data_4258 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H Chemical Shift Assignments of the Palindromic 12mer d(TTTGACGCGTCAA)2 (MCB12T) which Contains the Recognition Site for the Yeast Transcription Factor Mbp1. ; _BMRB_accession_number 4258 _BMRB_flat_file_name bmr4258.str _Entry_type new _Submission_date 1998-10-29 _Accession_date 1998-10-29 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 McIntosh Pauline B . 2 Taylor Ian A . 3 Smerdon Steven J . 4 Frenkiel Thomas A . 5 Lane Andrew N . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 94 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-14 update BMRB 'update DNA residue label to two-letter code' 1999-11-23 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; 1H, 15N and 13C Assignments of the DNA Binding Domain of Transcription Factor Mbp1 from Saccharomyces cerevisiae in Both Its Free and DNA Bound Forms and H1 Assignments of the Free DNA ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 99281467 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 McIntosh Pauline B . 2 Taylor Ian A . 3 Smerdon Steven J . 4 Frenkiel Thomas A . 5 Lane Andrew N . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_volume 13 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 397 _Page_last 398 _Year 1999 _Details . loop_ _Keyword Cell Cycle Mbp1 'NMR assignments' stop_ save_ ################################## # Molecular system description # ################################## save_system_MCB12T _Saveframe_category molecular_system _Mol_system_name MCB12T _Abbreviation_common MCB12T _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA STRAND 1' $MCB12T 'DNA STRAND 2' $MCB12T stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state dimer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function ; MCB12T contains the recognition sequence (ACGCGTCA) for the transcription factor Mbp1. MCB12T is derived from the Mlu 1 cell cycle box (MCB) element found in the promoters of numerous genes involved in DNA sythesis in S. cerevisiae. ; stop_ _Database_query_date . _Details ; Palindromic 12mer containing the recognition sequence of the transcription factor Mbp1. ; save_ ######################## # Monomeric polymers # ######################## save_MCB12T _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common '12MER containing the mlu1 cell cycle box' _Abbreviation_common MCB12T _Molecular_mass . _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence TTTGACGCGTCAA loop_ _Residue_seq_code _Residue_label 1 DT 2 DT 3 DT 4 DG 5 DA 6 DC 7 DG 8 DC 9 DG 10 DT 11 DC 12 DA 13 DA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain _Fraction $MCB12T 'Baker's yeast' 4932 Eukaryota . Saccharomyces cerevisiae BL21/DE3 nucleus stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $MCB12T chemically_synthesized . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details ; Sample 1 is a 12base pair palindromic DNA duplex d(TTTGACGCGTCAA)2 (MCB12T) containing the Mbp1 recognition site ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MCB12T 1.0 mM . 'Na phosphate' 40 mM . NaCl 100 mM . D2O 10 % . H2O 90 % . