14 ? ? C6 A A 14 ? ? N1 A A 14 ? ? 120.89 117.70 3.19 0.50 N 6 1 C5 A A 20 ? ? C6 A A 20 ? ? N1 A A 20 ? ? 120.78 117.70 3.08 0.50 N 7 1 C5 A A 23 ? ? C6 A A 23 ? ? N1 A A 23 ? ? 121.37 117.70 3.67 0.50 N 8 1 "O4'" A U 29 ? ? "C1'" A U 29 ? ? N1 A U 29 ? ? 112.91 108.50 4.41 0.70 N 9 2 "O4'" A U 11 ? ? "C1'" A U 11 ? ? N1 A U 11 ? ? 112.74 108.50 4.24 0.70 N 10 3 C5 A A 3 ? ? C6 A A 3 ? ? N1 A A 3 ? ? 120.97 117.70 3.27 0.50 N 11 3 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 113.69 108.50 5.19 0.70 N 12 3 C5 A A 5 ? ? C6 A A 5 ? ? N1 A A 5 ? ? 120.86 117.70 3.16 0.50 N 13 3 "O4'" A U 11 ? ? "C1'" A U 11 ? ? N1 A U 11 ? ? 113.42 108.50 4.92 0.70 N 14 3 C5 A A 14 ? ? C6 A A 14 ? ? N1 A A 14 ? ? 121.03 117.70 3.33 0.50 N 15 3 "O4'" A A 15 ? ? "C1'" A A 15 ? ? N9 A A 15 ? ? 113.30 108.50 4.80 0.70 N 16 3 C5 A A 15 ? ? C6 A A 15 ? ? N1 A A 15 ? ? 121.16 117.70 3.46 0.50 N 17 3 N3 A U 16 ? ? C2 A U 16 ? ? O2 A U 16 ? ? 117.98 122.20 -4.22 0.70 N 18 3 C5 A A 20 ? ? C6 A A 20 ? ? N1 A A 20 ? ? 120.92 117.70 3.22 0.50 N 19 3 N3 A C 22 ? ? C2 A C 22 ? ? O2 A C 22 ? ? 117.53 121.90 -4.37 0.70 N 20 3 C5 A A 23 ? ? C6 A A 23 ? ? N1 A A 23 ? ? 121.86 117.70 4.16 0.50 N 21 3 C5 A A 26 ? ? C6 A A 26 ? ? N1 A A 26 ? ? 120.74 117.70 3.04 0.50 N 22 3 "O4'" A U 27 ? ? "C1'" A U 27 ? ? N1 A U 27 ? ? 113.18 108.50 4.68 0.70 N 23 3 "O4'" A U 29 ? ? "C1'" A U 29 ? ? N1 A U 29 ? ? 112.95 108.50 4.45 0.70 N 24 4 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 112.87 108.50 4.37 0.70 N 25 5 C5 A A 3 ? ? C6 A A 3 ? ? N1 A A 3 ? ? 120.85 117.70 3.15 0.50 N 26 5 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 113.38 108.50 4.88 0.70 N 27 5 C5 A A 7 ? ? C6 A A 7 ? ? N1 A A 7 ? ? 121.36 117.70 3.66 0.50 N 28 5 C5 A A 12 ? ? C6 A A 12 ? ? N1 A A 12 ? ? 121.07 117.70 3.37 0.50 N 29 5 "C4'" A C 13 ? ? "C3'" A C 13 ? ? "C2'" A C 13 ? ? 96.11 102.60 -6.49 1.00 N 30 5 C5 A A 14 ? ? C6 A A 14 ? ? N1 A A 14 ? ? 120.87 117.70 3.17 0.50 N 31 5 C4 A A 15 ? ? C5 A A 15 ? ? C6 A A 15 ? ? 113.61 117.00 -3.39 0.50 N 32 5 C5 A A 15 ? ? C6 A A 15 ? ? N1 A A 15 ? ? 121.20 117.70 3.50 0.50 N 33 5 N1 A A 15 ? ? C6 A A 15 ? ? N6 A A 15 ? ? 