data_1BAE # _entry.id 1BAE # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.390 _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 1BAE pdb_00001bae 10.2210/pdb1bae/pdb WWPDB D_1000171523 ? ? # 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 1998-01-14 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-03-14 5 'Structure model' 1 4 2024-04-10 # _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' 6 4 'Structure model' 'Experimental preparation' 7 4 'Structure model' Other 8 4 'Structure model' 'Source and taxonomy' 9 5 'Structure model' 'Data collection' 10 5 'Structure model' 'Database references' 11 5 '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' citation 2 4 'Structure model' ndb_struct_conf_na 3 4 'Structure model' pdbx_database_status 4 4 'Structure model' pdbx_entity_src_syn 5 4 'Structure model' pdbx_nmr_ensemble 6 4 'Structure model' pdbx_nmr_exptl 7 4 'Structure model' pdbx_nmr_exptl_sample 8 4 'Structure model' pdbx_nmr_exptl_sample_conditions 9 4 'Structure model' pdbx_nmr_representative 10 4 'Structure model' pdbx_nmr_sample_details 11 4 'Structure model' pdbx_nmr_software 12 4 'Structure model' pdbx_nmr_spectrometer 13 4 'Structure model' pdbx_struct_assembly 14 4 'Structure model' pdbx_struct_assembly_prop 15 4 'Structure model' pdbx_struct_oper_list 16 5 'Structure model' chem_comp_atom 17 5 'Structure model' chem_comp_bond 18 5 'Structure model' database_2 19 5 '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' '_citation.page_last' 2 4 'Structure model' '_citation.pdbx_database_id_DOI' 3 4 'Structure model' '_citation.pdbx_database_id_PubMed' 4 4 'Structure model' '_pdbx_database_status.process_site' 5 4 'Structure model' '_pdbx_nmr_ensemble.conformer_selection_criteria' 6 4 'Structure model' '_pdbx_nmr_exptl_sample_conditions.label' 7 4 'Structure model' '_pdbx_nmr_exptl_sample_conditions.pH_units' 8 4 'Structure model' '_pdbx_nmr_exptl_sample_conditions.pressure' 9 4 'Structure model' '_pdbx_nmr_software.authors' 10 5 'Structure model' '_database_2.pdbx_DOI' 11 5 'Structure model' '_database_2.pdbx_database_accession' 12 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1BAE _pdbx_database_status.recvd_initial_deposition_date 1997-07-28 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Nonin, S.' 1 ? 'Tuan, A.P.' 2 ? 'Leroy, J.L.' 3 ? # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability. ; Structure 5 1231 1246 1997 STRUE6 UK 0969-2126 2005 ? 9331414 '10.1016/S0969-2126(97)00273-6' 1 'Structure and Conversion Kinetics of a Bi-Stable DNA I-Motif: Broken Symmetry in the [D(5Mcctcc)]4 Tetramer' J.Mol.Biol. 261 399 414 1996 JMOBAK UK 0022-2836 0070 ? 8780782 10.1006/jmbi.1996.0472 2 ;Solution Structures of the I-Motif Tetramers of D(Tcc), D(5Methylcct) and D(T5Methylcc): Novel Noe Connections between Amino Protons and Sugar Protons ; Structure 3 101 120 1995 STRUE6 UK 0969-2126 2005 ? 7743125 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nonin, S.' 1 ? primary 'Phan, A.T.' 2 ? primary 'Leroy, J.L.' 3 ? 1 'Nonin, S.' 4 ? 1 'Leroy, J.L.' 5 ? 2 'Leroy, J.L.' 6 ? 