data_30710 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of enterococcal cytolysin L (CylLL") produced by Enterococcus faecalis ; _BMRB_accession_number 30710 _BMRB_flat_file_name bmr30710.str _Entry_type original _Submission_date 2020-01-08 _Accession_date 2020-01-08 _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" 164 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-07-05 original BMRB . stop_ _Original_release_date 2020-01-10 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 'cytolysin L' _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 3446.074 _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 38 _Mol_residue_sequence ; XXPVCAVAAXAAAAXAACGW VGGGIFTGVXVVVXLKHC ; loop_ _Residue_seq_code _Residue_label 1 ABA 2 DBU 3 PRO 4 VAL 5 CYS 6 ALA 7 VAL 8 ALA 9 ALA 10 DBU 11 ALA 12 ALA 13 ALA 14 ALA 15 DHA 16 ALA 17 ALA 18 CYS 19 GLY 20 TRP 21 VAL 22 GLY 23 GLY 24 GLY 25 ILE 26 PHE 27 THR 28 GLY 29 VAL 30 DBU 31 VAL 32 VAL 33 VAL 34 DAL 35 LEU 36 LYS 37 HIS 38 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_ save_chem_comp_DHA _Saveframe_category polymer_residue _Mol_type 'PEPTIDE LINKING' _Name_common '2-AMINO-ACRYLIC ACID' _BMRB_code DHA _PDB_code DHA _Standard_residue_derivative . _Molecular_mass 87.077 _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 . ? HB1 HB1 H . 0 . ? HB2 HB2 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 HB1 ? ? SING CB HB2 ? ? 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 . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '2.0 mM cytolysin L, methanol' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2.0 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_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H 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 6 0.1 pH pressure 1 0 atm temperature 296 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' 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 ABA HA H 4.104 0.000 1 2 1 1 ABA HG1 H 1.332 0.000 1 3 1 1 ABA HG2 H 1.332 0.000 1 4 1 1 ABA HG3 H 1.332 0.000 1 5 2 2 DBU HB H 5.838 0.011 1 6 2 2 DBU HG1 H 1.851 0.000 1 7 2 2 DBU HG2 H 1.851 0.000 1 8 2 2 DBU HG3 H 1.851 0.000 1 9 3 3 PRO HA H 4.370 0.001 1 10 3 3 PRO HB2 H 2.099 0.004 2 11 3 3 PRO HB3 H 2.404 0.001 2 12 3 3 PRO HG2 H 2.116 0.000 2 13 3 3 PRO HG3 H 2.116 0.000 2 14 3 3 PRO HD2 H 3.759 0.004 2 15 3 3 PRO HD3 H 4.016 0.003 2 16 4 4 VAL HA H 3.682 0.003 1 17 4 4 VAL HB H 2.290 0.003 1 18 4 4 VAL HG1 H 1.094 0.000 2 19 4 4 VAL HG2 H 1.016 0.000 2 20 5 5 CYS H H 7.520 0.006 1 21 5 5 CYS HA H 4.153 0.001 1 22 5 5 CYS HB2 H 2.563 0.000 2 23 5 5 CYS HB3 H 3.190 0.009 2 24 6 6 ALA H H 8.217 0.005 1 25 6 6 ALA HA H 4.029 0.001 1 26 6 6 ALA HB H 1.450 0.013 1 27 7 7 VAL H H 7.831 0.005 1 28 7 7 VAL HA H 3.570 0.002 1 29 7 7 VAL HB H 2.165 0.002 1 30 7 7 VAL HG1 H 1.119 0.003 2 31 7 7 VAL HG2 H 0.952 0.000 2 32 8 8 ALA H H 8.051 0.002 1 33 8 8 ALA HA H 4.112 0.002 1 34 8 8 ALA HB H 1.415 0.048 1 35 9 9 ALA H H 8.316 0.003 1 36 9 9 ALA HA H 4.112 0.002 1 37 9 9 ALA HB H 1.572 0.001 1 38 10 10 DBU H H 9.173 0.000 1 39 10 10 DBU HB H 6.296 0.000 1 40 10 10 DBU HG1 H 1.762 0.000 1 41 10 10 DBU HG2 H 1.762 0.000 1 42 10 10 DBU HG3 H 1.762 0.000 1 43 11 11 ALA H H 8.232 0.038 1 44 11 11 ALA HA H 4.151 0.001 1 45 11 11 ALA HB H 1.455 0.016 1 46 12 12 ALA H H 8.036 0.005 1 47 12 12 ALA HA H 4.063 0.001 1 48 12 12 ALA HB H 1.497 0.002 1 49 13 13 ALA H H 8.047 0.003 1 50 13 13 ALA HA H 4.034 0.002 1 51 13 13 ALA HB H 1.512 0.004 1 52 14 14 ALA H H 7.947 0.002 1 53 14 14 ALA HA H 4.311 0.001 1 54 15 15 DHA H H 9.391 0.000 1 55 16 16 ALA H H 8.946 0.001 