data_4536 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural basis for uracil DNA glycosylase interaction with uracil: NMR study ; _BMRB_accession_number 4536 _BMRB_flat_file_name bmr4536.str _Entry_type original _Submission_date 1999-11-25 _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 Kumar1 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" 197 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2000-09-01 original author 'original release' 2010-07-14 update BMRB 'update DNA residue label to two-letter code' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural basis for uracil DNA glycosylase interaction with uracil: NMR study' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 10756190 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ghosh M. . . 2 Kumar1 V. . . 3 Varshney U. . . 4 Chary K. V.R. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 28 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1906 _Page_last 1912 _Year 2000 _Details . loop_ _Keyword 'double helix' 'hairpin dna' 'hairpin loop' 'udg-uracil interaction' uracil stop_ save_ ################################## # Molecular system description # ################################## save_hairpin_system _Saveframe_category molecular_system _Mol_system_name 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*UP*TP*TP*GP*GP*AP*TP*CP*CP*T)-3' _Abbreviation_common hairpin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA hairpin' $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 'URACIL CONTAINING HAIRPIN DNA' _Abbreviation_common hairpin _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; CTAGAGGATCCTXTTGGATC 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 DUR 14 DT 15 DT 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_ ###################### # Polymer residues # ###################### save_chem_comp_DUR _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 2'-DEOXYURIDINE _BMRB_code . _PDB_code DUR _Standard_residue_derivative . _Molecular_mass 228.202 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jun 9 14:06:26 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N1 N1 N . 0 . ? C2 C2 C . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O2 O2 O . 0 . ? O4 O4 O . 0 . ? C1' C1' C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4' C4' C . 0 . ? O3' O3' O . 0 . ? O4' O4' O . 0 . ? C5' C5' C . 0 . ? O5' O5' O . 0 . ? HN3 HN3 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? H1' H1' H . 0 . ? H2'1 H2'1 H . 0 . ? H2'2 H2'2 H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? HO3' HO3' H . 0 . ? H5'1 H5'1 H . 0 . ? H5'2 H5'2 H . 0 . ? HO5' HO5' H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N1 C2 ? ? SING N1 C6 ? ? SING N1 C1' ? ? SING C2 N3 ? ? DOUB C2 O2 ? ? SING N3 C4 ? ? SING N3 HN3 ? ? SING C4 C5 ? ? DOUB C4 O4 ? ? DOUB C5 C6 ? ? SING C5 H5 ? ? SING C6 H6 ? ? SING C1' C2' ? ? SING C1' O4' ? ? SING C1' H1' ? ? SING C2' C3' ? ? SING C2' H2'1 ? ? SING C2' H2'2 ? ? SING C3' C4' ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING C4' O4' ? ? SING C4' C5' ? ? SING C4' H4' ? ? SING O3' HO3' ? ? SING C5' O5' ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? SING O5' HO5' ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $hairpin . . . . . . 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 'not reported' . . . . . 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 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 $hairpin 5 mM . D2O 10 % . H2O 90 % . