data_18590 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; S. aureus pepA1 NMR structure ; _BMRB_accession_number 18590 _BMRB_flat_file_name bmr18590.str _Entry_type original _Submission_date 2012-07-11 _Accession_date 2012-07-11 _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 Sayed N. . . 2 Nonin-Lecomte Sylvie . . 3 Rety S. . . 4 Felden B. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 94 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-04-22 original BMRB . stop_ _Original_release_date 2012-07-11 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Functional and structural insights of a Staphylococcus aureus apoptotic-like membrane peptide from a toxin-antitoxin module. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23129767 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sayed Nour . . 2 Nonin-Lecomte Sylvie . . 3 Rety Stephane . . 4 Felden Brice . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 287 _Journal_issue 52 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 43454 _Page_last 43463 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'S. aureus pepA1 NMR structure' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label PEPA1 $PEPA1 stop_ _System_molecular_weight 3459.2068 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state 'all free' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_PEPA1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PEPA1 _Molecular_mass 3459.2068 _Mol_thiol_state 'all free' _Details 'FULL TOXIN OF THE TYPE I T/A SYSTEM' ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; MLIFVHIIAPVISGCAIAFF SYWLSRRNTK ; loop_ _Residue_seq_code _Residue_label 1 MET 2 LEU 3 ILE 4 PHE 5 VAL 6 HIS 7 ILE 8 ILE 9 ALA 10 PRO 11 VAL 12 ILE 13 SER 14 GLY 15 CYS 16 ALA 17 ILE 18 ALA 19 PHE 20 PHE 21 SER 22 TYR 23 TRP 24 LEU 25 SER 26 ARG 27 ARG 28 ASN 29 THR 30 LYS 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 $PEPA1 'Staphylococcus aureus' 1280 Bacteria . Staphylococcus aureus stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $PEPA1 'chemical synthesis' . . . . n/a . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '5 mmol/l' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $PEPA1 5 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AutoDep _Saveframe_category software _Name AutoDep _Version 4.3 loop_ _Vendor _Address _Electronic_address 'Sen et al.' . . stop_ loop_ _Task collection stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version any loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_Analysis _Saveframe_category software _Name Analysis _Version any loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_CNS_2 _Saveframe_category software _Name CNS _Version 2 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement stop_ _Details 'refinement in explicit DMSO, conformer1= minimized average over the 20 best structures' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Bruker_Avance-600 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_1 save_ save_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_1 save_ save_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name COSY _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'pH [3.8], temp [288], pressure [1], ionStrength [0.0]' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.0 . mM pH 3.800 . pH pressure 1.000 . atm temperature 288.000 . 