data_15068 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure-Activity Analysis of Quorum-Sensing Signaling Peptides from Streptococcus mutans ; _BMRB_accession_number 15068 _BMRB_flat_file_name bmr15068.str _Entry_type new _Submission_date 2006-12-06 _Accession_date 2006-12-06 _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 Syvitski R. T. . 2 Jakeman D. L. . 3 Li Y. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 112 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-17 update BMRB 'complete entry citation' 2007-02-01 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure-Activity Analysis of Quorum-Sensing Signaling Peptides from Streptococcus mutans' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16936029 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Syvitski Raymond T. . 2 Tian Xiao-Lin . . 3 Sampara Kamal . . 4 Salman Alan . . 5 Lee Song F. . 6 Jakeman David L. . 7 Li Yung-Hua . . stop_ _Journal_abbreviation 'J. Bacteriol.' _Journal_name_full 'Journal of Bacteriology' _Journal_volume 189 _Journal_issue 4 _Journal_ASTM JOBAAY _Journal_ISSN 1098-5530 _Journal_CSD 0767 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1441 _Page_last 1450 _Year 2007 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name UA159 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label UA159 $signaling_peptide_UA159sp 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_signaling_peptide_UA159sp _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common signaling_peptide_UA159sp _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; SGSLSTFFRLFNRSFTQALG X ; loop_ _Residue_seq_code _Residue_label 1 SER 2 GLY 3 SER 4 LEU 5 SER 6 THR 7 PHE 8 PHE 9 ARG 10 LEU 11 PHE 12 ASN 13 ARG 14 SER 15 PHE 16 THR 17 GLN 18 ALA 19 LEU 20 GLY 21 LYS_NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-31 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 2I2J "Nmr Structure Of Ua159sp In Tfe" 95.24 21 100.00 100.00 4.49e-03 DBJ BAH87262 "competence stimulating peptide, precursor [Streptococcus mutans NN2025]" 95.24 46 100.00 100.00 1.58e-03 DBJ BAL68595 "competence stimulating peptide precursor [Streptococcus mutans LJ23]" 95.24 46 100.00 100.00 1.61e-03 EMBL CAL29378 "competence stimulating peptide [Streptococcus mutans]" 95.24 46 100.00 100.00 1.61e-03 EMBL CAL29379 "competence stimulating peptide [Streptococcus mutans]" 95.24 46 100.00 100.00 1.61e-03 EMBL CAL29380 "competence stimulating peptide [Streptococcus mutans]" 95.24 46 100.00 100.00 1.54e-03 EMBL CAL29381 "competence stimulating peptide [Streptococcus mutans]" 85.71 43 100.00 100.00 3.97e-02 EMBL CAL29382 "competence stimulating peptide [Streptococcus mutans]" 95.24 46 100.00 100.00 1.54e-03 GB AAK01541 "competence stimulating protein precursor [Streptococcus mutans]" 95.24 46 100.00 100.00 1.61e-03 GB AAK01542 "competence stimulating protein precursor [Streptococcus mutans]" 95.24 46 100.00 100.00 1.54e-03 GB AAK01543 "competence stimulating protein precursor [Streptococcus mutans]" 95.24 46 100.00 100.00 1.54e-03 GB AAK01545 "competence stimulating protein precursor [Streptococcus mutans]" 95.24 46 100.00 100.00 1.54e-03 GB AAK01546 "competence stimulating protein precursor [Streptococcus mutans]" 95.24 46 100.00 100.00 1.54e-03 REF NP_722220 "competence stimulating peptide [Streptococcus mutans UA159]" 95.24 46 100.00 100.00 1.54e-03 REF WP_002267610 "competence protein [Streptococcus mutans]" 95.24 46 100.00 100.00 1.54e-03 REF WP_002270250 "competence protein [Streptococcus mutans]" 95.24 46 100.00 100.00 1.61e-03 REF WP_002273928 "competence stimulating peptide, precursor [Streptococcus mutans]" 85.71 43 100.00 100.00 3.97e-02 REF