data_20032 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of Gelatinase Biosynthesis-Activating Pheromone (GBAP), a 11-residue peptide lactone, from the Gram-positive bacterium Enterococcus faecalis ; _BMRB_accession_number 20032 _BMRB_flat_file_name bmr20032.str _Entry_type new _Submission_date 2008-07-16 _Accession_date 2008-07-16 _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 Nagata Koji . . 2 Nishiguchi Kenzo . . 3 Kameda Yasuhiro . . 4 Sonomoto Kenji . . 5 Nakayama Jiro . . 6 Tanokura Masaru . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 60 "15N chemical shifts" 10 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-04-04 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure-Activity Relationship of Gelatinase Biosynthesis-Activating Pheromone of Enterococcus faecalis' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18996993 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nishiguchi Kenzo . . 2 Nagata Koji . . 3 Tanokura Masaru . . 4 Sonomoto Kenji . . 5 Nakayama Jiro . . stop_ _Journal_abbreviation 'J. Bacteriol.' _Journal_name_full 'Journal of Bacteriology' _Journal_volume 191 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 641 _Page_last 650 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name GBAP _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label GBAP $GBAP 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_GBAP _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common GBAP _Molecular_mass 1303.470 _Mol_thiol_state 'not present' loop_ _Biological_function pheromone autoinducer quormone stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence QNSPNIFGQWM loop_ _Residue_seq_code _Residue_label 1 GLN 2 ASN 3 SER 4 PRO 5 ASN 6 ILE 7 PHE 8 GLY 9 GLN 10 TRP 11 MET stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name single covalent GBAP 3 SER OG GBAP 11 MET C stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $GBAP '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 $GBAP 'recombinant technology' . . . . . 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 $GBAP 1.5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % '[U-100% 2H]' stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_NMRPipe _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_NMRDraw _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing 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_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_4 _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 temperature 283 . K pH 6.0 . pH 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 water H 1 protons ppm 4.916 na direct . . . 1.0 water N 15 protons ppm 118.396 na indirect . . . 0.10134 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D DQF-COSY' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-15N HSQC' 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 GBAP _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 GLN H H 8.316 . 1 2 1 1 GLN HB2 H 2.281 . 2 3 1 1 GLN HB3 H 2.281 . 2 4 1 1 GLN HG2 H 1.283 . 2 5 1 1 GLN HG3 H 1.283 . 2 6 1 1 GLN N N 110.4 . 1 7 2 2 ASN H H 8.132 . 1 8 2 2 ASN HB2 H 3.627 . 2 9 2 2 ASN HB3 H 3.838 . 2 10 3 3 SER H H 8.670 . 1 11 3 3 SER HA H 4.710 . 1 12 3 3 SER HB2 H 4.163 . 2 13 3 3 SER HB3 H 4.163 . 2 14 3 3 SER N N 117.0 . 1 15 4 4 PRO HA H 4.547 . 1 16 4 4 PRO HB2 H 1.742 . 2 17 4 4 PRO HB3 H 2.217 . 2 18 4 4 PRO HD2 H 3.524 . 2 19 4 4 PRO HD3 H 3.731 . 2 20 4 4 PRO HG2 H 1.910 . 2 21 4 4 PRO HG3 H 1.975 . 2 22 5 5 ASN HA H 4.463 . 1 23 5 5 ASN HB2 H 1.295 . 2 24 5 5 ASN HB3 H 2.293 . 2 25 5 5 ASN N N 119.2 . 1 26 6 6 ILE H H 8.446 . 1 27 6 6 ILE HA H 4.037 . 1 28 6 6 ILE HB H 1.654 . 1 29 6 6 ILE HG12 H 0.910 . 2 30 6 6 ILE HG13 H 1.256 . 2 31 6 6 ILE N N 126.2 . 1 32 7 7 PHE HA H 4.269 . 1 33 7 7 PHE HB2 H 2.995 . 2 34 7 7 PHE HB3 H 3.308 . 2 35 7 7 PHE HD1 H 7.206 . 3 36 7 7 PHE HD2 H 7.206 . 3 37 7 7 PHE HE1 H 7.311 . 3 38 7 7 PHE HE2 H 7.311 . 3 39 7 7 PHE HZ H 7.255 . 1 40 7 7 PHE N N 125.5 . 1 41 8 8 GLY H H 7.957 . 1 42 8 8 GLY HA2 H 3.519 . 2 43 8 8 GLY HA3 H 4.100 . 2 44 8 8 GLY N N 106.2 . 1 45 9 9 GLN H H 7.659 . 1 46 9 9 GLN HA H 4.462 . 1 47 9 9 GLN HB2 H 1.877 . 2 48 9 9 GLN HB3 H 2.006 . 2 49 9 9 GLN HG2 H 2.187 . 2 50 9 9 GLN HG3 H 2.248 . 2 51 9 9 GLN N N 119.6 . 1 52 10 10 TRP H H 8.683 . 1 53 10 10 TRP HA H 4.561 . 1 54 10 10 TRP HB2 H 3.106 . 2 55 10 10 TRP HB3 H 3.217 . 2 56 10 10 TRP HD1 H 7.260 . 1 57 10 10 TRP HE1 H 10.15 . 1 58 10 10 TRP HE3 H 7.748 . 1 59 10 10 TRP HH2 H 7.165 . 1 60 10 10 TRP HZ2 H 7.458 . 1 61 10 10 TRP HZ3 H 7.230 . 1 62 10 10 TRP N N 124.1 . 1 63 10 10 TRP NE1 N 129.2 . 1 64 11 11 MET H H 8.637 . 1 65 11 11 MET HA H 4.549 . 1 66 11 11 MET HB2 H 1.995 . 2 67 11 11 MET HB3 H 2.194 . 2 68 11 11 MET HG2 H 2.423 . 2 69 11 11 MET HG3 H 2.573 . 2 70 11 11 MET N N 124.3 . 1 stop_ save_ save_constraint_statistics _Saveframe_category constraint_statistics _Text_data_format . _Text_data . _NOE_interproton_distance_evaluation . _NOE_pseudoatom_corrections . _Details . save_