data_1YBL # _entry.id 1YBL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 1YBL pdb_00001ybl 10.2210/pdb1ybl/pdb RCSB RCSB031347 ? ? WWPDB D_1000031347 ? ? # 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 2005-01-11 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-06-06 5 'Structure model' 1 4 2024-05-01 # _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' 'Derived calculations' 5 4 'Structure model' 'Experimental preparation' 6 4 'Structure model' 'Source and taxonomy' 7 5 'Structure model' 'Data collection' 8 5 'Structure model' 'Database references' # 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' ndb_struct_conf_na 2 4 'Structure model' ndb_struct_na_base_pair 3 4 'Structure model' ndb_struct_na_base_pair_step 4 4 'Structure model' pdbx_entity_src_syn 5 4 'Structure model' pdbx_nmr_exptl_sample_conditions 6 4 'Structure model' pdbx_struct_assembly 7 4 'Structure model' pdbx_struct_assembly_prop 8 4 'Structure model' pdbx_struct_oper_list 9 4 'Structure model' struct_conn 10 5 'Structure model' chem_comp_atom 11 5 'Structure model' chem_comp_bond 12 5 'Structure model' database_2 # 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' '_ndb_struct_na_base_pair.hbond_type_28' 2 4 'Structure model' '_ndb_struct_na_base_pair_step.tip' 3 4 'Structure model' '_ndb_struct_na_base_pair_step.twist' 4 4 'Structure model' '_pdbx_nmr_exptl_sample_conditions.temperature' 5 5 'Structure model' '_database_2.pdbx_DOI' 6 5 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.entry_id 1YBL _pdbx_database_status.status_code REL _pdbx_database_status.recvd_initial_deposition_date 2004-12-21 _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 N _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 294D 'The X-ray structure of the same i-motif tetramer' unspecified PDB 1YBN 'i-motif, different sequence, topology 1' unspecified PDB 1YBR 'i-motif, different sequence, topology 2' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Esmaili, N.' 1 'Leroy, J.-L.' 2 # _citation.id primary _citation.title 'i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 33 _citation.page_first 213 _citation.page_last 224 _citation.year 2005 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15647504 _citation.pdbx_database_id_DOI 10.1093/nar/gki160 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Esmaili, N.' 1 ? primary 'Leroy, J.-L.' 2 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-D(*AP*AP*CP*CP*CP*C)-3'" _entity.formula_weight 1738.183 _entity.pdbx_number_of_molecules 4 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DA)(DA)(DC)(DC)(DC)(DC)' _entity_poly.pdbx_seq_one_letter_code_can AACCCC _entity_poly.pdbx_strand_id A,B,C,D _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 DA n 1 2 DA n 1 3 DC n 1 4 DC n 1 5 DC n 1 6 DC 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 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 # 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 DA 1 1 1 DA A A . n A 1 2 DA 2 2 2 DA A A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DC 