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1 loop_ _Task COLLECTION 'DATA ANALYSIS' stop_ _Details VARIAN save_ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 97 loop_ _Task 'STRUCTURE SOLUTION' stop_ _Details MSI save_ save_UXNMR _Saveframe_category software _Name UXNMR _Version 3.0 loop_ _Task COLLECTION stop_ _Details BRUKER save_ save_FELIX _Saveframe_category software _Name FELIX _Version 97 loop_ _Task 'DATA ANALYSIS' PROCESSING 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_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_E-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _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 pressure 1 . atm temperature 305 . K 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 pressure 1 . atm temperature 295 . K 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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label . H 1 . ppm . . . . . . $entry_citation $entry_citation 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 'DNA hairpin' _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 H6 H 7.70 0.01 1 2 . 1 DC H1' H 5.78 0.01 1 3 . 1 DC H2' H 2.16 0.01 1 4 . 1 DC H2'' H 2.41 0.01 1 5 . 1 DC H3' H 4.65 0.01 1 6 . 1 DC H5' H 3.74 0.01 4 7 . 1 DC H5'' H 3.74 0.01 4 8 . 2 DT H6 H 7.49 0.01 1 9 . 2 DT H71 H 1.81 0.01 2 10 . 2 DT H72 H 1.81 0.01 2 11 . 2 DT H73 H 1.81 0.01 2 12 . 2 DT H1' H 5.97 0.01 1 13 . 2 DT H2' H 2.16 0.01 1 14 . 2 DT H2'' H 2.45 0.01 1 15 . 2 DT H3' H 4.67 0.01 1 16 . 2 DT H4' H 3.97 0.01 1 17 . 3 DA H2 H 7.23 0.01 1 18 . 3 DA H8 H 8.07 0.01 1 19 . 3 DA H1' H 5.89 0.01 1 20 . 3 DA H2' H 2.39 0.01 1 21 . 3 DA H2'' H 2.49 0.01 1 22 . 3 DA H3' H 4.82 0.01 1 23 . 3 DA H4' H 3.96 0.01 1 24 . 3 DA H5' H 3.86 0.01 4 25 . 3 DA H5'' H 3.86 0.01 4 26 . 4 DG H8 H 7.70 0.01 1 27 . 4 DG H2'' H 2.41 0.01 1 28 . 5 DA H2 H 7.47 0.01 1 29 . 5 DA H8 H 8.11 0.01 1 30 . 5 DA H1' H 5.88 0.01 1 31 . 5 DA H2' H 2.70 0.01 1 32 . 5 DA H2'' H 2.78 0.01 1 33 . 6 DG H1 H 12.79 0.01 1 34 . 6 DG H8 H 7.65 0.01 1 35 . 6 DG H1' H 5.54 0.01 1 36 . 6 DG H2' H 2.55 0.01 1 37 . 6 DG H2'' H 2.67 0.01 1 38 . 6 DG H3' H 4.99 0.01 1 39 . 7 DG H1 H 12.62 0.01 1 40 . 7 DG H8 H 7.67 0.01 1 41 . 7 DG H1' H 5.71 0.01 1 42 . 7 DG H2' H 2.67 0.01 1 43 . 7 DG H2'' H 2.77 0.01 1 44 . 7 DG H3' H 4.97 0.01 1 45 . 7 DG H4' H 4.18 0.01 1 46 . 8 DA H2 H 7.84 0.01 1 47 . 8 DA H8 H 8.14 0.01 1 48 . 8 DA H1' H 6.26 0.01 1 49 . 8 DA H2' H 2.60 0.01 1 50 . 8 DA H2'' H 2.95 0.01 1 51 . 8 DA H3' H 4.82 0.01 1 52 . 8 DA H4' H 4.47 0.01 1 53 . 8 DA H5' H 4.25 0.01 4 54 . 8 DA H5'' H 4.25 0.01 4 55 . 9 DT H3 H 13.60 0.01 5 56 . 9 DT H6 H 7.15 0.01 1 57 . 9 DT H71 H 1.32 0.01 2 58 . 9 DT H72 H 1.32 0.01 2 59 . 9 DT H73 H 1.32 0.01 2 60 . 9 DT H1' H 5.94 0.01 1 61 . 9 DT H2' H 2.08 0.01 1 62 . 9 DT H2'' H 2.51 0.01 1 63 . 9 DT H3' H 4.86 0.01 1 64 . 9 DT H4' H 4.30 0.01 1 65 . 9 DT H5' H 4.21 0.01 2 66 . 9 DT H5'' H 4.17 0.01 2 67 . 10 DC H41 H 8.37 0.01 1 68 . 10 DC H42 H 6.77 0.01 1 69 . 10 DC H5 H 5.60 0.01 1 70 . 10 DC H6 H 7.52 0.01 1 71 . 10 DC H1' H 6.00 0.01 1 72 . 10 DC H2' H 2.09 0.01 1 73 . 10 DC H2'' H 2.26 0.01 1 74 . 10 DC H3' H 4.81 0.01 1 75 . 10 DC H4' H 4.22 0.01 1 76 . 10 DC H5' H 4.13 0.01 4 77 . 10 DC H5'' H 4.13 0.01 4 78 . 11 DC H41 H 8.58 0.01 1 79 . 11 DC H42 H 6.96 0.01 1 80 . 11 DC H5 H 5.60 0.01 1 81 . 11 DC H6 H 7.53 0.01 1 82 . 11 DC H1' H 6.09 0.01 1 83 . 