data_30238 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of chemically synthesized antilisterial Pediocin PA-1 analog. ; _BMRB_accession_number 30238 _BMRB_flat_file_name bmr30238.str _Entry_type original _Submission_date 2017-01-23 _Accession_date 2017-01-23 _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 Bedard F. . . 2 Hammami R. . . 3 Zirah S. . . 4 Rebuffat S. . . 5 Fliss I. . . 6 Biron E. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 196 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-06-21 original BMRB . stop_ _Original_release_date 2017-03-15 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Total Synthesis, Antimicrobial Activity and Conformational Analy-sis of the Class IIa Bacteriocin Pediocin PA-1. ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bedard F. . . 2 Hammami R. . . 3 Zirah S. . . 4 Rebuffat S. . . 5 Fliss I. . . 6 Biron E. . . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Bacteriocin pediocin PA-1' _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 4617.172 _Mol_thiol_state . _Details 'Pediocin PA-1 M31L' ############################## # Polymer residue sequence # ############################## _Residue_count 44 _Mol_residue_sequence ; KYYGNGVTCGKHSCSVDWGK ATTCIINNGALAWATGGHQG NHKC ; loop_ _Residue_seq_code _Residue_label 1 LYS 2 TYR 3 TYR 4 GLY 5 ASN 6 GLY 7 VAL 8 THR 9 CYS 10 GLY 11 LYS 12 HIS 13 SER 14 CYS 15 SER 16 VAL 17 ASP 18 TRP 19 GLY 20 LYS 21 ALA 22 THR 23 THR 24 CYS 25 ILE 26 ILE 27 ASN 28 ASN 29 GLY 30 ALA 31 LEU 32 ALA 33 TRP 34 ALA 35 THR 36 GLY 37 GLY 38 HIS 39 GLN 40 GLY 41 ASN 42 HIS 43 LYS 44 CYS 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 'Pediococcus acidilactici' 1254 Bacteria . Pediococcus acidilactici 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 _Details $entity_1 'chemical synthesis' . . . . . 'Pediocin PA-1 producer' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '3.33 mg/mL NA- Pediocin PA-1 M31L, trifluoroethanol/water' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 3.33 mg/mL 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CS-Rosetta _Version 3.7 loop_ _Vendor _Address _Electronic_address 'Shen, Vernon, Baker and Bax' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name TOPSPIN _Version 3.5 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 600 _Details Cyroprobe save_ ############################# # NMR applied experiments # ############################# save_2D_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_2D_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _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 pH 2.8 0.2 pH pressure 1 . atm temperature 313 0.1 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 H 1 'methyl protons' ppm 0.000 internal direct . . . 