6 6 6 DC C A . n B 1 1 DA 1 1 1 DA A B . n B 1 2 DA 2 2 2 DA A B . n B 1 3 DC 3 3 3 DC C B . n B 1 4 DC 4 4 4 DC C B . n B 1 5 DC 5 5 5 DC C B . n B 1 6 DC 6 6 6 DC C B . n C 1 1 DA 1 1 1 DA A C . n C 1 2 DA 2 2 2 DA A C . n C 1 3 DC 3 3 3 DC C C . n C 1 4 DC 4 4 4 DC C C . n C 1 5 DC 5 5 5 DC C C . n C 1 6 DC 6 6 6 DC C C . n D 1 1 DA 1 1 1 DA A D . n D 1 2 DA 2 2 2 DA A D . n D 1 3 DC 3 3 3 DC C D . n D 1 4 DC 4 4 4 DC C D . n D 1 5 DC 5 5 5 DC C D . n D 1 6 DC 6 6 6 DC C D . n # _exptl.entry_id 1YBL _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1YBL _struct.title 'NMR structure of the i-motif tetramer of d(AACCCC)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YBL _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA; i-motif; hemiprotonated cytidine; tetrahymena; telomer, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 1 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1YBL _struct_ref.pdbx_db_accession 1YBL _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1YBL A 1 ? 6 ? 1YBL 1 ? 6 ? 1 6 2 1 1YBL B 1 ? 6 ? 1YBL 1 ? 6 ? 1 6 3 1 1YBL C 1 ? 6 ? 1YBL 1 ? 6 ? 1 6 4 1 1YBL D 1 ? 6 ? 1YBL 1 ? 6 ? 1 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 4660 ? 1 MORE 38 ? 1 'SSA (A^2)' 2410 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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 ? _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_ _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 DA 2 N6 ? ? ? 1_555 C DA 2 N7 ? ? A DA 2 C DA 2 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog2 hydrog ? ? A DA 2 N7 ? ? ? 1_555 C DA 2 N6 ? ? A DA 2 C DA 2 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog3 hydrog ? ? A DC 3 N4 ? ? ? 1_555 C DC 3 O2 ? ? A DC 3 C DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog4 hydrog ? ? A DC 3 O2 ? ? ? 1_555 C DC 3 N4 ? ? A DC 3 C DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog5 hydrog ? ? A DC 4 N4 ? ? ? 1_555 C DC 4 O2 ? ? A DC 4 C DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog6 hydrog ? ? A DC 4 O2 ? ? ? 1_555 C DC 4 N4 ? ? A DC 4 C DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog7 hydrog ? ? A DC 5 N4 ? ? ? 1_555 C DC 5 O2 ? ? A DC 5 C DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog8 hydrog ? ? A DC 5 O2 ? ? ? 1_555 C DC 5 N4 ? ? A DC 5 C DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog9 hydrog ? ? A DC 6 N4 ? ? ? 1_555 C DC 6 O2 ? ? A DC 6 C DC 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog10 hydrog ? ? A DC 6 O2 ? ? ? 1_555 C DC 6 N4 ? ? A DC 6 C DC 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog11 hydrog ? ? B DA 2 N6 ? ? ? 1_555 D DA 2 N7 ? ? B DA 2 D DA 2 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog12 hydrog ? ? B DA 2 N7 ? ? ? 1_555 D DA 2 N6 ? ? B DA 2 D DA 2 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog13 hydrog ? ? B DC 3 N4 ? ? ? 1_555 D DC 3 O2 ? ? B DC 3 D DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog14 hydrog ? ? B DC 3 O2 ? ? ? 