data_34270 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; AapA1 V26A toxin from helicobacter pylori 26695 ; _BMRB_accession_number 34270 _BMRB_flat_file_name bmr34270.str _Entry_type original _Submission_date 2018-05-11 _Accession_date 2018-05-11 _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 Korkut D. N. . 2 Salgado G. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 179 "15N chemical shifts" 30 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-09-06 update BMRB 'update entry citation' 2018-05-18 original author 'original release' stop_ _Original_release_date 2018-05-16 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural insights into the AapA1 toxin of Helicobacter pylori. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 31476357 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Korkut D. N. . 2 Alves I. D. . 3 Vogel A. . . 4 Chabas S. . . 5 Sharma C. M. . 6 Martinez D. . . 7 Loquet A. . . 8 Salgado G. F. . 9 Darfeuille F. . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta Gen. Subj.' _Journal_volume . _Journal_issue . _Journal_ISSN 1872-8006 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 129423 _Page_last 129423 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Uncharacterized protein' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass 3443.265 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; MATKHGKNSWKTLYLKISFL GCKVVALLKR ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ALA 3 THR 4 LYS 5 HIS 6 GLY 7 LYS 8 ASN 9 SER 10 TRP 11 LYS 12 THR 13 LEU 14 TYR 15 LEU 16 LYS 17 ILE 18 SER 19 PHE 20 LEU 21 GLY 22 CYS 23 LYS 24 VAL 25 VAL 26 ALA 27 LEU 28 LEU 29 LYS 30 ARG 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 $entity_1 'Helicobacter pylori SS1' 102617 Bacteria . Helicobacter pylori 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 1 mM no labeling AapA1 V26A, 10 mM deuterated acetic acid, 10 mM deuterated DTT, 40 % deuterated TFE, trifluoroethanol/water. ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' 'acetic acid' 10 mM [U-2H] DTT 10 mM [U-2H] TFE 40 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name ARIA _Version . loop_ _Vendor _Address _Electronic_address "Linge, O'Donoghue and Nilges" . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name CcpNMR _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 800 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _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' 10 . mM pH 4.7 . pH pressure 1 . atm temperature 303 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 0.000 internal indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.000 internal indirect . . . 0.10132912 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_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 1 MET HA H 4.123 . 1 2 1 1 MET HG2 H 2.179 . 1 3 2 2 ALA H H 8.598 0.002 1 4 2 2 ALA HA H 4.493 . 1 5 2 2 ALA HB H 1.420 0.001 1 6 2 2 ALA N N 126.799 . 1 7 3 3 THR H H 8.030 0.0 1 8 3 3 THR HA H 4.364 0.003 1 9 3 3 THR HB H 4.197 0.002 1 10 3 3 THR HG2 H 1.177 0.0 1 11 3 3 THR N N 113.180 . 1 12 4 4 LYS H H 8.191 0.001 1 13 4 4 LYS HA H 4.312 . 