2 'Gueron, M.' 7 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*MCYP*CP*TP*TP*TP*AP*CP*C)-3') ; _entity.formula_weight 2271.602 _entity.pdbx_number_of_molecules 2 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details 'I-MOTIF DIMER FORMED BY TWO D(5MCCTTTACC) STRANDS' # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(MCY)(DC)(DT)(DT)(DT)(DA)(DC)(DC)' _entity_poly.pdbx_seq_one_letter_code_can CCTTTACC _entity_poly.pdbx_strand_id A,B _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 MCY n 1 2 DC n 1 3 DT n 1 4 DT n 1 5 DT n 1 6 DA n 1 7 DC n 1 8 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 MCY 'DNA linking' n "5-METHYL-2'-DEOXYCYTIDINE" ? 'C10 H15 N3 O4' 241.244 # 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 MCY 1 1 1 MCY MCY A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DC 8 8 8 DC C A . n B 1 1 MCY 1 1 1 MCY MCY B . n B 1 2 DC 2 2 2 DC C B . n B 1 3 DT 3 3 3 DT T B . n B 1 4 DT 4 4 4 DT T B . n B 1 5 DT 5 5 5 DT T B . n B 1 6 DA 6 6 6 DA A B . n B 1 7 DC 7 7 7 DC C B . n B 1 8 DC 8 8 8 DC C B . n # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' 3.1 ? 1 X-PLOR refinement 3.1 ? 2 X-PLOR phasing 3.1 ? 3 # _cell.entry_id 1BAE _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BAE _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _exptl.entry_id 1BAE _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _database_PDB_matrix.entry_id 1BAE _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 # _struct.entry_id 1BAE _struct.title ;STRUCTURE OF DNA (5'-D 5MCCTTTACC-3')2, NMR, 1 STRUCTURE ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1BAE _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DEOXYRIBONUCLEIC ACID, DNA DIMER OF 5MCCTTTACC, I-MOTIF, DIMER, 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 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1BAE _struct_ref.pdbx_db_accession 1BAE _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 1BAE A 1 ? 8 ? 1BAE 1 ? 8 ? 1 8 2 1 1BAE B 1 ? 8 ? 1BAE 1 ? 8 ? 1 8 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # 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)' 650 ? 1 MORE -6 ? 1 'SSA (A^2)' 2890 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 covale1 covale both ? A MCY 1 "O3'" ? ? ? 1_555 A DC 2 P ? ? A MCY 1 A DC 2 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale2 covale both ? B MCY 1 "O3'" ? ? ? 1_555 B DC 2 P ? ? B MCY 1 B DC 2 1_555 ? ? ? ? ? ? ? 1.613 ? ? hydrog1 hydrog ? ? A MCY 1 N4 ? ? ? 1_555 B DC 7 O2 ? ? A MCY 1 B DC 7 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog2 hydrog ? ? A MCY 1 O2 ? ? ? 1_555 B DC 7 N4 ? ? A MCY 1 B DC 7 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog3 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DC 8 O2 ? ? A DC 2 B DC 8 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog4 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DC 8 N4 ? ? A DC 2 B DC 8 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog5 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B MCY 1 O2 ? ? A DC 7 B MCY 1 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog6 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B MCY 1 N4 ? ? A DC 7 B MCY 1 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog7 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DC 2 O2 ? ? A DC 8 B DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog8 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DC 2 N4 ? ? A DC 8 B DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 110.58 108.30 2.28 0.30 N 2 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.97 108.30 2.67 0.30 N 3 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 110.46 108.30 2.16 0.30 N 4 1 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 111.26 108.30 2.96 0.30 N 5 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 110.87 108.30 2.57 0.30 N 6 1 N7 A DA 6 ? ? C8 A DA 6 ? ? N9 A DA 6 ? ? 