data_27580 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Backbone 1H, 15N and 13C Chemical shifts of N-terminal domain of antitoxin VapB46 from Mycobacterium tuberculosis ; _BMRB_accession_number 27580 _BMRB_flat_file_name bmr27580.str _Entry_type original _Submission_date 2018-08-18 _Accession_date 2018-08-18 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Assignment for determination of DNA binding interface' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Roy Madhurima . . 2 De Soumya . . 3 Das Amit K. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 46 "13C chemical shifts" 148 "15N chemical shifts" 46 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-03-22 update BMRB 'update entry citation' 2019-01-02 original author 'original release' stop_ _Original_release_date 2018-08-20 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural characterization of VapB46 antitoxin from Mycobacterium tuberculosis: insights into VapB46-DNA binding. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30576065 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Roy Madhurima . . 2 Kundu Anirban . . 3 Bhunia Anirban . . 4 'Das Gupta' Sujoy . . 5 De Soumya . . 6 Das 'Amit Kumar' K. . stop_ _Journal_abbreviation 'FEBS J.' _Journal_name_full 'The FEBS journal' _Journal_volume 286 _Journal_issue 6 _Journal_ISSN 1742-4658 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1174 _Page_last 1190 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name VapB46 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label VapB46 $VapB46 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_VapB46 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common VapB46 _Molecular_mass . _Mol_thiol_state 'all free' loop_ _Biological_function 'DNA binding' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 66 _Mol_residue_sequence ; MRGSHHHHHHGSMTPTACAT VSTMTSVGVRALRQRASELL RRVEAGETIEITDRGRPVAL LSPLPQ ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -11 MET 2 -10 ARG 3 -9 GLY 4 -8 SER 5 -7 HIS 6 -6 HIS 7 -5 HIS 8 -4 HIS 9 -3 HIS 10 -2 HIS 11 -1 GLY 12 0 SER 13 1 MET 14 2 THR 15 3 PRO 16 4 THR 17 5 ALA 18 6 CYS 19 7 ALA 20 8 THR 21 9 VAL 22 10 SER 23 11 THR 24 12 MET 25 13 THR 26 14 SER 27 15 VAL 28 16 GLY 29 17 VAL 30 18 ARG 31 19 ALA 32 20 LEU 33 21 ARG 34 22 GLN 35 23 ARG 36 24 ALA 37 25 SER 38 26 GLU 39 27 LEU 40 28 LEU 41 29 ARG 42 30 ARG 43 31 VAL 44 32 GLU 45 33 ALA 46 34 GLY 47 35 GLU 48 36 THR 49 37 ILE 50 38 GLU 51 39 ILE 52 40 THR 53 41 ASP 54 42 ARG 55 43 GLY 56 44 ARG 57 45 PRO 58 46 VAL 59 47 ALA 60 48 LEU 61 49 LEU 62 50 SER 63 51 PRO 64 52 LEU 65 53 PRO 66 54 GLN 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 $VapB46 'Mycobacterium tuberculosis' 1773 Bacteria . Mycobacterium tuberculosis 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 $VapB46 'recombinant technology' . Escherichia coli . pQE30 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 $VapB46 0.3 mM '[U-13C; U-15N]' 'potassium phosphate' 50 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' DTT 2 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Zhengrong and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_3D_CBCA(CO)NH_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CBCA(CO)NH' _Sample_label $sample_1 save_ save_3D_HNCACB_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_3D_HNCO_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCO' _Sample_label $sample_1 save_ save_3D_HN(CA)CO_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HN(CA)CO' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.2 . M pH 6.5 . pH pressure 1 . atm temperature 308 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_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 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-15N HSQC' '3D CBCA(CO)NH' '3D HNCACB' '3D HNCO' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name VapB46 _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 13 MET C C 173.4 . . 