data_30702 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of enterococcal cytolysin S (CylLS") produced by Enterococcus faecalis ; _BMRB_accession_number 30702 _BMRB_flat_file_name bmr30702.str _Entry_type original _Submission_date 2019-12-30 _Accession_date 2019-12-30 _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 Bobeica S. C. . 2 'van der Donk' W. A. . 3 Zhu L. . . 4 Tang W. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 113 "13C chemical shifts" 23 "15N chemical shifts" 16 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-07-05 original BMRB . stop_ _Original_release_date 2020-01-09 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; The sequence of the enterococcal cytolysin imparts unusual lanthionine stereochemistry. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23314913 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tang W. . . 2 'van der Donk' W. A. . stop_ _Journal_abbreviation 'Nat. Chem. Biol.' _Journal_volume 9 _Journal_issue 3 _Journal_ISSN 1552-4469 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 157 _Page_last 159 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'enterococcal cytolysin S' _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 2037.470 _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; XXPACFXIGLGVGALFXAKF C ; loop_ _Residue_seq_code _Residue_label 1 ABA 2 DBU 3 PRO 4 ALA 5 CYS 6 PHE 7 DBU 8 ILE 9 GLY 10 LEU 11 GLY 12 VAL 13 GLY 14 ALA 15 LEU 16 PHE 17 DAL 18 ALA 19 LYS 20 PHE 21 CYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_ABA _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 'ALPHA-AMINOBUTYRIC ACID' _BMRB_code ABA _PDB_code ABA _Standard_residue_derivative . _Molecular_mass 103.120 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HB3 HB3 H . 0 . ? HB2 HB2 H . 0 . ? HG1 HG1 H . 0 . ? HG3 HG3 H . 0 . ? HG2 HG2 H . 0 . ? HXT HXT 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 N CA ? ? SING N H ? ? SING N HN2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB3 ? ? SING CB HB2 ? ? SING CG HG1 ? ? SING CG HG3 ? ? SING CG HG2 ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DAL _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-ALANINE _BMRB_code DAL _PDB_code DAL _Standard_residue_derivative . _Molecular_mass 89.093 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB1 HB1 H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HXT HXT 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 N CA ? ? SING N H ? ? SING N H2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB HB1 ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DBU _Saveframe_category polymer_residue _Mol_type 'PEPTIDE LINKING' _Name_common '(2Z)-2-AMINOBUT-2-ENOIC ACID' _BMRB_code DBU _PDB_code DBU _Standard_residue_derivative . _Molecular_mass 101.104 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HB HB H . 