117.80 113.80 4.00 0.50 N 7 1 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? N1 A DC 7 ? ? 110.20 108.30 1.90 0.30 N 8 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 110.74 108.30 2.44 0.30 N 9 1 "O4'" B DC 2 ? ? "C1'" B DC 2 ? ? N1 B DC 2 ? ? 110.62 108.30 2.32 0.30 N 10 1 "O4'" B DT 3 ? ? "C1'" B DT 3 ? ? N1 B DT 3 ? ? 110.99 108.30 2.69 0.30 N 11 1 "O4'" B DT 4 ? ? "C1'" B DT 4 ? ? N1 B DT 4 ? ? 110.44 108.30 2.14 0.30 N 12 1 "O4'" B DT 5 ? ? "C1'" B DT 5 ? ? N1 B DT 5 ? ? 111.34 108.30 3.04 0.30 N 13 1 "O4'" B DA 6 ? ? "C1'" B DA 6 ? ? N9 B DA 6 ? ? 110.90 108.30 2.60 0.30 N 14 1 N7 B DA 6 ? ? C8 B DA 6 ? ? N9 B DA 6 ? ? 117.77 113.80 3.97 0.50 N 15 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 110.16 108.30 1.86 0.30 N 16 1 "O4'" B DC 8 ? ? "C1'" B DC 8 ? ? N1 B DC 8 ? ? 110.74 108.30 2.44 0.30 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 MCY 1 A MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" 2 B MCY 1 B MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" # _pdbx_nmr_ensemble.entry_id 1BAE _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the least restraint violations' # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 1BAE _pdbx_nmr_representative.selection_criteria 'fewest violations' # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.details _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.type '8 mM d(5mCCTTTACC)' ? sample_1 1 '90% H2O/10% D2O' solution '8 mM d(5mCCTTTACC)' ? sample_2 2 99.99% solution # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id 'd(5mCCTTTACC)' 8 ? mM ? 1 'd(5mCCTTTACC)' 8 ? mM ? 2 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 270 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 4.3 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K _pdbx_nmr_exptl_sample_conditions.label 1 _pdbx_nmr_exptl_sample_conditions.pH_units pH _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 NOESY 1 2 1 NOESY 2 3 1 TOCSY 2 # _pdbx_nmr_refine.entry_id 1BAE _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _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 refinement X-PLOR 3.1 BRUNGER 1 'structure solution' X-PLOR 3.1 BRUNGER 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 DT OP3 O N N 71 DT P P N N 72 DT OP1 O N N 73 DT OP2 O N N 74 DT "O5'" O N N 75 DT "C5'" C N N 76 DT "C4'" C N R 77 DT "O4'" O N N 78 DT "C3'" C N S 79 DT "O3'" O N N 80 DT "C2'" C N N 81 DT "C1'" C N R 82 DT N1 N N N 83 DT C2 C N N 84 DT O2 O N N 85 DT N3 N N N 86 DT C4 C N N 87 DT O4 O N N 88 DT C5 C N N 89 DT C7 C N N 90 DT C6 C N N 91 DT HOP3 H N N 92 DT HOP2 H N N 93 DT "H5'" H N N 94 DT "H5''" H N N 95 DT "H4'" H N N 96 DT "H3'" H N N 97 DT "HO3'" H N N 98 DT "H2'" H N N 99 DT "H2''" H N N 100 DT "H1'" H N N 101 DT H3 H N N 102 DT H71 H N N 103 DT H72 H N N 104 DT H73 H N N 105 DT H6 H N N 106 MCY N1 N N N 107 MCY C2 C N N 108 MCY N3 N N N 109 MCY C4 C N N 110 MCY C5 C N N 111 MCY C6 C N N 112 MCY O2 O N N 113 MCY N4 N N N 114 MCY "C1'" C N R 115 MCY "C2'" C N N 116 MCY "C3'" C N S 117 MCY "C4'" C N R 118 MCY "O4'" O N N 119 MCY "O3'" O N N 120 MCY "C5'" C N N 121 MCY "O5'" O N N 122 MCY C5A C N N 123 MCY H6 H N N 124 MCY HN41 H N N 125 MCY