1_555 D DC 3 N4 ? ? B DC 3 D DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog15 hydrog ? ? B DC 4 N4 ? ? ? 1_555 D DC 4 O2 ? ? B DC 4 D DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog16 hydrog ? ? B DC 4 O2 ? ? ? 1_555 D DC 4 N4 ? ? B DC 4 D DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog17 hydrog ? ? B DC 5 N4 ? ? ? 1_555 D DC 5 O2 ? ? B DC 5 D DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog18 hydrog ? ? B DC 5 O2 ? ? ? 1_555 D DC 5 N4 ? ? B DC 5 D DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog19 hydrog ? ? B DC 6 N4 ? ? ? 1_555 D DC 6 O2 ? ? B DC 6 D DC 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog20 hydrog ? ? B DC 6 O2 ? ? ? 1_555 D DC 6 N4 ? ? B DC 6 D DC 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 H41 _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 DC _pdbx_validate_close_contact.auth_seq_id_1 4 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 N3 _pdbx_validate_close_contact.auth_asym_id_2 D _pdbx_validate_close_contact.auth_comp_id_2 DC _pdbx_validate_close_contact.auth_seq_id_2 4 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.45 # 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 DA 1 ? ? "C1'" A DA 1 ? ? N9 A DA 1 ? ? 111.78 108.30 3.48 0.30 N 2 1 N7 A DA 1 ? ? C8 A DA 1 ? ? N9 A DA 1 ? ? 117.73 113.80 3.93 0.50 N 3 1 C8 A DA 1 ? ? N9 A DA 1 ? ? C4 A DA 1 ? ? 103.19 105.80 -2.61 0.40 N 4 1 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 112.71 108.30 4.41 0.30 N 5 1 N7 A DA 2 ? ? C8 A DA 2 ? ? N9 A DA 2 ? ? 117.55 113.80 3.75 0.50 N 6 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 112.55 108.30 4.25 0.30 N 7 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 112.25 108.30 3.95 0.30 N 8 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 112.23 108.30 3.93 0.30 N 9 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 111.31 108.30 3.01 0.30 N 10 1 "O4'" B DA 1 ? ? "C1'" B DA 1 ? ? N9 B DA 1 ? ? 111.61 108.30 3.31 0.30 N 11 1 N7 B DA 1 ? ? C8 B DA 1 ? ? N9 B DA 1 ? ? 117.67 113.80 3.87 0.50 N 12 1 C8 B DA 1 ? ? N9 B DA 1 ? ? C4 B DA 1 ? ? 103.14 105.80 -2.66 0.40 N 13 1 "O4'" B DA 2 ? ? "C1'" B DA 2 ? ? N9 B DA 2 ? ? 112.49 108.30 4.19 0.30 N 14 1 N7 B DA 2 ? ? C8 B DA 2 ? ? N9 B DA 2 ? ? 117.56 113.80 3.76 0.50 N 15 1 "O4'" B DC 3 ? ? "C1'" B DC 3 ? ? N1 B DC 3 ? ? 112.45 108.30 4.15 0.30 N 16 1 "O4'" B DC 4 ? ? "C1'" B DC 4 ? ? N1 B DC 4 ? ? 113.09 108.30 4.79 0.30 N 17 1 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 112.26 108.30 3.96 0.30 N 18 1 "O4'" B DC 6 ? ? "C1'" B DC 6 ? ? N1 B DC 6 ? ? 110.86 108.30 2.56 0.30 N 19 1 "O4'" C DA 1 ? ? "C1'" C DA 1 ? ? N9 C DA 1 ? ? 111.76 108.30 3.46 0.30 N 20 1 N7 C DA 1 ? ? C8 C DA 1 ? ? N9 C DA 1 ? ? 117.74 113.80 3.94 0.50 N 21 1 C8 C DA 1 ? ? N9 C DA 1 ? ? C4 C DA 1 ? ? 103.22 105.80 -2.58 0.40 N 22 1 "O4'" C DA 2 ? ? "C1'" C DA 2 ? ? N9 C DA 2 ? ? 112.79 108.30 4.49 0.30 N 23 1 N7 C DA 2 ? ? C8 C DA 2 ? ? N9 C DA 2 ? ? 117.45 113.80 3.65 0.50 N 24 1 "O4'" C DC 3 ? ? "C1'" C DC 3 ? ? N1 C DC 3 ? ? 112.21 108.30 3.91 0.30 N 25 1 "O4'" C DC 4 ? ? "C1'" C DC 4 ? ? N1 C DC 4 ? ? 