11 DC H2' H 2.11 0.01 1 84 . 11 DC H2'' H 2.45 0.01 1 85 . 11 DC H3' H 4.81 0.01 1 86 . 11 DC H4' H 4.21 0.01 1 87 . 12 DT H6 H 7.59 0.01 1 88 . 12 DT H71 H 1.81 0.01 2 89 . 12 DT H72 H 1.81 0.01 2 90 . 12 DT H73 H 1.81 0.01 2 91 . 12 DT H1' H 6.14 0.01 1 92 . 12 DT H2' H 2.21 0.01 1 93 . 12 DT H2'' H 2.42 0.01 1 94 . 12 DT H3' H 4.82 0.01 1 95 . 12 DT H4' H 4.22 0.01 1 96 . 12 DT H5' H 4.16 0.01 2 97 . 12 DT H5'' H 4.06 0.01 2 98 . 13 DUR H5 H 5.81 0.01 1 99 . 13 DUR H6 H 7.80 0.01 1 100 . 13 DUR H1' H 6.13 0.01 1 101 . 13 DUR H2' H 2.11 0.01 1 102 . 13 DUR H2'' H 2.39 0.01 1 103 . 13 DUR H3' H 4.66 0.01 1 104 . 13 DUR H4' H 4.22 0.01 1 105 . 13 DUR H5' H 4.05 0.01 2 106 . 13 DUR H5'' H 3.97 0.01 2 107 . 14 DT H6 H 7.59 0.01 1 108 . 14 DT H71 H 1.67 0.01 2 109 . 14 DT H72 H 1.67 0.01 2 110 . 14 DT H73 H 1.67 0.01 2 111 . 14 DT H1' H 6.13 0.01 1 112 . 14 DT H2' H 2.02 0.01 1 113 . 14 DT H2'' H 2.28 0.01 1 114 . 14 DT H3' H 4.67 0.01 1 115 . 14 DT H4' H 4.02 0.01 1 116 . 14 DT H5' H 3.88 0.01 2 117 . 14 DT H5'' H 3.75 0.01 2 118 . 15 DT H6 H 7.34 0.01 1 119 . 15 DT H71 H 1.76 0.01 2 120 . 15 DT H72 H 1.76 0.01 2 121 . 15 DT H73 H 1.76 0.01 2 122 . 15 DT H1' H 5.86 0.01 1 123 . 15 DT H2' H 2.01 0.01 1 124 . 15 DT H2'' H 2.31 0.01 1 125 . 15 DT H3' H 4.65 0.01 1 126 . 15 DT H4' H 4.12 0.01 1 127 . 15 DT H5' H 3.94 0.01 2 128 . 15 DT H5'' H 3.81 0.01 2 129 . 16 DG H1 H 13.10 0.01 1 130 . 16 DG H8 H 7.90 0.01 1 131 . 16 DG H1' H 5.53 0.01 1 132 . 16 DG H2' H 2.65 0.01 1 133 . 16 DG H2'' H 2.75 0.01 1 134 . 16 DG H3' H 4.92 0.01 1 135 . 16 DG H4' H 4.30 0.01 1 136 . 16 DG H5' H 4.02 0.01 4 137 . 16 DG H5'' H 4.02 0.01 4 138 . 17 DG H1 H 12.75 0.01 1 139 . 17 DG H8 H 7.78 0.01 1 140 . 17 DG H1' H 5.74 0.01 1 141 . 17 DG H2' H 2.64 0.01 1 142 . 17 DG H2'' H 2.77 0.01 1 143 . 17 DG H3' H 5.01 0.01 1 144 . 17 DG H4' H 4.42 0.01 1 145 . 17 DG H5' H 4.41 0.01 2 146 . 17 DG H5'' H 4.17 0.01 2 147 . 18 DA H2 H 7.88 0.01 1 148 . 18 DA H8 H 8.19 0.01 1 149 . 18 DA H1' H 6.31 0.01 1 150 . 18 DA H2' H 2.83 0.01 1 151 . 18 DA H2'' H 2.96 0.01 1 152 . 18 DA H3' H 5.01 0.01 1 153 . 18 DA H4' H 4.48 0.01 1 154 . 18 DA H5' H 4.26 0.01 4 155 . 18 DA H5'' H 4.26 0.01 4 156 . 19 DT H3 H 13.60 0.01 5 157 . 19 DT H6 H 7.17 0.01 1 158 . 19 DT H71 H 1.33 0.01 2 159 . 19 DT H72 H 1.33 0.01 2 160 . 19 DT H73 H 1.33 0.01 2 161 . 19 DT H1' H 5.94 0.01 1 162 . 19 DT H2' H 2.09 0.01 1 163 . 19 DT H2'' H 2.50 0.01 1 164 . 19 DT H3' H 4.87 0.01 1 165 . 19 DT H4' H 4.31 0.01 1 166 . 19 DT H5' H 4.22 0.01 2 167 . 19 DT H5'' H 4.17 0.01 2 168 . 20 DC H41 H 8.19 0.01 1 169 . 20 DC H42 H 6.61 0.01 1 170 . 20 DC H5 H 5.55 0.01 1 171 . 20 DC H6 H 7.54 0.01 1 172 . 20 DC H1' H 5.94 0.01 1 173 . 20 DC H2' H 2.22 0.01 1 174 . 20 DC H2'' H 2.50 0.01 1 175 . 20 DC H3' H 4.82 0.01 1 176 . 20 DC H4' H 4.20 0.01 1 177 . 20 DC H5' H 4.13 0.01 4 178 . 20 DC H5'' H 4.13 0.01 4 179 . 21 DC H41 H 8.27 0.01 1 180 . 21 DC H42 H 6.82 0.01 1 181 . 21 DC H5 H 5.58 0.01 1 182 . 21 DC H6 H 7.56 0.01 1 183 . 21 DC H1' H 5.94 0.01 1 184 . 21 DC H2' H 2.10 0.01 1 185 . 21 DC H2'' H 2.47 0.01 1 186 . 21 DC H3' H 4.83 0.01 1 187 . 22 DT H6 H 7.46 0.01 1 188 . 22 DT H71 H 1.70 0.01 2 189 . 22 DT H72 H 1.70 0.01 2 190 . 22 DT H73 H 1.70 0.01 2 191 . 22 DT H1' H 6.24 0.01 1 192 . 22 DT H2' H 2.27 0.01 1 193 . 22 DT H2'' H 2.27 0.01 1 194 . 22 DT H3' H 4.58 0.01 1 195 . 22 DT H4' H 4.15 0.01 1 196 . 22 DT H5' H 4.04 0.01 4 197 . 22 DT H5'' H 4.04 0.01 4 stop_ save_