data_6274 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H chemical shift assignments for the triloop DNA hairpin 5'- GTACACAGTAC - 3' ; _BMRB_accession_number 6274 _BMRB_flat_file_name bmr6274.str _Entry_type new _Submission_date 2004-07-23 _Accession_date 2004-07-27 _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 Lamoureux Michele . . 2 Patard Louis . . 3 Cordier Christine . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 101 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-19 update BMRB 'update DNA residue label to two-letter code' 2006-08-16 update author 'complete the citation' 2004-12-14 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 6273 'GTTCACAGAAC mutant' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Spectroscopic and structural impact of a stem base-pair change in DNA hairpins: GTTC-ACA-GAAC versus GTAC-ACA-GTAC. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16530466 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lamoureux Michele . . 2 Patard Louis . . 3 Hernandez Belen . . 4 Couesnon Thierry . . 5 Santini Guillaume P. . 6 Cognet Jean A. . 7 Gouyette Catherine . . 8 Cordier Christine . . stop_ _Journal_abbreviation 'Spectrochim. Acta. A. Mol. Biomol. Spectrosc.' _Journal_volume 65 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 84 _Page_last 94 _Year 2006 _Details . loop_ _Keyword hairpin stop_ save_ ################################## # Molecular system description # ################################## save_system_ACA _Saveframe_category molecular_system _Mol_system_name 'GTACACAGTAC DNA hairpin' _Abbreviation_common ACA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'hairpin DNA' $hairpin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_hairpin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA hairpin' _Abbreviation_common hairpin _Molecular_mass 3493 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence GTACACAGTAC loop_ _Residue_seq_code _Residue_label 1 DG 2 DT 3 DA 4 DC 5 DA 6 DC 7 DA 8 DG 9 DT 10 DA 11 DC 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 _Details $hairpin 'Vibrio cholerae' 666 Eubacteria . vibrio cholerae ; The mutant GTTCACAGAAC sequence has the natural source as above. The sequence of this entry was chemically synthesized. ; 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 $hairpin 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $hairpin 8 mM . phosphate 20.6 mM . EDTA 1.0 mM . D2O 10 '% v/v' . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $hairpin 8 mM . phosphate 20.6 mM . EDTA 1.0 mM . D2O 99.9 '% v/v' . stop_ save_ ############################ # Computer software used # ############################ save_GIFA _Saveframe_category software _Name GIFA _Version 4.2 loop_ _Task 'Processing of the specta' integration stop_ _Details ; Delsuc, M.A, 1989 In : Skilling, J. (Ed) Maximum Entropy and Bayesian Methods. Kluwer Academic Publishers, Dordrecht. Pons, J.L., Malliavin, T.E., Delsuc, M.A. Gifa V4 : a complete package for NMR data set processing. J. Biomol. NMR,1996, 8, 445-452 ; save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _Sample_label . save_ save_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H TOCSY' _Sample_label . save_ save_1H-1H_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H DQF-COSY' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _BMRB_pulse_sequence_accession_number . _Details 'Broad Band or inverse Broad Band probes were employed' save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H TOCSY' _BMRB_pulse_sequence_accession_number . _Details 'Broad Band or inverse Broad Band probes