112.32 108.30 4.02 0.30 N 26 1 "O4'" C DC 5 ? ? "C1'" C DC 5 ? ? N1 C DC 5 ? ? 112.30 108.30 4.00 0.30 N 27 1 "O4'" C DC 6 ? ? "C1'" C DC 6 ? ? N1 C DC 6 ? ? 111.12 108.30 2.82 0.30 N 28 1 "O4'" D DA 1 ? ? "C1'" D DA 1 ? ? N9 D DA 1 ? ? 111.79 108.30 3.49 0.30 N 29 1 N7 D DA 1 ? ? C8 D DA 1 ? ? N9 D DA 1 ? ? 117.75 113.80 3.95 0.50 N 30 1 C8 D DA 1 ? ? N9 D DA 1 ? ? C4 D DA 1 ? ? 103.10 105.80 -2.70 0.40 N 31 1 "O4'" D DA 2 ? ? "C1'" D DA 2 ? ? N9 D DA 2 ? ? 112.56 108.30 4.26 0.30 N 32 1 N7 D DA 2 ? ? C8 D DA 2 ? ? N9 D DA 2 ? ? 117.56 113.80 3.76 0.50 N 33 1 "O4'" D DC 3 ? ? "C1'" D DC 3 ? ? N1 D DC 3 ? ? 112.47 108.30 4.17 0.30 N 34 1 "O4'" D DC 4 ? ? "C1'" D DC 4 ? ? N1 D DC 4 ? ? 111.54 108.30 3.24 0.30 N 35 1 "O4'" D DC 5 ? ? "C1'" D DC 5 ? ? N1 D DC 5 ? ? 112.10 108.30 3.80 0.30 N 36 1 "O4'" D DC 6 ? ? "C1'" D DC 6 ? ? N1 D DC 6 ? ? 111.14 108.30 2.84 0.30 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 DA A 1 ? ? 0.088 'SIDE CHAIN' 2 1 DA A 2 ? ? 0.056 'SIDE CHAIN' 3 1 DC A 3 ? ? 0.058 'SIDE CHAIN' 4 1 DC A 4 ? ? 0.081 'SIDE CHAIN' 5 1 DA B 1 ? ? 0.091 'SIDE CHAIN' 6 1 DA B 2 ? ? 0.059 'SIDE CHAIN' 7 1 DC B 3 ? ? 0.068 'SIDE CHAIN' 8 1 DC B 4 ? ? 0.076 'SIDE CHAIN' 9 1 DA C 1 ? ? 0.088 'SIDE CHAIN' 10 1 DA C 2 ? ? 0.055 'SIDE CHAIN' 11 1 DC C 3 ? ? 0.061 'SIDE CHAIN' 12 1 DC C 4 ? ? 0.083 'SIDE CHAIN' 13 1 DA D 1 ? ? 0.091 'SIDE CHAIN' 14 1 DA D 2 ? ? 0.060 'SIDE CHAIN' 15 1 DC D 3 ? ? 0.068 'SIDE CHAIN' 16 1 DC D 4 ? ? 0.087 'SIDE CHAIN' # _pdbx_nmr_ensemble.entry_id 1YBL _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'back calculated data agree with experimental NOESY spectrum' _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 1YBL _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'fewest violations' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents 'pH 4.5 to 6' _pdbx_nmr_sample_details.solvent_system 'H2O/D2O solution' _pdbx_nmr_sample_details.label ? _pdbx_nmr_sample_details.type ? _pdbx_nmr_sample_details.details ? # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 273 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 4.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength 'no added salt' _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K _pdbx_nmr_exptl_sample_conditions.label ? _pdbx_nmr_exptl_sample_conditions.pH_units ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units ? # 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 2 '2D TOCSY' 2 # _pdbx_nmr_details.entry_id 1YBL _pdbx_nmr_details.text 'This structure was determined using standard 2D homonuclear techniques' # _pdbx_nmr_refine.entry_id 1YBL _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details '96 NOE-derived distances constraints and 12 distance restraints for hydrogen bonds derived from proton exchange measurements' _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal 'structure solution' X-PLOR 3.851 'Brunger A.T.' 1 refinement X-PLOR 3.851 'Brunger A.T.' 2 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 # _ndb_struct_conf_na.entry_id 1YBL _ndb_struct_conf_na.feature 'double helix' # 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 DA 2 1_555 C DA 2 1_555 -5.903 4.335 0.010 12.162 44.826 -179.749 1 A_DA2:DA2_C A 2 ? C 2 ? 