0 . ? HG1 HG1 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HXT HXT 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 N CA ? ? SING N H ? ? SING N H2 ? ? DOUB CA CB ? ? SING CA C ? ? SING CB CG ? ? SING CB HB ? ? SING CG HG1 ? ? SING CG HG2 ? ? SING CG HG3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ 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 'Enterococcus faecalis' 1351 Bacteria . Enterococcus faecalis 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 'recombinant technology' . Escherichia coli . pRSFDuet-1 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1.0 mM [U-99% 13C; U-99% 15N] Cytolysin S, methanol' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.0 mM '[U-99% 13C; U-99% 15N]' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '1.0 mM Cytolysin S, CD3OH' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.0 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name Sparky _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_4 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model VNMRS _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_3D_HNCACB_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_3D_HN(CO)CA_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HN(CO)CA' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_5 _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 pH 6 0.1 pH pressure 1 0.001 atm temperature 277 0.1 K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6 0.1 pH pressure 1 0.001 atm temperature 277 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 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 TOCSY' '2D 1H-1H NOESY' '3D HNCACB' '3D HN(CO)CA' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_2 $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 ABA HA H 4.255 0.000 1 2 1 1 ABA HB2 H 3.854 0.001 1 3 1 1 ABA HG1 H 1.408 0.002 1 4 1 1 ABA HG2 H 1.408 0.002 1 5 1 1 ABA HG3 H 1.408 0.002 1 6 2 2 DBU HB H 5.929 0.002 1 7 2 2 DBU HG1 H 1.829 0.002 1 8 2 2 DBU HG2 H 1.829 0.002 1 9 2 2 DBU HG3 H 1.829 0.002 1 10 3 3 PRO HA H 4.418 0.002 1 11 3 3 PRO HB2 H 2.127 0.002 2 12 3 3 PRO HB3 H 2.415 0.001 2 13 3 3 PRO HG2 H 2.073 0.003 2 14 3 3 PRO HG3 H 2.073 0.003 2 15 3 3 PRO HD2 H 3.768 0.002 2 16 3 3 PRO HD3 H 3.977 0.002 2 17 4 4 ALA H H 8.209 0.014 1 18 4 4 ALA HA H 4.258 0.001 1 19 4 4 ALA HB H 1.512 0.003 1 20 5 5 CYS H H 7.846 0.003 1 21 5 5 CYS HA H 4.449 0.005 1 22 5 5 CYS HB2 H 2.610 0.003 2 23 5 5 CYS HB3 H 3.329 0.004 2 24 5 5 CYS N N 114.659 0.000 1 25 6 6 PHE H H 8.170 0.002 1 26 6 6 PHE HA H 4.393 0.004 1 27 6 6 PHE HB2 H 3.216 0.004 2 28 6 6 PHE HB3 H 3.295 0.005 2 29 6 6 PHE HD1 H 7.270 0.003 3 30 6 6 PHE HD2 H 7.270 0.003 3 31 6 6 PHE HE1 H 7.260 0.022 3 32 6 6 PHE HE2 H 7.260 0.022 3 33 6 6 PHE HZ H 7.209 0.003 1 34 6 6 PHE CA C 60.592 0.000 1 35 6 6 PHE CB C 38.876 0.000 1 36 6 6 PHE N N 119.646 0.000 1 37 7 7 DBU H H 9.428 0.003 1 38 7 7 DBU N N 118.359 0.028 1 39 7 7 DBU HB H 6.295 0.002 1 40 7 7 DBU HG1 H 1.670 0.004 1 41 7 7 DBU HG2 H 1.670 0.004 1 42 7 7 DBU HG3 H 1.670 0.004 1 43 8 8 ILE H H 7.891 0.004 1 44 8 8 ILE HA H 3.906 0.002 1 45 8 8 ILE HB H 2.045 0.002 1 46 8 8 ILE HG12 H 1.286 0.119 2 47 8 8 ILE HG13 H 1.816 0.003 2 48 8 8 ILE HG2 H 1.122 0.137 1 49 8 8 ILE HD1 H 0.949 0.009 1 50 8 8 ILE CA C 64.352 0.000 1 51 8 8 ILE CB C 37.562 0.000 1 52 8 8 ILE N N 119.348 0.029 1 53 9 9 GLY H H 8.067 0.006 1 54 9 9 GLY HA2 H 3.713 0.003 2 55 9 9 GLY HA3 H 3.873 0.004 2 56 9 9 GLY CA C 46.809 0.033 1 57 10 10 LEU H