114.76 118.60 -3.84 0.60 N 34 5 "O4'" A U 18 ? ? "C1'" A U 18 ? ? N1 A U 18 ? ? 112.89 108.50 4.39 0.70 N 35 5 C5 A A 20 ? ? C6 A A 20 ? ? N1 A A 20 ? ? 120.90 117.70 3.20 0.50 N 36 5 C5 A A 23 ? ? C6 A A 23 ? ? N1 A A 23 ? ? 121.31 117.70 3.61 0.50 N 37 5 N1 A G 24 ? ? C6 A G 24 ? ? O6 A G 24 ? ? 115.00 119.90 -4.90 0.60 N 38 5 "O4'" A U 29 ? ? "C1'" A U 29 ? ? N1 A U 29 ? ? 112.95 108.50 4.45 0.70 N 39 7 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 112.85 108.50 4.35 0.70 N 40 7 C5 A A 7 ? ? C6 A A 7 ? ? N1 A A 7 ? ? 120.98 117.70 3.28 0.50 N 41 7 "C5'" A A 10 ? ? "C4'" A A 10 ? ? "C3'" A A 10 ? ? 106.48 115.20 -8.72 1.40 N 42 7 "C4'" A C 13 ? ? "C3'" A C 13 ? ? "C2'" A C 13 ? ? 96.13 102.60 -6.47 1.00 N 43 7 "O4'" A A 15 ? ? "C1'" A A 15 ? ? N9 A A 15 ? ? 112.85 108.50 4.35 0.70 N 44 7 C4 A A 15 ? ? C5 A A 15 ? ? C6 A A 15 ? ? 113.89 117.00 -3.11 0.50 N 45 7 C5 A A 15 ? ? N7 A A 15 ? ? C8 A A 15 ? ? 100.60 103.90 -3.30 0.50 N 46 7 N7 A A 15 ? ? C8 A A 15 ? ? N9 A A 15 ? ? 117.04 113.80 3.24 0.50 N 47 7 "C5'" A A 20 ? ? "C4'" A A 20 ? ? "C3'" A A 20 ? ? 105.97 115.20 -9.23 1.40 N 48 7 C5 A A 20 ? ? C6 A A 20 ? ? N1 A A 20 ? ? 120.97 117.70 3.27 0.50 N 49 7 C5 A A 23 ? ? C6 A A 23 ? ? N1 A A 23 ? ? 121.28 117.70 3.58 0.50 N 50 7 C5 A A 28 ? ? C6 A A 28 ? ? N1 A A 28 ? ? 120.85 117.70 3.15 0.50 N 51 8 "C5'" A G 9 ? ? "C4'" A G 9 ? ? "C3'" A G 9 ? ? 104.81 115.20 -10.39 1.40 N 52 8 "C5'" A A 10 ? ? "C4'" A A 10 ? ? "C3'" A A 10 ? ? 105.86 115.20 -9.34 1.40 N 53 9 C5 A A 3 ? ? C6 A A 3 ? ? N1 A A 3 ? ? 121.21 117.70 3.51 0.50 N 54 9 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 113.98 108.50 5.48 0.70 N 55 9 C5 A A 5 ? ? C6 A A 5 ? ? N1 A A 5 ? ? 121.23 117.70 3.53 0.50 N 56 9 "O4'" A U 6 ? ? "C1'" A U 6 ? ? N1 A U 6 ? ? 113.14 108.50 4.64 0.70 N 57 9 C5 A A 7 ? ? C6 A A 7 ? ? N1 A A 7 ? ? 121.75 117.70 4.05 0.50 N 58 9 C5 A A 10 ? ? C6 A A 10 ? ? N1 A A 10 ? ? 121.10 117.70 3.40 0.50 N 59 9 "O4'" A U 11 ? ? "C1'" A U 11 ? ? N1 A U 11 ? ? 113.75 108.50 5.25 0.70 N 60 9 C5 A A 12 ? ? C6 A A 12 ? ? N1 A A 12 ? ? 