2 8 1 A DC 3 1_555 C DC 3 1_555 1.910 1.912 0.028 -19.333 1.265 179.961 2 A_DC3:DC3_C A 3 ? C 3 ? 15 2 1 D DC 6 1_555 B DC 6 1_555 -1.989 -0.191 -0.019 -2.092 2.983 -179.342 3 D_DC6:DC6_B D 6 ? B 6 ? 15 2 1 A DC 4 1_555 C DC 4 1_555 -2.129 -0.130 0.004 3.691 1.771 -179.951 4 A_DC4:DC4_C A 4 ? C 4 ? 15 2 1 D DC 5 1_555 B DC 5 1_555 -2.043 -0.547 -0.028 0.484 -12.646 -179.293 5 D_DC5:DC5_B D 5 ? B 5 ? 15 2 1 A DC 5 1_555 C DC 5 1_555 -1.856 -0.685 0.014 0.360 -11.305 -179.916 6 A_DC5:DC5_C A 5 ? C 5 ? 15 2 1 D DC 4 1_555 B DC 4 1_555 -2.337 -0.002 -0.352 3.038 0.584 -174.504 7 D_DC4:DC4_B D 4 ? B 4 ? 15 2 1 A DC 6 1_555 C DC 6 1_555 -1.681 -0.317 0.039 -2.346 3.886 -179.783 8 A_DC6:DC6_C A 6 ? C 6 ? 15 2 1 D DC 3 1_555 B DC 3 1_555 -2.154 -1.743 0.002 18.970 -0.920 -179.541 9 D_DC3:DC3_B D 3 ? B 3 ? 15 2 1 D DA 2 1_555 B DA 2 1_555 -6.098 4.271 -0.003 12.468 44.231 -179.380 10 D_DA2:DA2_B D 2 ? B 2 ? 2 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 DA 2 1_555 C DA 2 1_555 A DC 3 1_555 C DC 3 1_555 -0.014 0.010 2.214 -0.089 0.018 -122.295 -0.006 -0.009 2.214 -0.010 -0.051 -122.295 1 AA_DA2DC3:DC3DA2_CC A 2 ? C 2 ? A 3 ? C 3 ? 1 A DC 3 1_555 C DC 3 1_555 D DC 6 1_555 B DC 6 1_555 2.172 2.078 0.087 125.167 -128.281 -58.935 -1.017 1.107 0.017 64.281 62.721 -179.328 2 AD_DC3DC6:DC6DC3_BC A 3 ? C 3 ? D 6 ? B 6 ? 1 D DC 6 1_555 B DC 6 1_555 A DC 4 1_555 C DC 4 1_555 -2.098 2.577 -0.048 -140.510 -111.404 -65.680 -1.307 -1.025 -0.062 55.799 -70.378 -179.424 3 DA_DC6DC4:DC4DC6_CB D 6 ? B 6 ? A 4 ? C 4 ? 1 A DC 4 1_555 C DC 4 1_555 D DC 5 1_555 B DC 5 1_555 -3.014 2.738 0.028 118.685 134.866 8.187 1.336 1.536 0.066 67.554 -59.449 179.653 4 AD_DC4DC5:DC5DC4_BC A 4 ? C 4 ? D 5 ? B 5 ? 1 D DC 5 1_555 B DC 5 1_555 A DC 5 1_555 C DC 5 1_555 -1.621 1.731 -0.044 -132.235 -121.677 -81.149 -0.879 -0.796 -0.044 60.874 -66.156 -179.771 5 DA_DC5DC5:DC5DC5_CB D 5 ? B 5 ? A 5 ? C 5 ? 1 A DC 5 1_555 C DC 5 1_555 D DC 4 1_555 B DC 4 1_555 -3.124 2.584 0.032 116.757 132.689 -31.186 -1.338 -1.522 0.127 -67.238 59.165 -176.864 6 AD_DC5DC4:DC4DC5_BC A 5 ? C 5 ? D 4 ? B 4 ? 1 D DC 4 1_555 B DC 4 1_555 A DC 6 1_555 C DC 6 1_555 -1.976 2.662 0.182 -137.947 -110.249 46.236 1.361 0.951 -0.037 -55.771 69.782 176.864 7 DA_DC4DC6:DC6DC4_CB D 4 ? B 4 ? A 6 ? C 6 ? 1 A DC 6 1_555 C DC 6 1_555 D DC 3 1_555 B DC 3 1_555 -2.058 2.136 -0.031 127.865 125.950 79.997 1.072 1.025 0.005 63.040 -63.999 179.601 8 AD_DC6DC3:DC3DC6_BC A 6 ? C 6 ? D 3 ? B 3 ? 1 D DC 3 1_555 B DC 3 1_555 D DA 2 1_555 B DA 2 1_555 -0.016 -0.002 -2.253 -0.079 -0.114 -57.280 -0.002 -0.014 -2.253 0.119 -0.082 -57.281 9 DD_DC3DA2:DA2DC3_BB D 3 ? B 3 ? D 2 ? B 2 ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 500 _pdbx_nmr_spectrometer.type ? # _atom_sites.entry_id 1YBL _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_