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_assigned_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D TOCSY' '2D NOESY' 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 2 2 TYR H H 8.408 . . 2 2 2 TYR HA H 4.679 . . 3 2 2 TYR HB2 H 2.947 . . 4 2 2 TYR HB3 H 2.947 . . 5 2 2 TYR HD1 H 7.112 . . 6 2 2 TYR HD2 H 7.112 . . 7 2 2 TYR HE1 H 6.795 . . 8 2 2 TYR HE2 H 6.795 . . 9 3 3 TYR H H 8.030 . . 10 3 3 TYR HA H 4.525 . . 11 3 3 TYR HB2 H 3.048 . . 12 3 3 TYR HB3 H 2.777 . . 13 3 3 TYR HD1 H 7.067 . . 14 3 3 TYR HD2 H 7.067 . . 15 3 3 TYR HE1 H 6.787 . . 16 3 3 TYR HE2 H 6.787 . . 17 4 4 GLY H H 7.003 . . 18 4 4 GLY HA2 H 3.978 . . 19 4 4 GLY HA3 H 3.765 . . 20 5 5 ASN H H 8.089 . . 21 5 5 ASN HA H 4.683 . . 22 5 5 ASN HB2 H 2.834 . . 23 5 5 ASN HB3 H 2.834 . . 24 5 5 ASN HD21 H 7.320 . . 25 5 5 ASN HD22 H 6.585 . . 26 6 6 GLY H H 8.281 . . 27 6 6 GLY HA2 H 4.034 . . 28 6 6 GLY HA3 H 3.894 . . 29 7 7 VAL H H 7.797 . . 30 7 7 VAL HA H 4.272 . . 31 7 7 VAL HB H 2.100 . . 32 7 7 VAL HG1 H 0.908 . . 33 7 7 VAL HG2 H 0.908 . . 34 8 8 THR H H 8.173 . . 35 8 8 THR HA H 4.594 . . 36 8 8 THR HB H 4.179 . . 37 8 8 THR HG2 H 1.187 . . 38 9 9 CYS H H 8.387 . . 39 9 9 CYS HA H 4.989 . . 40 9 9 CYS HB2 H 3.156 . . 41 9 9 CYS HB3 H 2.975 . . 42 10 10 GLY H H 8.323 . . 43 10 10 GLY HA2 H 4.040 . . 44 10 10 GLY HA3 H 3.917 . . 45 11 11 LYS H H 8.265 . . 46 11 11 LYS HA H 4.165 . . 47 11 11 LYS HB2 H 1.792 . . 48 11 11 LYS HB3 H 1.792 . . 49 11 11 LYS HG2 H 1.397 . . 50 11 11 LYS HG3 H 1.397 . . 51 11 11 LYS HD2 H 1.690 . . 52 11 11 LYS HD3 H 1.690 . . 53 11 11 LYS HE2 H 2.983 . . 54 11 11 LYS HE3 H 2.983 . . 55 12 12 HIS H H 8.184 . . 56 12 12 HIS HA H 4.612 . . 57 12 12 HIS HB2 H 3.360 . . 58 12 12 HIS HB3 H 3.221 . . 59 12 12 HIS HD2 H 7.294 . . 60 12 12 HIS HE1 H 8.500 . . 61 13 13 SER H H 7.913 . . 62 13 13 SER HA H 4.544 . . 63 13 13 SER HB2 H 3.967 . . 64 13 13 SER HB3 H 3.967 . . 65 14 14 CYS H H 8.488 . . 66 14 14 CYS HA H 5.029 . . 67 14 14 CYS HB2 H 3.118 . . 68 14 14 CYS HB3 H 2.965 . . 69 15 15 SER H H 8.423 . . 70 15 15 SER HA H 4.501 . . 71 15 15 SER HB2 H 3.857 . . 72 15 15 SER HB3 H 3.857 . . 73 16 16 VAL H H 8.085 . . 74 16 16 VAL HB H 1.921 . . 75 16 16 VAL HG1 H 0.907 . . 76 16 16 VAL HG2 H 0.803 . . 77 17 17 ASP H H 8.000 . . 78 17 17 ASP HA H 4.455 . . 79 17 17 ASP HB2 H 3.233 . . 80 17 17 ASP HB3 H 3.233 . . 81 18 18 TRP H H 7.964 . . 82 18 18 TRP HA H 4.479 . . 83 18 18 TRP HB2 H 3.366 . . 84 18 18 TRP HB3 H 3.257 . . 85 18 18 TRP HD1 H 7.230 . . 86 18 18 TRP HE1 H 9.690 . . 87 18 18 TRP HE3 H 7.521 . . 88 18 18 TRP HZ2 H 7.406 . . 89 18 18 TRP HZ3 H 7.058 . . 90 18 18 TRP HH2 H 7.156 . . 91 19 19 GLY H H 8.370 . . 92 19 19 GLY HA2 H 3.910 . . 93 19 19 GLY HA3 H 3.809 . . 94 20 20 LYS H H 7.876 . . 95 20 20 LYS HA H 4.211 . . 96 20 20 LYS HB2 H 1.690 . . 97 20 20 LYS HB3 H 1.690 . . 98 20 20 LYS HG2 H 1.411 . . 99 20 20 LYS HG3 H 1.411 . . 100 20 20 LYS HD2 H 1.584 . . 