1 14 4 4 LYS HB2 H 1.706 0.001 2 15 4 4 LYS HB3 H 1.794 . 2 16 4 4 LYS HG2 H 1.368 . 2 17 4 4 LYS HG3 H 1.426 . 2 18 4 4 LYS HD2 H 1.662 . 1 19 4 4 LYS HD3 H 1.662 . 1 20 4 4 LYS HE2 H 2.967 . 1 21 4 4 LYS HE3 H 2.967 . 1 22 4 4 LYS N N 122.538 . 1 23 5 5 HIS H H 8.375 0.003 1 24 5 5 HIS HA H 4.738 . 1 25 5 5 HIS HB2 H 3.163 . 2 26 5 5 HIS HB3 H 3.296 . 2 27 5 5 HIS HD1 H 8.552 . 1 28 5 5 HIS HD2 H 7.286 . 1 29 5 5 HIS N N 118.390 . 1 30 6 6 GLY H H 8.354 0.001 1 31 6 6 GLY HA2 H 3.973 0.001 2 32 6 6 GLY HA3 H 4.058 0.0 2 33 6 6 GLY N N 109.381 . 1 34 7 7 LYS H H 8.256 0.001 1 35 7 7 LYS HA H 4.305 0.001 1 36 7 7 LYS HB2 H 1.773 0.001 2 37 7 7 LYS HB3 H 1.860 0.003 2 38 7 7 LYS HG2 H 1.417 0.004 2 39 7 7 LYS HG3 H 1.473 0.0 2 40 7 7 LYS HD2 H 1.694 . 1 41 7 7 LYS HD3 H 1.694 . 1 42 7 7 LYS HE2 H 2.987 . 1 43 7 7 LYS HE3 H 2.987 . 1 44 7 7 LYS N N 120.661 . 1 45 8 8 ASN H H 8.420 0.001 1 46 8 8 ASN HA H 4.714 0.001 1 47 8 8 ASN HB2 H 2.747 0.002 1 48 8 8 ASN HB3 H 2.747 0.002 1 49 8 8 ASN HD21 H 7.455 . 1 50 8 8 ASN HD22 H 6.752 . 1 51 8 8 ASN N N 118.263 . 1 52 8 8 ASN ND2 N 111.687 0.006 1 53 9 9 SER H H 8.195 0.001 1 54 9 9 SER HA H 4.393 0.001 1 55 9 9 SER HB2 H 3.868 0.004 2 56 9 9 SER HB3 H 3.919 0.0 2 57 9 9 SER N N 116.318 . 1 58 10 10 TRP H H 7.983 0.001 1 59 10 10 TRP HA H 4.475 0.001 1 60 10 10 TRP HB2 H 3.305 0.003 2 61 10 10 TRP HB3 H 3.369 0.004 2 62 10 10 TRP HD1 H 7.297 0.001 1 63 10 10 TRP HE1 H 9.836 0.001 1 64 10 10 TRP HE3 H 7.482 0.002 1 65 10 10 TRP HZ2 H 7.386 0.003 1 66 10 10 TRP HZ3 H 6.941 0.001 1 67 10 10 TRP HH2 H 7.086 . 1 68 10 10 TRP N N 122.485 . 1 69 10 10 TRP NE1 N 127.575 . 1 70 11 11 LYS H H 7.605 0.001 1 71 11 11 LYS HA H 3.804 0.001 1 72 11 11 LYS HB2 H 1.604 0.001 2 73 11 11 LYS HB3 H 1.712 0.0 2 74 11 11 LYS HG2 H 1.061 0.003 2 75 11 11 LYS HG3 H 1.092 0.002 2 76 11 11 LYS HD2 H 1.584 0.002 1 77 11 11 LYS HD3 H 1.584 0.002 1 78 11 11 LYS HE2 H 2.887 0.002 1 79 11 11 LYS HE3 H 2.887 0.002 1 80 11 11 LYS N N 119.195 . 1 81 12 12 THR H H 7.579 0.003 1 82 12 12 THR HA H 3.934 0.0 1 83 12 12 THR HB H 4.235 0.001 1 84 12 12 THR HG2 H 1.250 0.002 1 85 12 12 THR N N 111.430 . 1 86 13 13 LEU H H 7.517 0.001 1 87 13 13 LEU HA H 4.106 0.002 1 88 13 13 LEU HB2 H 1.798 0.002 1 89 13 13 LEU HB3 H 1.798 0.002 1 90 13 13 LEU HG H 1.654 0.002 1 91 13 13 LEU HD2 H 0.896 0.002 1 92 13 13 LEU N N 122.443 . 1 93 14 14 TYR H H 8.127 0.001 1 94 14 14 TYR HA H 4.099 0.001 1 95 14 14 TYR HB2 H 2.940 0.002 2 96 14 14 TYR HB3 H 3.013 0.001 2 97 14 14 TYR HD1 H 7.016 0.002 1 98 14 14 TYR HD2 H 7.016 0.002 1 99 14 14 TYR HE1 H 6.790 0.002 1 100 14 14 TYR HE2 H 6.790 0.002 1 101 14 14 TYR N N 117.893 . 1 102 15 15 LEU H H 8.105 0.001 1 103 15 15 LEU HA H 3.928 0.004 1 104 15 15 LEU HB2 H 1.878 0.001 1 105 15 15 LEU HB3 H 1.878 0.001 1 106 15 15 LEU HG H 1.562 0.001 1 107 15 15 LEU HD2 H 0.894 0.001 1 108 15 15 LEU N N 120.685 . 1 109 16 16 LYS H H 7.878 0.001 1 110 16 16 LYS HA H 4.025 0.002 1 111 16 16 LYS HB2 H 1.941 0.002 2 112 16 16 LYS HB3 H 2.027 0.001 2 113 16 16 LYS HG2 H 1.405 0.001 1 114 16 16 LYS HG3 H 1.405 0.001 1 115 16 16 LYS HD2 H 1.659 0.001 1 116 16 16 LYS HD3 H 1.659 0.001 1 117 16 16 LYS HE2 H 2.893 0.002 1 118 16 16 LYS HE3 H 2.893 0.002 1 119 16 16 LYS N N 118.956 . 