2 1 13 MET CA C 52.88 . . 3 1 13 MET CB C 30.15 . . 4 2 14 THR H H 8.148 . . 5 2 14 THR C C 170.2 . . 6 2 14 THR CA C 57.23 . . 7 2 14 THR CB C 67.24 . . 8 2 14 THR N N 118.8 . . 9 3 15 PRO CA C 61.08 . . 10 3 15 PRO CB C 29.33 . . 11 4 16 THR H H 7.789 . . 12 4 16 THR CA C 59.97 . . 13 4 16 THR CB C 67.83 . . 14 4 16 THR N N 120.3 . . 15 5 17 ALA CA C 51.24 . . 16 5 17 ALA CB C 16.74 . . 17 6 18 CYS H H 7.992 . . 18 6 18 CYS C C 173.6 . . 19 6 18 CYS CA C 52.38 . . 20 6 18 CYS CB C 27.63 . . 21 6 18 CYS N N 124.1 . . 22 7 19 ALA H H 7.312 . . 23 7 19 ALA C C 175.9 . . 24 7 19 ALA CA C 54.82 . . 25 7 19 ALA CB C 16.1 . . 26 7 19 ALA N N 123.2 . . 27 8 20 THR C C 172.9 . . 28 8 20 THR CA C 59.73 . . 29 9 21 VAL H H 7.984 . . 30 9 21 VAL C C 173 . . 31 9 21 VAL CA C 59.59 . . 32 9 21 VAL CB C 30.11 . . 33 9 21 VAL N N 119.6 . . 34 10 22 SER H H 8.369 . . 35 10 22 SER CA C 55.87 . . 36 10 22 SER CB C 61.41 . . 37 10 22 SER N N 120.2 . . 38 11 23 THR H H 8.154 . . 39 11 23 THR C C 173.3 . . 40 11 23 THR CA C 58.99 . . 41 11 23 THR CB C 67.29 . . 42 11 23 THR N N 116.8 . . 43 12 24 MET H H 8.298 . . 44 12 24 MET C C 173.5 . . 45 12 24 MET CA C 53.14 . . 46 12 24 MET CB C 31.47 . . 47 12 24 MET N N 124.2 . . 48 13 25 THR H H 8.74 . . 49 13 25 THR C C 169.9 . . 50 13 25 THR CA C 60.5 . . 51 13 25 THR CB C 67.12 . . 52 13 25 THR N N 121.1 . . 53 14 26 SER H H 8.104 . . 54 14 26 SER C C 171.7 . . 55 14 26 SER CA C 53.92 . . 56 14 26 SER CB C 62.2 . . 57 14 26 SER N N 120.8 . . 58 15 27 VAL H H 9.105 . . 59 15 27 VAL C C 171.5 . . 60 15 27 VAL CA C 56.81 . . 61 15 27 VAL CB C 32.93 . . 62 15 27 VAL N N 121.9 . . 63 16 28 GLY H H 8.116 . . 64 16 28 GLY C C 173 . . 65 16 28 GLY CA C 41.43 . . 66 16 28 GLY N N 109.1 . . 67 17 29 VAL H H 8.251 . . 68 17 29 VAL C C 174.9 . . 69 17 29 VAL CA C 63.69 . . 70 17 29 VAL CB C 29.08 . . 71 17 29 VAL N N 120 . . 72 18 30 ARG H H 8.511 . . 73 18 30 ARG C C 175.5 . . 74 18 30 ARG CA C 57.05 . . 75 18 30 ARG CB C 26.77 . . 76 18 30 ARG N N 120.4 . . 77 19 31 ALA H H 7.706 . . 78 19 31 ALA C C 176.7 . . 79 19 31 ALA CA C 51.96 . . 80 19 31 ALA CB C 15.84 . . 81 19 31 ALA N N 122.4 . . 82 20 32 LEU H H 7.801 . . 83 20 32 LEU C C 173.8 . . 84 20 32 LEU CA C 55.45 . . 85 20 32 LEU CB C 38.93 . . 86 20 32 LEU N N 119.6 . . 87 21 33 ARG H H 7.593 . . 88 21 33 ARG C C 175.9 . . 89 21 33 ARG CA C 56.66 . . 90 21 33 ARG CB C 27.96 . . 91 21 33 ARG N N 113.7 . . 92 22 34 GLN H H 7.952 . . 93 22 34 GLN C C 175.4 . . 94 22 34 GLN CA C 55.02 . . 95 22 34 GLN CB C 27.69 . . 96 22 34 GLN N N 115.8 . . 97 23 35 ARG H H 8.521 . . 98 23 35 ARG C C 173.5 . . 99 23 35 ARG CA C 52.58 . . 100 23 35 ARG CB C 26.57 . . 101 23 35 ARG N N 118.1 . . 102 24 36 ALA H H 7.271 . . 103 24 36 ALA C C 175.9 . . 104 24 36 ALA CA C 54.77 . . 105 24 36 ALA CB C 16.03 . . 106 24 36 ALA N N 122.9 . . 107 25 37 SER H H 8.414 . . 108 25 37 SER CA C 59.87 . . 109 25 37 SER N N 111 . . 110 26 38 GLU H H 8.013 . . 111 26 38 GLU C C 176.8 . . 112 26 38 GLU CA C 56.7 . . 113 26 38 GLU CB C 26.47 . . 114 26 38 GLU N N 124.1 . . 115 27 39 LEU H H 8.285 . . 