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_list _Saveframe_category NMR_spectrometer _Manufacturer . _Model . _Field_strength . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions _Saveframe_category sample_conditions _Details ; The samples were equilibrated for 30 minutes under these conditions before the spectra were collected. ; loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.6 0.2 n/a temperature 288 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis DSS H 1 'methyl protons' ppm 0.0 . direct . . . stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chemical_shifts _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'DNA STRAND 1' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 DT H6 H 7.39 . 1 2 . 1 DT H71 H 1.55 . 2 3 . 1 DT H72 H 1.55 . 2 4 . 1 DT H73 H 1.55 . 2 5 . 1 DT H1' H 5.93 . 1 6 . 1 DT H2' H 2.1 . 1 7 . 1 DT H2'' H 2.43 . 1 8 . 1 DT H3' H 4.06 . 1 9 . 2 DT H3 H 13.4 . 1 10 . 2 DT H6 H 7.6 . 1 11 . 2 DT H71 H 1.81 . 2 12 . 2 DT H72 H 1.81 . 2 13 . 2 DT H73 H 1.81 . 2 14 . 2 DT H1' H 6.06 . 1 15 . 2 DT H2' H 2.28 . 1 16 . 2 DT H2'' H 2.34 . 1 17 . 2 DT H3' H 4.85 . 1 18 . 3 DT H3 H 13.93 . 1 19 . 3 DT H6 H 7.42 . 1 20 . 3 DT H71 H 1.75 . 2 21 . 3 DT H72 H 1.75 . 2 22 . 3 DT H73 H 1.75 . 2 23 . 3 DT H1' H 5.66 . 1 24 . 3 DT H2' H 2.06 . 1 25 . 3 DT H2'' H 2.38 . 1 26 . 3 DT H3' H 4.88 . 1 27 . 4 DG H1 H 12.68 . 1 28 . 4 DG H8 H 7.98 . 1 29 . 4 DG H1' H 5.49 . 1 30 . 4 DG H2' H 2.74 . 1 31 . 4 DG H2'' H 2.79 . 1 32 . 4 DG H3' H 5.03 . 1 33 . 5 DA H2 H 7.78 . 1 34 . 5 DA H8 H 8.21 . 1 35 . 5 DA H1' H 6.19 . 1 36 . 5 DA H2' H 2.66 . 1 37 . 5 DA H2'' H 2.87 . 1 38 . 5 DA H3' H 5.05 . 1 39 . 6 DC H41 H 8.1 . 1 40 . 6 DC H42 H 6.5 . 1 41 . 6 DC H5 H 5.19 . 1 42 . 6 DC H6 H 7.17 . 1 43 . 6 DC H1' H 5.52 . 1 44 . 6 DC H2' H 1.9 . 1 45 . 6 DC H2'' H 2.29 . 1 46 . 6 DC H3' H 4.8 . 1 47 . 7 DG H1 H 12.84 . 1 48 . 7 DG H8 H 7.82 . 1 49 . 7 DG H1' H 5.84 . 1 50 . 7 DG H2' H 2.57 . 1 51 . 7 DG H2'' H 2.67 . 1 52 . 7 DG H3' H 4.96 . 1 53 . 8 DC H41 H 8.24 . 1 54 . 8 DC H42 H 6.35 . 1 55 . 8 DC H5 H 5.29 . 1 56 . 8 DC H6 H 7.28 . 1 57 . 8 DC H1' H 5.63 . 1 58 . 8 DC H2' H 2.03 . 1 59 . 8 DC H2'' H 2.38 . 1 60 . 8 DC H3' H 4.83 . 1 61 . 9 DG H1 H 12.82 . 1 62 . 9 DG H8 H 7.9 . 1 63 . 9 DG H1' H 5.96 . 1 64 . 9 DG H2' H 2.61 . 1 65 . 9 DG H2'' H 2.78 . 1 66 . 9 DG H3' H 4.95 . 1 67 . 10 DT H3 H 13.74 . 1 68 . 10 DT H6 H 7.21 . 1 69 . 10 DT H71 H 1.4 . 1 70 . 10 DT H72 H 1.4 . 1 71 . 10 DT H73 H 1.4 . 1 72 . 10 DT H1' H 5.93 . 1 73 . 10 DT H2' H 2.02 . 1 74 . 10 DT H2'' H 2.40 . 1 75 . 10 DT H3' H 4.89 . 1 76 . 11 DC H41 H 8.45 . 1 77 . 11 DC H42 H 6.9 . 1 78 . 11 DC H5 H 5.68 . 1 79 . 11 DC H6 H 7.46 . 1 80 . 11 DC H1' H 5.26 . 1 81 . 11 DC H2' H 1.86 . 1 82 . 11 DC H2'' H 2.16 . 1 83 . 11 DC H3' H 4.77 . 1 84 . 12 DA H2 H 7.56 . 1 85 . 12 DA H8 H 8.12 . 1 86 . 12 DA H1' H 5.89 . 1 87 . 12 DA H2' H 2.63 . 1 88 . 12 DA H2'' H 2.77 . 1 89 . 12 DA H3' H 5.00 . 1 90 . 13 DA H8 H 8.1 . 1 91 . 13 DA H1' H 6.2 . 1 92 . 13 DA H2' H 2.38 . 1 93 . 13 DA H2'' H 2.63 . 1 94 . 13 DA H3' H 5.00 . 1 stop_ save_