1 120 17 17 ILE H H 8.450 0.0 1 121 17 17 ILE HA H 3.804 0.002 1 122 17 17 ILE HB H 1.872 0.002 1 123 17 17 ILE HG12 H 1.228 0.001 1 124 17 17 ILE HG13 H 1.228 0.001 1 125 17 17 ILE HG2 H 0.898 0.002 1 126 17 17 ILE HD1 H 0.815 0.002 1 127 17 17 ILE N N 117.789 . 1 128 18 18 SER H H 8.090 0.001 1 129 18 18 SER HA H 4.119 0.0 1 130 18 18 SER HB2 H 3.668 0.002 2 131 18 18 SER HB3 H 3.885 0.0 2 132 18 18 SER N N 116.504 . 1 133 19 19 PHE H H 8.135 0.001 1 134 19 19 PHE HA H 4.392 0.003 1 135 19 19 PHE HB2 H 3.228 0.001 1 136 19 19 PHE HB3 H 3.228 0.001 1 137 19 19 PHE HD1 H 7.232 0.001 1 138 19 19 PHE HD2 H 7.232 0.001 1 139 19 19 PHE HE1 H 7.264 0.002 1 140 19 19 PHE HE2 H 7.264 0.002 1 141 19 19 PHE N N 122.180 . 1 142 20 20 LEU H H 8.201 0.001 1 143 20 20 LEU HA H 4.081 0.003 1 144 20 20 LEU HB2 H 1.851 0.002 1 145 20 20 LEU HB3 H 1.851 0.002 1 146 20 20 LEU HG H 1.641 0.001 1 147 20 20 LEU HD2 H 0.897 0.002 1 148 20 20 LEU N N 120.050 . 1 149 21 21 GLY H H 8.351 0.001 1 150 21 21 GLY HA2 H 3.796 0.002 2 151 21 21 GLY HA3 H 3.883 0.001 2 152 21 21 GLY N N 105.711 . 1 153 22 22 CYS H H 7.871 0.001 1 154 22 22 CYS HA H 4.219 0.001 1 155 22 22 CYS HB2 H 2.906 0.002 2 156 22 22 CYS HB3 H 3.045 0.002 2 157 22 22 CYS N N 117.411 . 1 158 23 23 LYS H H 7.818 0.002 1 159 23 23 LYS HA H 4.074 0.002 1 160 23 23 LYS HB2 H 1.857 0.002 2 161 23 23 LYS HB3 H 1.911 0.002 2 162 23 23 LYS HG2 H 1.356 0.0 2 163 23 23 LYS HG3 H 1.446 0.003 2 164 23 23 LYS HD2 H 1.622 0.002 1 165 23 23 LYS HD3 H 1.622 0.002 1 166 23 23 LYS HE2 H 2.843 0.004 1 167 23 23 LYS HE3 H 2.843 0.004 1 168 23 23 LYS N N 120.335 . 1 169 24 24 VAL H H 7.896 0.001 1 170 24 24 VAL HA H 3.701 0.001 1 171 24 24 VAL HB H 2.167 0.001 1 172 24 24 VAL HG1 H 0.916 0.001 2 173 24 24 VAL HG2 H 1.002 0.001 2 174 24 24 VAL N N 118.265 . 1 175 25 25 VAL H H 7.757 0.001 1 176 25 25 VAL HA H 3.613 0.001 1 177 25 25 VAL HB H 2.094 0.001 1 178 25 25 VAL HG1 H 0.924 0.002 2 179 25 25 VAL HG2 H 1.024 0.001 2 180 25 25 VAL N N 118.078 . 1 181 26 26 ALA H H 7.540 0.001 1 182 26 26 ALA HA H 4.059 0.001 1 183 26 26 ALA HB H 1.468 0.002 1 184 26 26 ALA N N 120.114 . 1 185 27 27 LEU H H 7.780 0.002 1 186 27 27 LEU HA H 4.156 0.001 1 187 27 27 LEU HB2 H 1.770 0.002 2 188 27 27 LEU HB3 H 1.915 . 2 189 27 27 LEU HG H 1.627 0.001 1 190 27 27 LEU HD2 H 0.860 0.0 1 191 27 27 LEU N N 117.467 . 1 192 28 28 LEU H H 7.951 0.001 1 193 28 28 LEU HA H 4.223 0.001 1 194 28 28 LEU HB2 H 1.854 0.0 1 195 28 28 LEU HB3 H 1.854 0.0 1 196 28 28 LEU HG H 1.523 0.0 1 197 28 28 LEU HD2 H 0.836 0.002 1 198 28 28 LEU N N 118.458 . 1 199 29 29 LYS H H 7.886 0.002 1 200 29 29 LYS HA H 4.258 0.0 1 201 29 29 LYS HB2 H 1.924 . 2 202 29 29 LYS HB3 H 1.852 . 2 203 29 29 LYS HG2 H 1.461 0.0 2 204 29 29 LYS HG3 H 1.529 . 2 205 29 29 LYS HD2 H 1.649 . 1 206 29 29 LYS HD3 H 1.649 . 1 207 29 29 LYS HE2 H 2.950 . 1 208 29 29 LYS HE3 H 2.950 . 1 209 29 29 LYS N N 117.930 . 1 stop_ save_