121.37 117.70 3.67 0.50 N 61 9 "C4'" A C 13 ? ? "C3'" A C 13 ? ? "C2'" A C 13 ? ? 95.67 102.60 -6.93 1.00 N 62 9 N3 A C 13 ? ? C2 A C 13 ? ? O2 A C 13 ? ? 117.45 121.90 -4.45 0.70 N 63 9 "O4'" A A 14 ? ? "C1'" A A 14 ? ? N9 A A 14 ? ? 113.91 108.50 5.41 0.70 N 64 9 C5 A A 14 ? ? C6 A A 14 ? ? N1 A A 14 ? ? 120.94 117.70 3.24 0.50 N 65 9 C4 A A 15 ? ? C5 A A 15 ? ? C6 A A 15 ? ? 113.64 117.00 -3.36 0.50 N 66 9 C5 A A 15 ? ? C6 A A 15 ? ? N1 A A 15 ? ? 122.17 117.70 4.47 0.50 N 67 9 C5 A A 15 ? ? N7 A A 15 ? ? C8 A A 15 ? ? 100.81 103.90 -3.09 0.50 N 68 9 N1 A A 15 ? ? C6 A A 15 ? ? N6 A A 15 ? ? 113.87 118.60 -4.73 0.60 N 69 9 "C5'" A A 20 ? ? "C4'" A A 20 ? ? "C3'" A A 20 ? ? 106.30 115.20 -8.90 1.40 N 70 9 "C5'" A A 20 ? ? "C4'" A A 20 ? ? "O4'" A A 20 ? ? 115.40 109.80 5.60 0.90 N 71 9 C5 A A 20 ? ? C6 A A 20 ? ? N1 A A 20 ? ? 121.14 117.70 3.44 0.50 N 72 9 "C5'" A U 21 ? ? "C4'" A U 21 ? ? "C3'" A U 21 ? ? 105.76 115.20 -9.44 1.40 N 73 9 C5 A A 23 ? ? C6 A A 23 ? ? N1 A A 23 ? ? 122.01 117.70 4.31 0.50 N 74 9 N1 A G 24 ? ? C6 A G 24 ? ? O6 A G 24 ? ? 114.88 119.90 -5.02 0.60 N 75 9 C5 A A 26 ? ? C6 A A 26 ? ? N1 A A 26 ? ? 121.17 117.70 3.47 0.50 N 76 9 C5 A A 28 ? ? C6 A A 28 ? ? N1 A A 28 ? ? 121.34 117.70 3.64 0.50 N 77 9 "O4'" A U 29 ? ? "C1'" A U 29 ? ? N1 A U 29 ? ? 113.12 108.50 4.62 0.70 N 78 9 N3 A C 30 ? ? C2 A C 30 ? ? O2 A C 30 ? ? 117.57 121.90 -4.33 0.70 N 79 10 "O4'" A A 14 ? ? "C1'" A A 14 ? ? N9 A A 14 ? ? 113.39 108.50 4.89 0.70 N 80 10 C5 A A 15 ? ? C6 A A 15 ? ? N1 A A 15 ? ? 120.84 117.70 3.14 0.50 N 81 12 C4 A A 3 ? ? C5 A A 3 ? ? C6 A A 3 ? ? 113.97 117.00 -3.03 0.50 N 82 12 N1 A A 3 ? ? C6 A A 3 ? ? N6 A A 3 ? ? 113.19 118.60 -5.41 0.60 N 83 12 C5 A A 7 ? ? C6 A A 7 ? ? N1 A A 7 ? ? 120.82 117.70 3.12 0.50 N 84 12 C5 A A 12 ? ? C6 A A 12 ? ? N1 A A 12 ? ? 121.04 117.70 3.34 0.50 N 85 12 "C4'" A C 13 ? ? "C3'" A C 13 ? ? "C2'" A C 13 ? ? 96.57 102.60 -6.03 1.00 N 86 12 C5 A A 14 ? ? C6 A A 14 ? ? N1 A A 14 ? ? 120.77 117.70 3.07 0.50 N 87 12 C5 A A 15 ? ? C6 A A 15 ? ? N1 A A 15 ? ? 121.35 117.70 3.65 0.50 N 88 12 C5 A A 15 ? ? N7 A A 15 ? ? C8 A A 15 ? ? 