were employed' save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H DQF-COSY' _BMRB_pulse_sequence_accession_number . _Details 'Broad Band or inverse Broad Band probes were employed' save_ ####################### # Sample conditions # ####################### save_Ex-cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH* 7.2 0.1 n/a temperature 283 0.5 K 'ionic strength' 0.08 0.001 M 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 _Indirect_shift_ratio H2O H 1 protons ppm 4.80 external direct cylindrical external parallel 1.0 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_GTTC_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Ex-cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'hairpin DNA' _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 DG H8 H 7.81 0.02 1 2 . 1 DG H1' H 5.83 0.02 1 3 . 1 DG H2' H 2.63 0.02 1 4 . 1 DG H2'' H 2.63 0.02 1 5 . 1 DG H3' H 4.65 0.02 1 6 . 1 DG H4' H 4.06 0.02 1 7 . 1 DG H5' H 3.68 0.02 1 8 . 1 DG H5'' H 3.63 0.02 1 9 . 2 DT H6 H 7.38 0.02 1 10 . 2 DT H71 H 1.27 0.02 2 11 . 2 DT H72 H 1.27 0.02 2 12 . 2 DT H73 H 1.27 0.02 2 13 . 2 DT H1' H 5.8 0.02 1 14 . 2 DT H2' H 2.17 0.02 1 15 . 2 DT H2'' H 2.49 0.02 1 16 . 2 DT H3' H 4.8 0.02 1 17 . 2 DT H4' H 4.16 0.02 1 18 . 2 DT H5' H 4.02 0.02 1 19 . 2 DT H5'' H 4.02 0.02 1 20 . 3 DA H2 H 7.43 0.02 1 21 . 3 DA H8 H 8.08 0.02 1 22 . 3 DA H1' H 6.08 0.02 1 23 . 3 DA H2' H 2.35 0.02 1 24 . 3 DA H2'' H 2.64 0.02 1 25 . 3 DA H3' H 4.86 0.02 1 26 . 3 DA H4' H 4.24 0.02 1 27 . 3 DA H5' H 4.04 0.02 1 28 . 3 DA H5'' H 3.96 0.02 1 29 . 4 DC H5 H 4.68 0.02 1 30 . 4 DC H6 H 6.64 0.02 1 31 . 4 DC H1' H 5.66 0.02 1 32 . 4 DC H2' H 1.37 0.02 1 33 . 4 DC H2'' H 1.88 0.02 1 34 . 4 DC H3' H 4.66 0.02 1 35 . 4 DC H4' H 4.05 0.02 1 36 . 4 DC H5' H 3.99 0.02 1 37 . 4 DC H5'' H 3.96 0.02 1 38 . 5 DA H2 H 8.2 0.02 1 39 . 5 DA H8 H 8.4 0.02 1 40 . 5 DA H1' H 5.77 0.02 1 41 . 5 DA H2' H 2.73 0.02 1 42 . 5 DA H2'' H 2.4 0.02 1 43 . 5 DA H3' H 4.74 0.02 1 44 . 5 DA H4' H 4.41 0.02 1 45 . 5 DA H5' H 3.94 0.02 1 46 . 5 DA H5'' H 3.94 0.02 1 47 . 6 DC H5 H 5.3 0.02 1 48 . 6 DC H6 H 7.29 0.02 1 49 . 6 DC H1' H 5.77 0.02 1 50 . 6 DC H2' H 1.62 0.02 1 51 . 6 DC H2'' H 1.95 0.02 1 52 . 6 DC H3' H 4.31 0.02 1 53 . 6 DC H4' H 2.23 0.02 1 54 . 6 DC H5' H 2.78 0.02 1 55 . 6 DC H5'' H 3.24 0.02 1 56 . 7 DA H2 H 7.98 0.02 1 57 . 7 DA H8 H 7.93 0.02 1 58 . 7 DA H1' H 6.08 0.02 1 59 . 7 DA H2' H 2.7 0.02 1 60 . 7 DA H2'' H 2.7 0.02 1 61 . 7 DA H3' H 4.7 0.02 1 62 . 7 DA H4' H 4.16 0.02 1 63 . 7 DA H5' H 3.82 0.02 1 64 . 7 DA H5'' H 3.65 0.02 1 65 . 8 DG H8 H 7.96 0.02 1 66 . 8 DG H1' H 5.41 0.02 1 67 . 8 DG H2' H 2.54 0.02 1 68 . 8 DG H2'' H 2.47 0.02 1 69 . 8 DG H3' H 4.78 0.02 1 70 . 8 DG H4' H 4.24 0.02 1 71 . 8 DG H5' H 4.03 0.02 1 72 . 8 DG H5'' H 3.99 0.02 1 73 . 9 DT H6 H 7.25 0.02 1 74 . 9 DT H71 H 1.29 0.02 2 75 . 9 DT H72 H 1.29 0.02 2 76 . 9 DT H73 H 1.29 0.02 2 77 . 9 DT H1' H 5.73 0.02 1 78 . 9 DT H2' H 2.14 0.02 1 79 . 9 DT H2'' H 2.45 0.02 1 80 . 9 DT H3' H 4.79 0.02 1 81 . 9 DT H4' H 4.15 0.02 1 82 . 9 DT H5' H 4.05 0.02 1 83 . 9 DT H5'' H 4.05 0.02 1 84 . 10 DA H2 H 7.25 0.02 1 85 . 10 DA H8 H 8.16 0.02 1 86 . 10 DA H1' H 6.16 0.02 1 87 . 10 DA H2' H 2.56 0.02 1 88 . 10 DA H2'' H 2.76 0.02 1 89 . 10 DA H3' H 4.88 0.02 1 90 . 10 DA H4' H 4.28 0.02 1 91 . 10 DA H5' H 4.05 0.02 1 92 . 10 DA H5'' H 4.04 0.02 1 93 . 11 DC H5 H 5.23 0.02 1 94 . 11 DC H6 H 7.27 0.02 1 95 . 11 DC H1' H 5.9 0.02 1 96 . 11 DC H2' H 1.97 0.02 1 97 . 11 DC H2'' H 1.99 0.02 1 98 . 11 DC H3' H 4.34 0.02 1 99 . 11 DC H4' H 3.87 0.02 1 100 . 11 DC H5' H 4.14 0.02 1 101 . 11 DC H5'' H 3.95 0.02 1 stop_ save_