H 8.071 0.006 1 58 10 10 LEU HA H 4.076 0.004 1 59 10 10 LEU HB2 H 1.564 0.000 2 60 10 10 LEU HB3 H 1.910 0.000 2 61 10 10 LEU HG H 1.435 0.003 1 62 10 10 LEU HD1 H 0.768 0.004 2 63 10 10 LEU CA C 57.199 0.023 1 64 10 10 LEU CB C 41.784 0.046 1 65 10 10 LEU N N 120.310 0.018 1 66 11 11 GLY H H 8.285 0.002 1 67 11 11 GLY HA2 H 3.794 0.005 2 68 11 11 GLY HA3 H 3.919 0.006 2 69 11 11 GLY CA C 46.856 0.032 1 70 11 11 GLY N N 106.677 0.028 1 71 12 12 VAL H H 8.483 0.002 1 72 12 12 VAL HA H 3.701 0.002 1 73 12 12 VAL HB H 2.203 0.002 1 74 12 12 VAL HG1 H 1.108 0.002 1 75 12 12 VAL HG2 H 0.982 0.002 1 76 12 12 VAL CA C 66.579 0.000 1 77 12 12 VAL CB C 31.454 0.000 1 78 12 12 VAL N N 120.477 0.023 1 79 13 13 GLY H H 8.592 0.004 1 80 13 13 GLY HA2 H 3.833 0.004 2 81 13 13 GLY HA3 H 3.950 0.004 2 82 13 13 GLY CA C 47.125 0.036 1 83 13 13 GLY N N 107.079 0.010 1 84 14 14 ALA H H 8.439 0.003 1 85 14 14 ALA HA H 4.235 0.001 1 86 14 14 ALA HB H 1.564 0.001 1 87 14 14 ALA CA C 54.945 0.000 1 88 14 14 ALA CB C 17.774 0.000 1 89 14 14 ALA N N 123.652 0.014 1 90 15 15 LEU H H 8.081 0.002 1 91 15 15 LEU HA H 4.068 0.004 1 92 15 15 LEU HB2 H 1.797 0.048 2 93 15 15 LEU HB3 H 1.902 0.023 2 94 15 15 LEU HG H 1.665 0.004 1 95 15 15 LEU HD1 H 0.939 0.003 2 96 15 15 LEU HD2 H 0.906 0.002 2 97 15 15 LEU CA C 57.473 0.000 1 98 15 15 LEU CB C 41.700 0.000 1 99 15 15 LEU N N 118.460 0.010 1 100 16 16 PHE H H 8.580 0.003 1 101 16 16 PHE HA H 4.176 0.002 1 102 16 16 PHE HB2 H 3.226 0.004 2 103 16 16 PHE HB3 H 3.330 0.006 2 104 16 16 PHE HD1 H 7.336 0.002 3 105 16 16 PHE HD2 H 7.336 0.002 3 106 16 16 PHE HE1 H 7.187 0.003 3 107 16 16 PHE HE2 H 7.187 0.003 3 108 16 16 PHE HZ H 7.088 0.001 1 109 16 16 PHE CA C 62.065 0.000 1 110 16 16 PHE CB C 39.303 0.000 1 111 16 16 PHE N N 118.565 0.014 1 112 17 17 DAL H H 9.188 0.001 1 113 17 17 DAL N N 121.042 0.010 1 114 17 17 DAL HA H 4.025 0.004 1 115 17 17 DAL HB1 H 2.677 0.006 2 116 17 17 DAL HB2 H 2.677 0.006 2 117 18 18 ALA H H 8.590 0.003 1 118 18 18 ALA HA H 3.971 0.002 1 119 18 18 ALA HB H 1.486 0.001 1 120 18 18 ALA CA C 55.200 0.000 1 121 18 18 ALA CB C 17.741 0.000 1 122 18 18 ALA N N 122.154 0.000 1 123 19 19 LYS H H 7.252 0.003 1 124 19 19 LYS HA H 4.045 0.005 1 125 19 19 LYS HB2 H 1.235 0.002 2 126 19 19 LYS HB3 H 1.235 0.002 2 127 19 19 LYS HG2 H 0.794 0.008 2 128 19 19 LYS HG3 H 0.932 0.005 2 129 19 19 LYS HD2 H 1.400 0.005 2 130 19 19 LYS HD3 H 1.400 0.005 2 131 19 19 LYS HE2 H 2.707 0.002 2 132 19 19 LYS HE3 H 2.707 0.002 2 133 19 19 LYS HZ H 7.753 0.002 4 134 19 19 LYS CA C 57.320 0.000 1 135 19 19 LYS CB C 33.630 0.000 1 136 19 19 LYS N N 111.687 0.008 1 137 20 20 PHE H H 8.038 0.004 1 138 20 20 PHE HA H 4.849 0.002 1 139 20 20 PHE HB2 H 2.091 0.002 2 140 20 20 PHE HB3 H 3.172 0.003 2 141 20 20 PHE HD1 H 6.918 0.002 3 142 20 20 PHE HD2 H 6.918 0.002 3 143 20 20 PHE HE1 H 7.135 0.003 3 144 20 20 PHE HE2 H 7.135 0.003 3 145 20 20 PHE CA C 57.409 0.000 1 146 20 20 PHE CB C 41.142 0.000 1 147 20 20 PHE N N 111.792 0.006 1 148 21 21 CYS H H 9.333 0.002 1 149 21 21 CYS HA H 4.493 0.002 1 150 21 21 CYS HB2 H 2.665 0.002 2 151 21 21 CYS HB3 H 3.636 0.003 2 152 21 21 CYS N N 120.491 0.075 1 stop_ save_