100.83 103.90 -3.07 0.50 N 89 12 C5 A A 20 ? ? C6 A A 20 ? ? N1 A A 20 ? ? 120.97 117.70 3.27 0.50 N 90 12 N3 A C 22 ? ? C2 A C 22 ? ? O2 A C 22 ? ? 117.48 121.90 -4.42 0.70 N 91 12 C5 A A 23 ? ? C6 A A 23 ? ? N1 A A 23 ? ? 121.01 117.70 3.31 0.50 N 92 12 C5 A A 26 ? ? C6 A A 26 ? ? N1 A A 26 ? ? 120.80 117.70 3.10 0.50 N 93 12 C5 A A 28 ? ? C6 A A 28 ? ? N1 A A 28 ? ? 120.87 117.70 3.17 0.50 N 94 13 C5 A A 3 ? ? C6 A A 3 ? ? N1 A A 3 ? ? 121.08 117.70 3.38 0.50 N 95 13 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 113.50 108.50 5.00 0.70 N 96 13 C5 A A 5 ? ? C6 A A 5 ? ? N1 A A 5 ? ? 121.25 117.70 3.55 0.50 N 97 13 "O4'" A U 6 ? ? "C1'" A U 6 ? ? N1 A U 6 ? ? 113.56 108.50 5.06 0.70 N 98 13 C5 A A 7 ? ? C6 A A 7 ? ? N1 A A 7 ? ? 120.76 117.70 3.06 0.50 N 99 13 "O4'" A U 8 ? ? "C1'" A U 8 ? ? N1 A U 8 ? ? 112.92 108.50 4.42 0.70 N 100 13 C5 A A 12 ? ? C6 A A 12 ? ? N1 A A 12 ? ? 121.40 117.70 3.70 0.50 N 101 13 "O4'" A C 13 ? ? "C1'" A C 13 ? ? N1 A C 13 ? ? 113.12 108.50 4.62 0.70 N 102 13 C5 A A 15 ? ? C6 A A 15 ? ? N1 A A 15 ? ? 121.43 117.70 3.73 0.50 N 103 13 C5 A A 20 ? ? C6 A A 20 ? ? N1 A A 20 ? ? 121.58 117.70 3.88 0.50 N 104 13 "O4'" A U 21 ? ? "C1'" A U 21 ? ? N1 A U 21 ? ? 112.82 108.50 4.32 0.70 N 105 13 "O4'" A C 22 ? ? "C1'" A C 22 ? ? N1 A C 22 ? ? 113.04 108.50 4.54 0.70 N 106 13 N3 A C 22 ? ? C2 A C 22 ? ? O2 A C 22 ? ? 117.67 121.90 -4.23 0.70 N 107 13 C5 A A 23 ? ? C6 A A 23 ? ? N1 A A 23 ? ? 121.96 117.70 4.26 0.50 N 108 13 N1 A G 24 ? ? C6 A G 24 ? ? O6 A G 24 ? ? 115.85 119.90 -4.05 0.60 N 109 13 C5 A A 26 ? ? C6 A A 26 ? ? N1 A A 26 ? ? 121.24 117.70 3.54 0.50 N 110 13 "O4'" A U 27 ? ? "C1'" A U 27 ? ? N1 A U 27 ? ? 112.86 108.50 4.36 0.70 N 111 13 C5 A A 28 ? ? C6 A A 28 ? ? N1 A A 28 ? ? 121.01 117.70 3.31 0.50 N 112 13 "O4'" A U 29 ? ? "C1'" A U 29 ? ? N1 A U 29 ? ? 113.25 108.50 4.75 0.70 N 113 13 "O4'" A C 30 ? ? "C1'" A C 30 ? ? N1 A C 30 ? ? 112.73 108.50 4.23 0.70 N 114 13 N3 A C 30 ? ? C2 A C 30 ? ? O2 A C 30 ? ? 117.27 121.90 -4.63 0.70 N 115 15 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 112.85 108.50 4.35 0.70 N 116 15 C5 A A 3 ? ? C6 A A 3 ? ? N1 A A 3 ? ? 