HN42 H N N 126 MCY "H1'" H N N 127 MCY "H2'" H N N 128 MCY "H2''" H N N 129 MCY "H3'" H N N 130 MCY "H4'" H N N 131 MCY "HO3'" H N N 132 MCY "H5'" H N N 133 MCY "H5''" H N N 134 MCY "HO5'" H N N 135 MCY H5A1 H N N 136 MCY H5A2 H N N 137 MCY H5A3 H N N 138 # 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 DT OP3 P sing N N 74 DT OP3 HOP3 sing N N 75 DT P OP1 doub N N 76 DT P OP2 sing N N 77 DT P "O5'" sing N N 78 DT OP2 HOP2 sing N N 79 DT "O5'" "C5'" sing N N 80 DT "C5'" "C4'" sing N N 81 DT "C5'" "H5'" sing N N 82 DT "C5'" "H5''" sing N N 83 DT "C4'" "O4'" sing N N 84 DT "C4'" "C3'" sing N N 85 DT "C4'" "H4'" sing N N 86 DT "O4'" "C1'" sing N N 87 DT "C3'" "O3'" sing N N 88 DT "C3'" "C2'" sing N N 89 DT "C3'" "H3'" sing N N 90 DT "O3'" "HO3'" sing N N 91 DT "C2'" "C1'" sing N N 92 DT "C2'" "H2'" sing N N 93 DT "C2'" "H2''" sing N N 94 DT "C1'" N1 sing N N 95 DT "C1'" "H1'" sing N N 96 DT N1 C2 sing N N 97 DT N1 C6 sing N N 98 DT C2 O2 doub N N 99 DT C2 N3 sing N N 100 DT N3 C4 sing N N 101 DT N3 H3 sing N N 102 DT C4 O4 doub N N 103 DT C4 C5 sing N N 104 DT C5 C7 sing N N 105 DT C5 C6 doub N N 106 DT C7 H71 sing N N 107 DT C7 H72 sing N N 108 DT C7 H73 sing N N 109 DT C6 H6 sing N N 110 MCY N1 C2 sing N N 111 MCY N1 C6 sing N N 112 MCY N1 "C1'" sing N N 113 MCY C2 N3 sing N N 114 MCY C2 O2 doub N N 115 MCY N3 C4 doub N N 116 MCY C4 C5 sing N N 117 MCY C4 N4 sing N N 118 MCY C5 C6 doub N N 119 MCY C5 C5A sing N N 120 MCY C6 H6 sing N N 121 MCY N4 HN41 sing N N 122 MCY N4 HN42 sing N N 123 MCY "C1'" "C2'" sing N N 124 MCY "C1'" "O4'" sing N N 125 MCY "C1'" "H1'" sing N N 126 MCY "C2'" "C3'" sing N N 127 MCY "C2'" "H2'" sing N N 128 MCY "C2'" "H2''" sing N N 129 MCY "C3'" "C4'" sing N N 130 MCY "C3'" "O3'" sing N N 131 MCY "C3'" "H3'" sing N N 132 MCY "C4'" "O4'" sing N N 133 MCY "C4'" "C5'" sing N N 134 MCY "C4'" "H4'" sing N N 135 MCY "O3'" "HO3'" sing N N 136 MCY "C5'" "O5'" sing N N 137 MCY "C5'" "H5'" sing N N 138 MCY "C5'" "H5''" sing N N 139 MCY "O5'" "HO5'" sing N N 140 MCY C5A H5A1 sing N N 141 MCY C5A H5A2 sing N N 142 MCY C5A H5A3 sing N N 143 # _ndb_struct_conf_na.entry_id 1BAE _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 DC 2 1_555 B DC 8 1_555 2.186 1.775 0.095 11.839 -2.758 179.963 1 A_DC2:DC8_B A 2 ? B 8 ? 15 2 1 B MCY 1 1_555 A DC 7 1_555 2.225 1.921 -0.098 -9.671 -13.582 178.921 2 B_MCY1:DC7_A B 1 ? A 7 ? 15 2 1 A MCY 1 1_555 B DC 7 1_555 2.226 1.920 -0.100 -9.665 -13.591 178.921 3 A_MCY1:DC7_B A 1 ? B 7 ? 15 2 1 B DC 2 1_555 A DC 8 1_555 2.186 1.777 0.093 11.821 -2.728 179.935 4 B_DC2:DC8_A B 2 ? A 8 ? 15 2 # 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 DC 2 1_555 B DC 8 1_555 B MCY 1 1_555 A DC 7 1_555 -3.138 1.976 -0.207 -142.058 -102.106 -130.470 -1.051 -1.482 -0.772 51.189 -71.218 -177.884 1 AB_DC2MCY1:DC7DC8_AB A 2 ? B 8 ? B 1 ? A 7 ? 1 B MCY 1 1_555 A DC 7 1_555 A MCY 1 1_555 B DC 7 1_555 1.364 -2.259 0.028 -127.174 -126.588 -174.831 1.130 0.682 0.000 63.294 -63.587 -179.975 2 BA_MCY1MCY1:DC7DC7_BA B 1 ? A 7 ? A 1 ? B 7 ? 1 A MCY 1 1_555 B DC 7 1_555 B DC 2 1_555 A DC 8 1_555 3.134 -1.978 0.220 142.062 102.053 131.513 -1.051 -1.481 0.772 51.157 -71.213 177.914 3 AB_MCY1DC2:DC8DC7_AB A 1 ? B 7 ? B 2 ? A 8 ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 'HOME BUILT' Home-built 360 ? 2 AMX Bruker 600 ? # _atom_sites.entry_id 1BAE _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_