data_4542 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of a uracil containing hairpin DNA ; _BMRB_accession_number 4542 _BMRB_flat_file_name bmr4542.str _Entry_type new _Submission_date 1999-08-20 _Accession_date 1999-12-06 _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 Ghosh M. . . 2 Kumar N. V. . 3 Varshney U. . . 4 Chary K. V.R. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 206 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2000-12-06 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural Characterization of a Uracil Containing Hairpin DNA by NMR and Molecular Dynamics ; _Citation_status published _Citation_type Journal _CAS_abstract_code . _MEDLINE_UI_code 99412438 _PubMed_ID 10481034 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ghosh M. . . 2 Kumar N. V. . 3 Varshney U. . . 4 Chary K. V.R. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 27 _Journal_issue 19 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3938 _Page_last 3944 _Year 1999 _Details . loop_ _Keyword uracil 'hairpin DNA' 'hairpin loop' 'double helix' stop_ save_ ################################## # Molecular system description # ################################## save_system_U-DNA _Saveframe_category molecular_system _Mol_system_name 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*TP*TP*UP*GP*GP*AP*TP*CP*CP*T)-3' _Abbreviation_common 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*TP*TP*UP*GP*GP*AP*TP*CP*CP*T)-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*TP*TP*UP*GP*GP*AP*TP*CP*CP*T)-3' $U-DNA 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_U-DNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*TP*TP*UP*GP*GP*AP*TP*CP*CP*T)-3' _Abbreviation_common 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*TP*TP*UP*GP*GP*AP*TP*CP*CP*T)-3' _Molecular_mass . _Mol_thiol_state 'not present' _Details 'Residue 15 is a uracil nucleotide.' ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; CTAGAGGATCCTTTUGGATC CT ; loop_ _Residue_seq_code _Residue_label 1 DC 2 DT 3 DA 4 DG 5 DA 6 DG 7 DG 8 DA 9 DT 10 DC 11 DC 12 DT 13 DT 14 DT 15 DU 16 DG 17 DG 18 DA 19 DT 20 DC 21 DC 22 DT 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 $U-DNA . . . . . . 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 $U-DNA . . . . . . 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 $U-DNA 5 mM . D2O 99 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $U-DNA 5 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1 loop_ _Task 'data collection' 'data analysis' stop_ _Details VARIAN save_ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 97 loop_ _Task 'structure calculation' stop_ _Details MSI save_ save_UXNMR _Saveframe_category software _Name UXNMR _Version 3.0 loop_ _Task 'data collection' stop_ _Details BRUKER save_ save_FELIX _Saveframe_category software _Name FELIX _Version 97 loop_ _Task 'data processing' 'data analysis' stop_ _Details MSI save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_E-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _Sample_label . save_ save_2D_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 . n/a temperature 305 . K pressure 1 . atm stop_ save_ save_sample_cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 . n/a temperature 295 . K pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_ref_1 _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 . H 1 . ppm . . . . . . 