101 20 20 LYS HD3 H 1.584 . . 102 21 21 ALA H H 7.941 . . 103 21 21 ALA HA H 4.111 . . 104 21 21 ALA HB H 1.425 . . 105 22 22 THR H H 7.800 . . 106 22 22 THR HA H 4.380 . . 107 22 22 THR HB H 4.020 . . 108 22 22 THR HG2 H 1.250 . . 109 27 27 ASN H H 8.127 . . 110 27 27 ASN HA H 4.688 . . 111 27 27 ASN HB2 H 2.839 . . 112 27 27 ASN HB3 H 2.839 . . 113 27 27 ASN HD21 H 7.352 . . 114 27 27 ASN HD22 H 6.793 . . 115 28 28 ASN H H 8.135 . . 116 28 28 ASN HA H 4.674 . . 117 28 28 ASN HB2 H 2.862 . . 118 28 28 ASN HB3 H 2.682 . . 119 28 28 ASN HD21 H 7.259 . . 120 28 28 ASN HD22 H 6.558 . . 121 29 29 GLY H H 8.243 . . 122 29 29 GLY HA2 H 3.945 . . 123 29 29 GLY HA3 H 3.945 . . 124 30 30 ALA H H 8.116 . . 125 30 30 ALA HA H 4.203 . . 126 30 30 ALA HB H 1.485 . . 127 31 31 LEU H H 7.810 . . 128 31 31 LEU HA H 4.090 . . 129 31 31 LEU HB2 H 1.770 . . 130 31 31 LEU HB3 H 1.770 . . 131 31 31 LEU HD1 H 0.810 . . 132 31 31 LEU HD2 H 0.570 . . 133 32 32 ALA H H 8.125 . . 134 32 32 ALA HA H 4.130 . . 135 32 32 ALA HB H 1.429 . . 136 33 33 TRP H H 7.838 . . 137 33 33 TRP HA H 4.412 . . 138 33 33 TRP HB2 H 3.391 . . 139 33 33 TRP HB3 H 3.391 . . 140 33 33 TRP HD1 H 7.237 . . 141 33 33 TRP HE1 H 9.670 . . 142 33 33 TRP HE3 H 7.575 . . 143 33 33 TRP HZ2 H 7.410 . . 144 33 33 TRP HZ3 H 7.097 . . 145 33 33 TRP HH2 H 7.168 . . 146 34 34 ALA H H 8.110 . . 147 34 34 ALA HA H 4.079 . . 148 34 34 ALA HB H 1.390 . . 149 35 35 THR H H 7.960 . . 150 35 35 THR HA H 4.540 . . 151 35 35 THR HB H 4.180 . . 152 35 35 THR HG2 H 1.160 . . 153 37 37 GLY H H 8.515 . . 154 37 37 GLY HA2 H 3.936 . . 155 37 37 GLY HA3 H 3.741 . . 156 38 38 HIS H H 7.946 . . 157 38 38 HIS HA H 4.697 . . 158 38 38 HIS HB2 H 3.319 . . 159 38 38 HIS HB3 H 3.140 . . 160 38 38 HIS HD2 H 7.946 . . 161 38 38 HIS HE1 H 8.510 . . 162 39 39 GLN H H 8.350 . . 163 39 39 GLN HA H 4.396 . . 164 39 39 GLN HB2 H 2.376 . . 165 39 39 GLN HB3 H 2.128 . . 166 39 39 GLN HG2 H 1.979 . . 167 39 39 GLN HG3 H 1.979 . . 168 40 40 GLY H H 8.200 . . 169 40 40 GLY HA2 H 3.930 . . 170 40 40 GLY HA3 H 3.930 . . 171 41 41 ASN H H 8.132 . . 172 41 41 ASN HA H 4.598 . . 173 41 41 ASN HB2 H 2.758 . . 174 41 41 ASN HB3 H 2.758 . . 175 41 41 ASN HD21 H 7.333 . . 176 41 41 ASN HD22 H 6.631 . . 177 42 42 HIS H H 8.300 . . 178 42 42 HIS HA H 4.758 . . 179 42 42 HIS HB2 H 3.289 . . 180 42 42 HIS HB3 H 3.152 . . 181 42 42 HIS HD2 H 7.287 . . 182 42 42 HIS HE1 H 8.527 . . 183 43 43 LYS H H 8.152 . . 184 43 43 LYS HA H 4.361 . . 185 43 43 LYS HB2 H 1.853 . . 186 43 43 LYS HB3 H 1.853 . . 187 43 43 LYS HG2 H 1.439 . . 188 43 43 LYS HG3 H 1.439 . . 189 43 43 LYS HD2 H 1.745 . . 190 43 43 LYS HD3 H 1.745 . . 191 43 43 LYS HE2 H 2.992 . . 192 43 43 LYS HE3 H 2.992 . . 193 44 44 CYS H H 7.920 . . 194 44 44 CYS HA H 4.538 . . 195 44 44 CYS HB2 H 3.295 . . 196 44 44 CYS HB3 H 3.004 . . stop_ save_