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 HDO H 1 protons ppm 4.91 internal indirect . . . 1 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 _Saveframe_category assigned_chemical_shifts _Details 'Origin nmrStar file /ebi/msd/pdb_root/Processing/prepare/4b19/ebi/chemicalshift2-depositBMRB_1.txt.csh' loop_ _Experiment_label NOESY TOCSY COSY 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 PEPA1 _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 LEU H H 9.11 0.02 1 2 2 2 LEU HA H 4.51 0.02 1 3 2 2 LEU HB2 H 1.92 0.02 2 4 2 2 LEU HB3 H 1.96 0.02 2 5 3 3 ILE H H 8.53 0.02 1 6 3 3 ILE HA H 4.03 0.02 1 7 3 3 ILE HB H 2.16 0.02 1 8 4 4 PHE H H 8.40 0.02 1 9 4 4 PHE HA H 4.51 0.02 1 10 4 4 PHE HB2 H 3.37 0.02 2 11 4 4 PHE HB3 H 3.38 0.02 2 12 5 5 VAL H H 7.96 0.02 1 13 5 5 VAL HA H 3.81 0.02 1 14 5 5 VAL HB H 2.28 0.02 1 15 6 6 HIS H H 8.06 0.02 1 16 6 6 HIS HA H 4.53 0.02 1 17 6 6 HIS HB2 H 3.50 0.02 1 18 6 6 HIS HB3 H 3.50 0.02 1 19 7 7 ILE H H 7.90 0.02 1 20 7 7 ILE HA H 4.25 0.02 1 21 7 7 ILE HB H 2.16 0.02 1 22 8 8 ILE H H 7.86 0.02 1 23 8 8 ILE HA H 4.25 0.02 1 24 8 8 ILE HB H 1.95 0.02 1 25 9 9 ALA H H 8.44 0.02 1 26 9 9 ALA HA H 4.39 0.02 1 27 10 10 PRO HA H 4.49 0.02 1 28 10 10 PRO HB2 H 2.40 0.02 2 29 10 10 PRO HB3 H 2.52 0.02 2 30 11 11 VAL H H 7.45 0.02 1 31 11 11 VAL HA H 3.97 0.02 1 32 11 11 VAL HB H 2.50 0.02 1 33 12 12 ILE H H 8.29 0.02 1 34 12 12 ILE HA H 3.86 0.02 1 35 12 12 ILE HB H 2.15 0.02 1 36 13 13 SER H H 8.51 0.02 1 37 13 13 SER HA H 4.35 0.02 1 38 13 13 SER HB2 H 4.06 0.02 2 39 13 13 SER HB3 H 4.04 0.02 2 40 14 14 GLY H H 8.45 0.02 1 41 14 14 GLY HA3 H 4.09 0.02 1 42 15 15 CYS H H 8.53 0.02 1 43 15 15 CYS HA H 4.33 0.02 1 44 15 15 CYS HB2 H 3.42 0.02 1 45 16 16 ALA H H 8.57 0.02 1 46 16 16 ALA HA H 4.35 0.02 1 47 17 17 ILE H H 8.61 0.02 1 48 17 17 ILE HA H 4.03 0.02 1 49 17 17 ILE HB H 2.22 0.02 1 50 18 18 ALA H H 8.62 0.02 1 51 18 18 ALA HA H 4.30 0.02 1 52 19 19 PHE H H 8.84 0.02 1 53 19 19 PHE HA H 4.44 0.02 1 54 19 19 PHE HB2 H 3.45 0.02 1 55 19 19 PHE HB3 H 3.45 0.02 1 56 20 20 PHE H H 9.11 0.02 1 57 20 20 PHE HA H 4.57 0.02 1 58 20 20 PHE HB2 H 3.53 0.02 2 59 20 20 PHE HB3 H 3.46 0.02 2 60 21 21 SER H H 8.85 0.02 1 61 21 21 SER HA H 4.32 0.02 1 62 21 21 SER HB2 H 4.14 0.02 2 63 21 21 SER HB3 H 4.12 0.02 2 64 22 22 TYR H H 8.52 0.02 1 65 22 22 TYR HA H 4.14 0.02 1 66 23 23 TRP H H 8.40 0.02 1 67 23 23 TRP HA H 4.13 0.02 1 68 23 23 TRP HB2 H 3.50 0.02 1 69 24 24 LEU H H 8.88 0.02 1 70 24 24 LEU HA H 3.98 0.02 1 71 24 24 LEU HB2 H 1.83 0.02 1 72 24 24 LEU HB3 H 1.83 0.02 1 73 25 25 SER H H 8.05 0.02 1 74 25 25 SER HA H 4.26 0.02 1 75 25 25 SER HB2 H 4.09 0.02 2 76 25 25 SER HB3 H 4.07 0.02 2 77 26 26 ARG HA H 4.11 0.02 1 78 26 26 ARG HB2 H 1.90 0.02 2 79 26 26 ARG HB3 H 1.79 0.02 2 80 26 26 ARG HE H 7.27 0.02 1 81 27 27 ARG H H 8.17 0.02 1 82 27 27 ARG HA H 4.14 0.02 1 83 27 27 ARG HB2 H 1.97 0.02 2 84 27 27 ARG HB3 H 1.89 0.02 2 85 27 27 ARG HE H 7.45 0.02 1 86 28 28 ASN HA H 4.86 0.02 1 87 28 28 ASN HB2 H 3.04 0.02 2 88 28 28 ASN HB3 H 2.90 0.02 2 89 29 29 THR H H 7.72 0.02 1 90 29 29 THR HA H 4.42 0.02 1 91 29 29 THR HB H 4.42 0.02 1 92 30 30 LYS H H 8.14 0.02 1 93 30 30 LYS HA H 4.60 0.02 1 94 30 30 LYS HB2 H 2.12 0.02 1 stop_ save_