120.73 117.70 3.03 0.50 N 117 15 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 113.32 108.50 4.82 0.70 N 118 15 C5 A A 7 ? ? C6 A A 7 ? ? N1 A A 7 ? ? 121.07 117.70 3.37 0.50 N 119 15 C5 A A 10 ? ? C6 A A 10 ? ? N1 A A 10 ? ? 121.25 117.70 3.55 0.50 N 120 15 C5 A A 12 ? ? C6 A A 12 ? ? N1 A A 12 ? ? 121.17 117.70 3.47 0.50 N 121 15 C5 A A 14 ? ? C6 A A 14 ? ? N1 A A 14 ? ? 121.44 117.70 3.74 0.50 N 122 15 C4 A A 15 ? ? C5 A A 15 ? ? C6 A A 15 ? ? 113.66 117.00 -3.34 0.50 N 123 15 C5 A A 15 ? ? C6 A A 15 ? ? N1 A A 15 ? ? 121.96 117.70 4.26 0.50 N 124 15 N1 A A 15 ? ? C6 A A 15 ? ? N6 A A 15 ? ? 114.89 118.60 -3.71 0.60 N 125 15 N3 A U 16 ? ? C2 A U 16 ? ? O2 A U 16 ? ? 117.76 122.20 -4.44 0.70 N 126 15 N1 A G 19 ? ? C6 A G 19 ? ? O6 A G 19 ? ? 115.46 119.90 -4.44 0.60 N 127 15 C5 A A 20 ? ? C6 A A 20 ? ? N1 A A 20 ? ? 121.20 117.70 3.50 0.50 N 128 15 C5 A A 23 ? ? C6 A A 23 ? ? N1 A A 23 ? ? 120.98 117.70 3.28 0.50 N 129 15 N1 A G 24 ? ? C6 A G 24 ? ? O6 A G 24 ? ? 115.76 119.90 -4.14 0.60 N 130 15 C5 A A 26 ? ? C6 A A 26 ? ? N1 A A 26 ? ? 121.11 117.70 3.41 0.50 N 131 15 C5 A A 28 ? ? C6 A A 28 ? ? N1 A A 28 ? ? 121.10 117.70 3.40 0.50 N 132 15 N3 A C 30 ? ? C2 A C 30 ? ? O2 A C 30 ? ? 117.62 121.90 -4.28 0.70 N 133 16 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 112.82 108.50 4.32 0.70 N 134 16 "C5'" A G 9 ? ? "C4'" A G 9 ? ? "C3'" A G 9 ? ? 106.06 115.20 -9.14 1.40 N 135 16 "C4'" A C 13 ? ? "C3'" A C 13 ? ? "C2'" A C 13 ? ? 95.73 102.60 -6.87 1.00 N 136 16 C5 A A 23 ? ? C6 A A 23 ? ? N1 A A 23 ? ? 120.94 117.70 3.24 0.50 N 137 17 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 113.47 108.50 4.97 0.70 N 138 17 "O4'" A U 8 ? ? "C1'" A U 8 ? ? N1 A U 8 ? ? 112.78 108.50 4.28 0.70 N 139 17 "O4'" A U 21 ? ? "C1'" A U 21 ? ? N1 A U 21 ? ? 112.76 108.50 4.26 0.70 N 140 18 "C4'" A C 13 ? ? "C3'" A C 13 ? ? "C2'" A C 13 ? ? 95.36 102.60 -7.24 1.00 N 141 18 "O4'" A A 14 ? ? "C1'" A A 14 ? ? N9 A A 14 ? ? 113.07 108.50 4.57 0.70 N 142 18 N9 A A 15 ? ? "C1'" A A 15 ? ? "C2'" A A 15 ? ? 105.21 112.00 -6.79 1.10 N 143 18 "O4'" A A 15 ? ? "C1'" A A 15 ? ? N9 A A 15 ? ? 