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_ref_1 _Mol_system_component_name 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*TP*TP*UP*GP*GP*AP*TP*CP*CP*T)-3' _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 DC H5 H 5.8 0.01 1 2 . 1 DC H6 H 7.71 0.01 1 3 . 1 DC H1' H 6.00 0.01 1 4 . 1 DC H2' H 2.18 0.01 1 5 . 1 DC H2'' H 2.46 0.01 1 6 . 1 DC H3' H 4.67 0.01 1 7 . 2 DT H6 H 7.51 0.01 1 8 . 2 DT H71 H 1.81 0.01 1 9 . 2 DT H72 H 1.81 0.01 1 10 . 2 DT H73 H 1.81 0.01 1 11 . 2 DT H1' H 5.98 0.01 1 12 . 2 DT H2' H 1.88 0.01 1 13 . 2 DT H2'' H 2.21 0.01 1 14 . 2 DT H3' H 4.67 0.01 1 15 . 2 DT H4' H 4.15 0.01 1 16 . 2 DT H5' H 3.99 0.01 4 17 . 2 DT H5'' H 3.99 0.01 4 18 . 3 DA H8 H 8.08 0.01 1 19 . 3 DA H1' H 5.98 0.01 1 20 . 3 DA H2' H 2.47 0.01 1 21 . 3 DA H2'' H 2.53 0.01 1 22 . 3 DA H3' H 4.85 0.01 1 23 . 3 DA H4' H 3.98 0.01 1 24 . 3 DA H5' H 3.89 0.01 4 25 . 3 DA H5'' H 3.89 0.01 4 26 . 4 DG H1' H 6.11 0.01 1 27 . 4 DG H2' H 2.58 0.01 1 28 . 4 DG H2'' H 2.72 0.01 1 29 . 5 DA H2 H 7.47 0.01 1 30 . 5 DA H8 H 8.12 0.01 1 31 . 5 DA H1' H 5.86 0.01 1 32 . 5 DA H2' H 2.71 0.01 1 33 . 5 DA H2'' H 2.78 0.01 1 34 . 5 DA H3' H 5.00 0.01 1 35 . 5 DA H4' H 4.37 0.01 1 36 . 5 DA H5' H 4.16 0.01 4 37 . 5 DA H5'' H 4.16 0.01 4 38 . 6 DG H1 H 12.78 0.01 1 39 . 6 DG H8 H 7.65 0.01 1 40 . 6 DG H1' H 5.55 0.01 1 41 . 6 DG H2' H 2.56 0.01 1 42 . 6 DG H2'' H 2.68 0.01 1 43 . 6 DG H3' H 4.84 0.01 1 44 . 6 DG H4' H 4.56 0.01 1 45 . 6 DG H5' H 4.20 0.01 4 46 . 6 DG H5'' H 4.20 0.01 4 47 . 7 DG H1 H 12.64 0.01 1 48 . 7 DG H8 H 7.67 0.01 1 49 . 7 DG H1' H 5.72 0.01 1 50 . 7 DG H2' H 2.68 0.01 1 51 . 7 DG H2'' H 2.78 0.01 1 52 . 7 DG H3' H 5.03 0.01 1 53 . 7 DG H4' H 4.18 0.01 1 54 . 7 DG H5' H 3.79 0.01 2 55 . 7 DG H5'' H 3.73 0.01 2 56 . 8 DA H2 H 7.85 0.01 1 57 . 8 DA H8 H 8.15 0.01 1 58 . 8 DA H1' H 6.27 0.01 1 59 . 8 DA H2' H 2.63 0.01 1 60 . 8 DA H2'' H 2.96 0.01 1 61 . 8 DA H3' H 5.01 0.01 1 62 . 8 DA H4' H 4.49 0.01 1 63 . 8 DA H5' H 4.27 0.01 4 64 . 8 DA H5'' H 4.27 0.01 4 65 . 9 DT H3 H 13.62 0.01 5 66 . 9 DT H6 H 7.17 0.01 1 67 . 9 DT H71 H 1.35 0.01 1 68 . 9 DT H72 H 1.35 0.01 1 69 . 9 DT H73 H 1.35 0.01 1 70 . 9 DT H1' H 5.96 0.01 1 71 . 9 DT H2' H 2.10 0.01 1 72 . 9 DT H2'' H 2.52 0.01 1 73 . 9 DT H3' H 4.88 0.01 1 74 . 9 DT H4' H 4.32 0.01 1 75 . 9 DT H5' H 4.21 0.01 4 76 . 9 DT H5'' H 4.21 0.01 4 77 . 10 DC H41 H 8.37 0.01 1 78 . 10 DC H42 H 6.77 0.01 1 79 . 10 DC H5 H 5.62 0.01 1 80 . 10 DC H6 H 7.59 0.01 1 81 . 10 DC H1' H 6.01 0.01 1 82 . 10 DC H2' H 2.12 0.01 1 83 . 10 DC H2'' H 2.52 0.01 1 84 . 10 DC H3' H 4.83 0.01 1 85 . 10 DC H4' H 4.22 0.01 1 86 . 10 DC H5' H 4.08 0.01 4 87 . 10 DC H5'' H 4.08 0.01 4 88 . 11 DC H41 H 8.58 0.01 1 89 . 11 DC H42 H 6.96 0.01 1 90 . 11 DC H5 H 5.62 0.01 1 91 . 11 DC H6 H 7.55 0.01 1 92 . 11 DC H1' H 6.07 0.01 1 93 . 11 DC H2' H 2.26 0.01 1 94 . 11 DC H2'' H 2.47 0.01 1 95 . 11 DC H3' H 4.83 0.01 1 96 . 12 DT H6 H 7.58 0.01 1 97 . 12 DT H71 H 1.82 0.01 1 98 . 12 DT H72 H 1.82 0.01 1 99 . 12 DT H73 H 1.82 0.01 1 100 . 