116 27 39 LEU C C 176.4 . . 117 27 39 LEU CA C 55.25 . . 118 27 39 LEU CB C 38.31 . . 119 27 39 LEU N N 120.3 . . 120 28 40 LEU H H 8.433 . . 121 28 40 LEU C C 176.6 . . 122 28 40 LEU CA C 54.91 . . 123 28 40 LEU CB C 37.76 . . 124 28 40 LEU N N 119.2 . . 125 29 41 ARG H H 7.63 . . 126 29 41 ARG C C 177.2 . . 127 29 41 ARG CA C 56.91 . . 128 29 41 ARG CB C 27.19 . . 129 29 41 ARG N N 120.4 . . 130 30 42 ARG H H 7.468 . . 131 30 42 ARG C C 176.4 . . 132 30 42 ARG CA C 56.78 . . 133 30 42 ARG CB C 26.98 . . 134 30 42 ARG N N 120.6 . . 135 31 43 VAL H H 8.026 . . 136 31 43 VAL C C 178 . . 137 31 43 VAL CA C 62.16 . . 138 31 43 VAL CB C 28.77 . . 139 31 43 VAL N N 123.7 . . 140 32 44 GLU H H 8.585 . . 141 32 44 GLU C C 175.3 . . 142 32 44 GLU CA C 56.99 . . 143 32 44 GLU CB C 26.77 . . 144 32 44 GLU N N 122.8 . . 145 33 45 ALA H H 7.273 . . 146 33 45 ALA C C 175.1 . . 147 33 45 ALA CA C 49.68 . . 148 33 45 ALA CB C 15.77 . . 149 33 45 ALA N N 119.7 . . 150 34 46 GLY H H 8.223 . . 151 34 46 GLY C C 171.7 . . 152 34 46 GLY CA C 42.63 . . 153 34 46 GLY N N 108 . . 154 35 47 GLU H H 8.1 . . 155 35 47 GLU C C 171.4 . . 156 35 47 GLU CA C 54.64 . . 157 35 47 GLU CB C 29.14 . . 158 35 47 GLU N N 125.2 . . 159 36 48 THR H H 7.862 . . 160 36 48 THR C C 171.2 . . 161 36 48 THR CA C 59.87 . . 162 36 48 THR CB C 67.79 . . 163 36 48 THR N N 116.6 . . 164 37 49 ILE H H 9.022 . . 165 37 49 ILE C C 171.6 . . 166 37 49 ILE CA C 56.7 . . 167 37 49 ILE CB C 38.48 . . 168 37 49 ILE N N 127.9 . . 169 38 50 GLU H H 8.745 . . 170 38 50 GLU C C 171.3 . . 171 38 50 GLU CA C 53.37 . . 172 38 50 GLU CB C 29.74 . . 173 38 50 GLU N N 129.5 . . 174 39 51 ILE H H 8.964 . . 175 39 51 ILE C C 174 . . 176 39 51 ILE CA C 55.56 . . 177 39 51 ILE CB C 35.17 . . 178 39 51 ILE N N 126.5 . . 179 40 52 THR H H 9.256 . . 180 40 52 THR C C 170.1 . . 181 40 52 THR CA C 56.56 . . 182 40 52 THR CB C 69.24 . . 183 40 52 THR N N 119.7 . . 184 41 53 ASP H H 8.709 . . 185 41 53 ASP C C 173.7 . . 186 41 53 ASP CA C 51.07 . . 187 41 53 ASP CB C 41.26 . . 188 41 53 ASP N N 118.7 . . 189 42 54 ARG H H 9.061 . . 190 42 54 ARG C C 174.2 . . 191 42 54 ARG CA C 54.55 . . 192 42 54 ARG CB C 24.76 . . 193 42 54 ARG N N 125.8 . . 194 43 55 GLY H H 8.625 . . 195 43 55 GLY C C 170.9 . . 196 43 55 GLY CA C 42.61 . . 197 43 55 GLY N N 104.7 . . 198 45 57 PRO C C 174 . . 199 45 57 PRO CA C 61 . . 200 45 57 PRO CB C 29.29 . . 201 46 58 VAL H H 9.207 . . 202 46 58 VAL C C 171.9 . . 203 46 58 VAL CA C 59.19 . . 204 46 58 VAL CB C 32.43 . . 205 46 58 VAL N N 117.8 . . 206 47 59 ALA H H 7.88 . . 207 47 59 ALA C C 171.5 . . 208 47 59 ALA CA C 48.8 . . 209 47 59 ALA CB C 21.13 . . 210 47 59 ALA N N 121.9 . . 211 48 60 LEU H H 8.992 . . 212 48 60 LEU C C 173 . . 213 48 60 LEU CA C 50.84 . . 214 48 60 LEU CB C 42.66 . . 215 48 60 LEU N N 119.2 . . 216 49 61 LEU H H 9.345 . . 217 49 61 LEU C C 172 . . 218 49 61 LEU CA C 50.93 . . 219 49 61 LEU CB C 41.53 . . 220 49 61 LEU N N 127.4 . . 221 50 62 SER H H 9.233 . . 222 50 62 SER CA C 53.15 . . 223 50 62 SER CB C 63.45 . . 224 50 62 SER N N 120.8 . . 225 51 63 PRO C C 174 . . 226 51 63 PRO CA C 59.76 . . 227 51 63 PRO CB C 29.51 . . 228 52 64 LEU H H 8.124 . . 229 52 64 LEU C C 172.9 . . 230 52 64 LEU CA C 50.86 . . 231 52 64 LEU CB C 38.37 . . 232 52 64 LEU N N 123.4 . . 233 53 65 PRO C C 173.4 . . 234 53 65 PRO CA C 60.64 . . 235 53 65 PRO CB C 29.05 . . 236 54 66 GLN H H 7.935 . . 237 54 66 GLN C C 178 . . 238 54 66 GLN CA C 54.67 . . 239 54 66 GLN CB C 28.1 . . 240 54 66 GLN N N 126.8 . . stop_ save_