1 56 16 16 ALA HA H 4.127 0.002 1 57 16 16 ALA HB H 1.481 0.005 1 58 17 17 ALA H H 8.318 0.001 1 59 17 17 ALA HA H 4.212 0.002 1 60 17 17 ALA HB H 1.638 0.001 1 61 18 18 CYS H H 8.020 0.002 1 62 18 18 CYS HA H 3.956 0.001 1 63 18 18 CYS HB2 H 2.884 0.003 2 64 18 18 CYS HB3 H 3.234 0.004 2 65 19 19 GLY H H 8.448 0.003 1 66 19 19 GLY HA2 H 3.766 0.000 2 67 19 19 GLY HA3 H 3.861 0.000 2 68 20 20 TRP H H 8.365 0.003 1 69 20 20 TRP HA H 4.483 0.002 1 70 20 20 TRP HB2 H 3.329 0.005 2 71 20 20 TRP HB3 H 3.400 0.003 2 72 20 20 TRP HD1 H 7.135 0.001 1 73 20 20 TRP HE1 H 10.351 0.000 1 74 20 20 TRP HE3 H 7.543 0.002 1 75 20 20 TRP HZ2 H 8.049 1.328 1 76 20 20 TRP HZ3 H 6.977 0.016 1 77 20 20 TRP HH2 H 7.086 0.079 1 78 21 21 VAL H H 8.173 0.002 1 79 21 21 VAL HA H 3.771 0.001 1 80 21 21 VAL HB H 2.178 0.001 1 81 21 21 VAL HG1 H 1.122 0.006 2 82 21 21 VAL HG2 H 0.979 0.002 2 83 22 22 GLY HA2 H 3.769 0.000 2 84 22 22 GLY HA3 H 3.870 0.000 2 85 23 23 GLY H H 8.419 0.002 1 86 23 23 GLY HA2 H 3.840 0.000 2 87 23 23 GLY HA3 H 3.901 0.000 2 88 24 24 GLY H H 8.287 0.000 1 89 24 24 GLY HA2 H 3.874 0.000 2 90 24 24 GLY HA3 H 3.874 0.000 2 91 25 25 ILE H H 8.273 0.001 1 92 25 25 ILE HA H 3.833 0.001 1 93 25 25 ILE HB H 1.956 0.004 1 94 25 25 ILE HG12 H 1.123 0.000 2 95 25 25 ILE HG13 H 1.726 0.001 2 96 25 25 ILE HG2 H 0.851 0.000 1 97 25 25 ILE HD1 H 0.854 0.000 1 98 26 26 PHE H H 8.304 0.002 1 99 26 26 PHE HA H 4.223 0.004 1 100 26 26 PHE HD1 H 7.202 0.029 3 101 26 26 PHE HD2 H 7.202 0.029 3 102 26 26 PHE HE1 H 7.223 0.002 3 103 26 26 PHE HE2 H 7.223 0.002 3 104 27 27 THR H H 8.183 0.001 1 105 27 27 THR HA H 3.728 0.001 1 106 27 27 THR HG2 H 1.189 0.001 1 107 28 28 GLY H H 8.180 0.001 1 108 28 28 GLY HA2 H 3.839 0.000 2 109 28 28 GLY HA3 H 3.839 0.000 2 110 29 29 VAL H H 8.309 0.001 1 111 29 29 VAL HA H 3.616 0.002 1 112 29 29 VAL HB H 2.301 0.006 1 113 29 29 VAL HG1 H 1.092 0.007 2 114 29 29 VAL HG2 H 0.912 0.001 2 115 30 30 DBU H H 9.345 0.001 1 116 30 30 DBU HB H 6.135 0.000 1 117 30 30 DBU HG1 H 1.363 0.002 1 118 30 30 DBU HG2 H 1.363 0.002 1 119 30 30 DBU HG3 H 1.363 0.002 1 120 31 31 VAL H H 8.138 0.001 1 121 31 31 VAL HA H 3.776 0.002 1 122 31 31 VAL HB H 2.319 0.000 1 123 31 31 VAL HG1 H 1.103 0.002 2 124 31 31 VAL HG2 H 0.953 0.001 2 125 32 32 VAL H H 7.664 0.002 1 126 32 32 VAL HA H 3.609 0.003 1 127 32 32 VAL HB H 2.305 0.001 1 128 32 32 VAL HG1 H 1.100 0.006 2 129 32 32 VAL HG2 H 0.959 0.002 2 130 33 33 VAL H H 8.436 0.001 1 131 33 33 VAL HA H 3.497 0.001 1 132 33 33 VAL HB H 2.067 0.001 1 133 33 33 VAL HG1 H 0.935 0.004 2 134 33 33 VAL HG2 H 0.908 0.006 2 135 34 34 DAL H H 8.720 0.002 1 136 34 34 DAL HA H 3.997 0.000 1 137 34 34 DAL HB1 H 2.600 0.003 2 138 34 34 DAL HB2 H 2.600 0.003 2 139 35 35 LEU H H 8.644 0.002 1 140 35 35 LEU HA H 4.069 0.003 1 141 35 35 LEU HB2 H 1.476 0.004 2 142 35 35 LEU HB3 H 2.021 0.009 2 143 35 35 LEU HG H 1.989 0.010 1 144 35 35 LEU HD1 H 0.915 0.001 1 145 35 35 LEU HD2 H 0.893 0.001 1 146 36 36 LYS H H 7.566 0.004 1 147 36 36 LYS HA H 4.294 0.004 1 148 36 36 LYS HB2 H 1.673 0.001 2 149 36 36 LYS HB3 H 1.673 0.001 2 150 36 36 LYS HG2 H 1.393 0.005 2 151 36 36 LYS HG3 H 1.393 0.005 2 152 36 36 LYS HD2 H 1.557 0.003 2 153 36 36 LYS HD3 H 1.557 0.003 2 154 36 36 LYS HE2 H 2.809 0.000 2 155 36 36 LYS HE3 H 2.854 0.001 2 156 37 37 HIS H H 8.362 0.004 1 157 37 37 HIS HA H 4.999 0.001 1 158 37 37 HIS HB2 H 2.905 0.002 2 159 37 37 HIS HB3 H 3.410 0.005 2 160 37 37 HIS HD2 H 7.289 0.000 1 161 38 38 CYS H H 9.482 0.001 1 162 38 38 CYS HA H 4.621 0.001 1 163 38 38 CYS HB2 H 2.745 0.004 2 164 38 38 CYS HB3 H 3.643 0.002 2 stop_ save_