115.00 108.50 6.50 0.70 N 144 18 N7 A A 15 ? ? C8 A A 15 ? ? N9 A A 15 ? ? 116.92 113.80 3.12 0.50 N 145 18 "C5'" A A 20 ? ? "C4'" A A 20 ? ? "C3'" A A 20 ? ? 105.18 115.20 -10.02 1.40 N 146 18 "C5'" A U 21 ? ? "C4'" A U 21 ? ? "C3'" A U 21 ? ? 105.64 115.20 -9.56 1.40 N 147 18 C5 A A 23 ? ? C6 A A 23 ? ? N1 A A 23 ? ? 120.93 117.70 3.23 0.50 N 148 18 C5 A A 28 ? ? C6 A A 28 ? ? N1 A A 28 ? ? 120.76 117.70 3.06 0.50 N 149 19 C5 A A 3 ? ? C6 A A 3 ? ? N1 A A 3 ? ? 121.34 117.70 3.64 0.50 N 150 19 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 113.91 108.50 5.41 0.70 N 151 19 C5 A A 5 ? ? C6 A A 5 ? ? N1 A A 5 ? ? 120.91 117.70 3.21 0.50 N 152 19 "O4'" A U 6 ? ? "C1'" A U 6 ? ? N1 A U 6 ? ? 113.77 108.50 5.27 0.70 N 153 19 C5 A A 7 ? ? C6 A A 7 ? ? N1 A A 7 ? ? 120.82 117.70 3.12 0.50 N 154 19 C5 A A 10 ? ? C6 A A 10 ? ? N1 A A 10 ? ? 121.11 117.70 3.41 0.50 N 155 19 "O4'" A U 11 ? ? "C1'" A U 11 ? ? N1 A U 11 ? ? 113.41 108.50 4.91 0.70 N 156 19 C5 A A 12 ? ? C6 A A 12 ? ? N1 A A 12 ? ? 120.95 117.70 3.25 0.50 N 157 19 "O4'" A A 14 ? ? "C1'" A A 14 ? ? N9 A A 14 ? ? 113.88 108.50 5.38 0.70 N 158 19 C5 A A 14 ? ? C6 A A 14 ? ? N1 A A 14 ? ? 121.42 117.70 3.72 0.50 N 159 19 N1 A A 14 ? ? C6 A A 14 ? ? N6 A A 14 ? ? 114.95 118.60 -3.65 0.60 N 160 19 C5 A A 15 ? ? C6 A A 15 ? ? N1 A A 15 ? ? 122.18 117.70 4.48 0.50 N 161 19 N1 A A 15 ? ? C6 A A 15 ? ? N6 A A 15 ? ? 114.90 118.60 -3.70 0.60 N 162 19 N1 A G 19 ? ? C6 A G 19 ? ? O6 A G 19 ? ? 116.14 119.90 -3.76 0.60 N 163 19 C5 A A 20 ? ? C6 A A 20 ? ? N1 A A 20 ? ? 121.21 117.70 3.51 0.50 N 164 19 "O4'" A U 21 ? ? "C1'" A U 21 ? ? N1 A U 21 ? ? 113.42 108.50 4.92 0.70 N 165 19 N3 A C 22 ? ? C2 A C 22 ? ? O2 A C 22 ? ? 117.62 121.90 -4.28 0.70 N 166 19 C5 A A 23 ? ? C6 A A 23 ? ? N1 A A 23 ? ? 121.39 117.70 3.69 0.50 N 167 19 N1 A A 23 ? ? C6 A A 23 ? ? N6 A A 23 ? ? 114.90 118.60 -3.70 0.60 N 168 19 N1 A G 24 ? ? C6 A G 24 ? ? O6 A G 24 ? ? 115.83 119.90 -4.07 0.60 N 169 19 C5 A A 26 ? ? C6 A A 26 ? ? N1 A A 26 ? ? 121.07 117.70 3.37 0.50 N 170 19 "O4'" A U 27 ? ? "C1'" A U 27 ? ? N1 A U 27 ? ? 112.80 108.50 4.30 0.70 N 171 19 C5 A A 28 ? ? C6 A A 28 ? ? N1 A A 28 ? ? 