data_21038 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; AIP-III_DL7 ; _BMRB_accession_number 21038 _BMRB_flat_file_name bmr21038.str _Entry_type new _Submission_date 2013-07-31 _Accession_date 2013-08-06 _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 Tal-Gan Yftah . . 2 Ivancic Monika . . 3 Cornilescu Gabriel . . 4 Cornilescu Claudia C. . 5 Blackwell Helen E. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 45 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-12-10 author 'original release; coordinate file annotated by PDBj' . stop_ loop_ _Related_BMRB_accession_number _Relationship 21035 AIP-III 21036 AIP-III_D4A 21037 AIP-III_DF5 21039 'AIP-III_F5A cyclic peptide' 21040 AIP-III_L7A 21041 tAIP-III 21042 tAIP-III_D2A 21045 AIP-I 21046 AIP-II 21047 AIP-IV stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural Characterization of an Autoinducing Peptide and Abiotic Analogs Reveals Key Features Essential for Activation and Inhibition of an AgrC Quorum Sensing Receptor in Staphylococcus aureus' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24219181 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tal-Gan Yftah . . 2 Ivancic Monika . . 3 Cornilescu Gabriel . . 4 Cornilescu Claudia C . 5 Blackwell Helen E . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'AIP-III_DL7 peptide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label AIP-III_DL7 $AIP-III_DL7 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_AIP-III_DL7 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common AIP-III_DL7 _Molecular_mass 818 _Mol_thiol_state 'all other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence INCDFLX loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 ILE 2 2 ASN 3 3 CYS 4 4 ASP 5 5 PHE 6 6 LEU 7 7 DLE stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DLE _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-LEUCINE _BMRB_code DLE _PDB_code DLE _Standard_residue_derivative . _Molecular_mass 131.173 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CD1 CD1 C . 0 . ? CD2 CD2 C . 0 . ? CG CG C . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD11 HD11 H . 0 . ? HD12 HD12 H . 0 . ? HD13 HD13 H . 0 . ? HD21 HD21 H . 0 . ? HD22 HD22 H . 0 . ? HD23 HD23 H . 0 . ? HG HG H . 0 . ? HXT HXT H . 0 . ? N N N . 0 . ? O O O . 0 . ? OXT OXT O . 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 CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD1 ? ? SING CG CD2 ? ? SING CG HG ? ? SING CD1 HD11 ? ? SING CD1 HD12 ? ? SING CD1 HD13 ? ? SING CD2 HD21 ? ? SING CD2 HD22 ? ? SING CD2 HD23 ? ? 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 $AIP-III_DL7 '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_name $AIP-III_DL7 synthetic . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $AIP-III_DL7 1 mM 'natural abundance' H2O 70 % . CD3CN 30 % . stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_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_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_ROESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _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 temperature 298 . K pH 3.65 . pH stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 'referenced CD3CN to 1.94ppm' 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 0.00 internal direct . . . 1.000000000 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_AIP-III_DL7_assignments _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H COSY' '2D 1H-1H ROESY' 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 AIP-III_DL7 _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 ILE HA H 3.747 0.002 1 2 1 1 ILE HB H 1.851 0.004 1 3 1 1 ILE HD1 H 0.835 0.002 4 4 1 1 ILE HG12 H 1.405 0.010 1 5 1 1 ILE HG13 H 1.114 0.009 1 6 1 1 ILE HG2 H 0.894 0.003 4 7 2 2 ASN H H 8.480 0.003 1 8 2 2 ASN HA H 4.618 0.001 1 9 2 2 ASN HB2 H 2.664 0.006 1 10 2 2 ASN HB3 H 2.578 0.003 1 11 2 2 ASN HD21 H 7.383 0.004 1 12 3 3 CYS H H 8.247 0.003 1 13 3 3 CYS HA H 4.325 0.004 1 14 3 3 CYS HB2 H 3.112 0.005 1 15 3 3 CYS HB3 H 2.955 0.003 1 16 4 4 ASP H H 8.431 0.003 1 17 4 4 ASP HA H 4.449 0.006 1 18 4 4 ASP HB2 H 2.575 0.003 2 19 4 4 ASP HB3 H 2.575 0.003 2 20 5 5 PHE H H 7.921 0.003 1 21 5 5 PHE HA H 4.355 0.002 1 22 5 5 PHE HB2 H 3.051 0.005 2 23 5 5 PHE HB3 H 3.051 0.005 2 24 5 5 PHE HD1 H 7.176 0.003 3 25 5 5 PHE HD2 H 7.176 0.003 3 26 5 5 PHE HE1 H 7.273 0.000 3 27 5 5 PHE HE2 H 7.273 0.000 3 28 6 6 LEU H H 7.994 0.004 1 29 6 6 LEU HA H 4.313 0.006 1 30 6 6 LEU HB2 H 1.470 0.007 2 31 6 6 LEU HB3 H 1.470 0.007 2 32 6 6 LEU HD1 H 0.801 0.009 2 33 6 6 LEU HD2 H 0.747 0.008 2 34 6 6 LEU HG H 1.190 0.002 1 35 7 7 DLE H H 8.649 0.003 1 36 7 7 DLE HA H 4.355 0.006 1 37 7 7 DLE HB2 H 1.544 0.004 2 38 7 7 DLE HB3 H 1.544 0.004 2 39 7 7 DLE HD11 H 0.823 0.009 2 40 7 7 DLE HD12 H 0.823 0.009 2 41 7 7 DLE HD13 H 0.823 0.009 2 42 7 7 DLE HD21 H 0.755 0.002 2 43 7 7 DLE HD22 H 0.755 0.002 2 44 7 7 DLE HD23 H 0.755 0.002 2 45 7 7 DLE HG H 1.483 0.001 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity 3 '6,3,6,3,6' stop_ save_