12 DT H1' H 6.14 0.01 1 101 . 12 DT H2' H 2.17 0.01 1 102 . 12 DT H2'' H 2.42 0.01 1 103 . 12 DT H3' H 4.83 0.01 1 104 . 12 DT H4' H 4.24 0.01 1 105 . 12 DT H5' H 4.19 0.01 2 106 . 12 DT H5'' H 4.07 0.01 2 107 . 13 DT H6 H 7.63 0.01 1 108 . 13 DT H71 H 1.85 0.01 1 109 . 13 DT H72 H 1.85 0.01 1 110 . 13 DT H73 H 1.85 0.01 1 111 . 13 DT H1' H 6.14 0.01 1 112 . 13 DT H2' H 2.09 0.01 1 113 . 13 DT H2'' H 2.35 0.01 1 114 . 13 DT H3' H 4.59 0.01 1 115 . 13 DT H4' H 4.23 0.01 1 116 . 13 DT H5' H 4.09 0.01 4 117 . 13 DT H5'' H 4.09 0.01 4 118 . 14 DT H6 H 7.51 0.01 1 119 . 14 DT H71 H 1.66 0.01 1 120 . 14 DT H72 H 1.66 0.01 1 121 . 14 DT H73 H 1.66 0.01 1 122 . 14 DT H1' H 5.97 0.01 1 123 . 14 DT H2' H 2.13 0.01 1 124 . 14 DT H2'' H 2.38 0.01 1 125 . 14 DT H3' H 4.7 0.01 1 126 . 14 DT H4' H 4.1 0.01 1 127 . 14 DT H5' H 3.91 0.01 2 128 . 14 DT H5'' H 3.79 0.01 2 129 . 15 DU H5 H 5.73 0.01 1 130 . 15 DU H6 H 7.56 0.01 1 131 . 15 DU H1' H 5.89 0.01 1 132 . 15 DU H2' H 2.17 0.01 1 133 . 15 DU H2'' H 2.4 0.01 1 134 . 15 DU H3' H 4.66 0.01 1 135 . 15 DU H4' H 4.16 0.01 1 136 . 15 DU H5' H 3.87 0.01 2 137 . 15 DU H5'' H 3.86 0.01 2 138 . 16 DG H1 H 13.12 0.01 1 139 . 16 DG H8 H 7.92 0.01 1 140 . 16 DG H1' H 5.59 0.01 1 141 . 16 DG H2' H 2.66 0.01 1 142 . 16 DG H2'' H 2.77 0.01 1 143 . 16 DG H3' H 4.95 0.01 1 144 . 16 DG H4' H 4.32 0.01 1 145 . 16 DG H5' H 4.19 0.01 4 146 . 16 DG H5'' H 4.19 0.01 4 147 . 17 DG H1 H 12.74 0.01 1 148 . 17 DG H8 H 7.78 0.01 1 149 . 17 DG H1' H 5.76 0.01 1 150 . 17 DG H2' H 2.66 0.01 1 151 . 17 DG H2'' H 2.78 0.01 1 152 . 17 DG H3' H 5.03 0.01 1 153 . 17 DG H4' H 4.15 0.01 1 154 . 17 DG H5' H 4.42 0.01 4 155 . 17 DG H5'' H 4.42 0.01 4 156 . 18 DA H2 H 7.89 0.01 1 157 . 18 DA H8 H 8.20 0.01 1 158 . 18 DA H1' H 6.33 0.01 1 159 . 18 DA H2' H 2.65 0.01 1 160 . 18 DA H2'' H 2.98 0.01 1 161 . 18 DA H3' H 5.03 0.01 1 162 . 18 DA H4' H 4.50 0.01 1 163 . 18 DA H5' H 4.28 0.01 4 164 . 18 DA H5'' H 4.28 0.01 4 165 . 19 DT H3 H 13.62 0.01 5 166 . 19 DT H6 H 7.18 0.01 1 167 . 19 DT H71 H 1.35 0.01 1 168 . 19 DT H72 H 1.35 0.01 1 169 . 19 DT H73 H 1.35 0.01 1 170 . 19 DT H1' H 5.96 0.01 1 171 . 19 DT H2' H 2.11 0.01 1 172 . 19 DT H2'' H 2.52 0.01 1 173 . 19 DT H3' H 4.88 0.01 1 174 . 19 DT H4' H 4.33 0.01 1 175 . 19 DT H5' H 4.24 0.01 4 176 . 19 DT H5'' H 4.24 0.01 4 177 . 20 DC H41 H 8.19 0.01 1 178 . 20 DC H42 H 6.61 0.01 1 179 . 20 DC H5 H 5.57 0.01 1 180 . 20 DC H6 H 7.57 0.01 1 181 . 20 DC H1' H 6.01 0.01 1 182 . 20 DC H2' H 2.23 0.01 1 183 . 20 DC H2'' H 2.51 0.01 1 184 . 20 DC H3' H 4.83 0.01 1 185 . 21 DC H41 H 8.27 0.01 1 186 . 21 DC H42 H 6.82 0.01 1 187 . 21 DC H5 H 5.6 0.01 1 188 . 21 DC H6 H 7.55 0.01 1 189 . 21 DC H1' H 5.96 0.01 1 190 . 21 DC H2' H 2.12 0.01 1 191 . 21 DC H2'' H 2.49 0.01 1 192 . 21 DC H3' H 4.81 0.01 1 193 . 21 DC H4' H 4.23 0.01 1 194 . 21 DC H5' H 4.17 0.01 4 195 . 21 DC H5'' H 4.17 0.01 4 196 . 22 DT H6 H 7.46 0.01 1 197 . 22 DT H71 H 1.71 0.01 1 198 . 22 DT H72 H 1.71 0.01 1 199 . 22 DT H73 H 1.71 0.01 1 200 . 22 DT H1' H 6.25 0.01 1 201 . 22 DT H2' H 2.28 0.01 1 202 . 22 DT H2'' H 2.28 0.01 1 203 . 22 DT H3' H 4.82 0.01 1 204 . 22 DT H4' H 4.60 0.01 1 205 . 22 DT H5' H 4.17 0.01 2 206 . 22 DT H5'' H 4.06 0.01 2 stop_ save_