121.33 117.70 3.63 0.50 N 172 19 "O4'" A U 29 ? ? "C1'" A U 29 ? ? N1 A U 29 ? ? 113.64 108.50 5.14 0.70 N 173 19 "O4'" A C 30 ? ? "C1'" A C 30 ? ? N1 A C 30 ? ? 112.89 108.50 4.39 0.70 N 174 19 N3 A C 30 ? ? C2 A C 30 ? ? O2 A C 30 ? ? 117.48 121.90 -4.42 0.70 N 175 20 "O4'" A A 15 ? ? "C1'" A A 15 ? ? N9 A A 15 ? ? 113.28 108.50 4.78 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 U A 16 ? ? 0.077 'SIDE CHAIN' 2 5 A A 15 ? ? 0.056 'SIDE CHAIN' 3 9 A A 23 ? ? 0.063 'SIDE CHAIN' 4 10 A A 26 ? ? 0.060 'SIDE CHAIN' 5 11 A A 7 ? ? 0.061 'SIDE CHAIN' 6 12 A A 15 ? ? 0.057 'SIDE CHAIN' 7 12 A A 23 ? ? 0.055 'SIDE CHAIN' 8 13 A A 15 ? ? 0.075 'SIDE CHAIN' 9 15 A A 15 ? ? 0.063 'SIDE CHAIN' 10 17 C A 13 ? ? 0.062 'SIDE CHAIN' 11 19 A A 15 ? ? 0.076 'SIDE CHAIN' 12 19 U A 17 ? ? 0.065 'SIDE CHAIN' 13 20 U A 16 ? ? 0.064 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1YLG 'a-form double helix' 1YLG 'hairpin loop' 1YLG 'bulge loop' 1YLG '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 31 1_555 -0.381 -0.174 0.095 4.961 -4.251 -0.319 1 A_G1:C31_A A 1 ? A 31 ? 19 1 1 A G 2 1_555 A C 30 1_555 -0.536 -0.232 -0.072 -3.868 -8.866 -1.235 2 A_G2:C30_A A 2 ? A 30 ? 19 1 1 A A 3 1_555 A U 29 1_555 0.039 -0.057 0.327 -2.248 -12.062 0.056 3 A_A3:U29_A A 3 ? A 29 ? 20 1 1 A U 4 1_555 A A 28 1_555 -0.069 -0.028 0.299 -1.857 -13.046 2.117 4 A_U4:A28_A A 4 ? A 28 ? 20 1 1 A A 5 1_555 A U 27 1_555 -0.203 0.037 0.548 -1.241 -20.522 6.665 5 A_A5:U27_A A 5 ? A 27 ? 20 1 1 A U 6 1_555 A A 26 1_555 0.008 -0.072 0.885 -5.642 -19.336 5.442 6 A_U6:A26_A A 6 ? A 26 ? 20 1 1 A A 7 1_555 A G 24 1_555 -0.651 1.464 -0.495 28.460 -10.929 -16.323 7 A_A7:G24_A A 7 ? A 24 ? 8 1 1 A U 8 1_555 A A 23 1_555 -0.733 0.144 0.242 7.988 -6.615 -11.679 8 A_U8:A23_A A 8 ? A 23 ? 20 1 1 A G 9 1_555 A C 22 1_555 -0.550 -0.317 0.318 2.024 -16.873 -7.855 9 A_G9:C22_A A 9 ? A 22 ? 19 1 1 A A 10 1_555 A U 21 1_555 0.165 -0.092 0.644 -3.714 -15.142 -2.020 10 A_A10:U21_A A 10 ? A 21 ? 20 1 1 A U 11 1_555 A A 20 1_555 -0.463 0.313 0.547 -3.950 -14.389 -13.657 11 A_U11:A20_A A 11 ? A 20 ? 20 1 1 A A 12 1_555 A G 19 1_555 -0.036 1.360 -0.843 -11.758 -28.212 -14.258 12 A_A12:G19_A A 12 ? A 19 ? 8 ? # 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 31 1_555 A G 2 1_555 A C 30 1_555 -0.160 -1.973 3.489 0.515 3.467 32.985 -4.060 0.369 3.268 6.085 -0.903 33.165 1 AA_G1G2:C30C31_AA A 1 ? A 31 ? A 2 ? A 30 ? 1 A G 2 1_555 A C 30 1_555 A A 3 1_555 A U 29 1_555 -0.104 -1.626 3.184 -1.757 -1.347 35.551 -2.467 -0.081 3.243 -2.203 2.874 35.617 2 AA_G2A3:U29C30_AA A 2 ? A 30 ? A 3 ? A 29 ? 1 A A 3 1_555 A U 29 1_555 A U 4 1_555 A A 28 1_555 0.063 -1.703 3.289 0.711 -4.978 30.068 -2.200 0.029 3.519 -9.512 -1.358 30.476 3 AA_A3U4:A28U29_AA A 3 ? A 29 ? A 4 ? A 28 ? 1 A U 4 1_555 A A 28 1_555 A A 5 1_555 A U 27 1_555 0.217 -1.400 2.874 -0.439 9.295 34.300 -3.417 -0.409 2.421 15.412 0.728 35.503 4 AA_U4A5:U27A28_AA A 4 ? A 28 ? A 5 ? A 27 ? 1 A A 5 1_555 A U 27 1_555 A U 6 1_555 A A 26 1_555 -0.010 -1.646 3.286 -2.117 -0.745 32.511 -2.803 -0.355 3.316 -1.328 3.776 32.587 5 AA_A5U6:A26U27_AA A 5 ? A 27 ? A 6 ? A 26 ? 1 A U 6 1_555 A A 26 1_555 A A 7 1_555 A G 24 1_555 0.886 -2.138 4.234 -17.710 -15.721 45.244 -0.986 -2.732 4.133 -18.982 21.383 50.777 6 AA_U6A7:G24A26_AA A 6 ? A 26 ? A 7 ? A 24 ? 1 A A 7 1_555 A G 24 1_555 A U 8 1_555 A A 23 1_555 0.273 -2.263 3.975 -7.974 -6.120 33.478 -2.597 -1.986 4.142 -10.338 13.471 34.913 7 AA_A7U8:A23G24_AA A 7 ? A 24 ? A 8 ? A 23 ? 1 A U 8 1_555 A A 23 1_555 A G 9 1_555 A C 22 1_555 -0.338 -1.541 3.410 -3.323 -2.848 34.572 -2.112 0.026 3.538 -4.769 5.564 34.839 8 AA_U8G9:C22A23_AA A 8 ? A 23 ? A 9 ? A 22 ? 1 A G 9 1_555 A C 22 1_555 A A 10 1_555 A U 21 1_555 0.543 -0.802 3.715 -1.132 -12.826 43.371 0.300 -0.826 3.780 -16.915 1.492 45.154 9 AA_G9A10:U21C22_AA A 9 ? A 22 ? A 10 ? A 21 ? 1 A A 10 1_555 A U 21 1_555 A U 11 1_555 A A 20 1_555 -0.353 -1.733 3.142 2.355 -3.508 30.530 -2.586 1.117 3.280 -6.622 -4.445 30.814 10 AA_A10U11:A20U21_AA A 10 ? A 21 ? A 11 ? A 20 ? 1 A U 11 1_555 A A 20 1_555 A A 12 1_555 A G 19 1_555 -0.628 -1.522 3.173 7.800 13.689 34.778 -3.845 1.824 2.252 21.585 -12.299 38.079 11 AA_U11A12:G19A20_AA A 11 ? A 20 ? A 12 ? A 19 ? #