WP_002278269 "competence stimulating peptide, precursor [Streptococcus mutans]" 95.24 46 100.00 100.00 1.71e-03 stop_ save_ ###################### # Polymer residues # ###################### save_LYS_NH2 _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common L-LYSINAMIDE _Abbreviation_common LYS_NH2 _BMRB_code LYS_NH2 _PDB_code . _Standard_residue_derivative LYS loop_ _Mol_label _Residue_seq_code $signaling_peptide_UA159sp 21 stop_ _Molecular_mass . _Mol_paramagnetic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? NT . N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? CE CE C . 0 . ? NZ NZ N . 1 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 1HB H . 0 . ? HB3 2HB H . 0 . ? HG2 1HG H . 0 . ? HG3 2HG H . 0 . ? HD2 1HD H . 0 . ? HD3 2HD H . 0 . ? HE2 1HE H . 0 . ? HE3 2HE H . 0 . ? HZ1 1HZ H . 0 . ? HZ2 2HZ H . 0 . ? HZ3 3HZ H . 0 . ? HT1 . H . 0 . ? HT2 . 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 CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD CE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING CE NZ ? ? SING CE HE2 ? ? SING CE HE3 ? ? SING NZ HZ1 ? ? SING NZ HZ2 ? ? SING NZ HZ3 ? ? SING NT C ? ? SING NT HT1 ? ? SING NT HT2 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $signaling_peptide_UA159sp . 1309 Bacteria . Streptococcus mutans 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 $signaling_peptide_UA159sp 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution _Details '2mM peptide, 100% TFE' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $signaling_peptide_UA159sp 2 mM none TFE 100 % none stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version 3.1 loop_ _Vendor _Address _Electronic_address 'Brunger A.T. et al.' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version 2.6 loop_ _Vendor _Address _Electronic_address Bruker . . stop_ loop_ _Task collection stop_ _Details . save_ save_Sparky _Saveframe_category software _Name Sparky _Version 3.1 loop_ _Vendor _Address _Electronic_address UCSF . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_nmr_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_150ms_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '150ms TOCSY' _Sample_label $sample save_ save_250ms_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '250ms NOESY' _Sample_label $sample save_ save_DOSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DOSY _Sample_label $sample save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pressure 1 . atm temperature 298 . 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.0 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 '150ms TOCSY' '250ms NOESY' DOSY stop_ loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name UA159 _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 SER HA H 4.505 0.006 1 2 1 1 SER HB2 H 2.795 0.006 2 3 1 1 SER HB3 H 3.336 0.011 2 4 4 4 LEU HA H 4.272 0.006 1 5 4 4 LEU HB2 H 1.662 0.001 1 6 4 4 LEU HB3 H 1.662 0.001 1 7 4 4 LEU HG H 1.720 0.010 1 8 4 4 LEU HD1 H 0.904 0.012 1 9 4 4 LEU HD2 H 0.973 0.009 1 10 5 5 SER H H 7.998 0.008 1 11 5 5 SER HA H 4.054 0.001 1 12 6 6 THR H H 7.785 0.011 1 13 6 6 THR HA H 4.282 0.009 1 14 6 6 THR HB H 3.950 0.008 1 15 6 6 THR HG2 H 1.253 0.007 1 16 7 7 PHE H H 7.941 0.011 1 17 7 7 PHE HA H 4.238 0.009 1 18 7 7 PHE HB3 H 3.203 0.012 2 19 7 7 PHE HD1 H 7.077 0.010 1 20 7 7 PHE HD2 H 7.077 0.010 1 21 7 7 PHE HE1 H 7.160 0.011 1 22 7 7 PHE HE2 H 7.160 0.011 1 23 8 8 PHE H H 8.438 0.008 1 24 8 8 PHE HA H 4.245 0.007 1 25 8 8 PHE HB3 H 3.254 0.009 2 26 8 8 PHE HD1 H 7.240 0.010 1 27 8 8 PHE HD2 H 7.240 0.010 1 28 8 8 PHE HE1 H 7.320 0.009 1 29 8 8 PHE HE2 H 7.320 0.009 1 30 9 9 ARG H H 8.074 0.010 1 31 9 9 ARG HA H 4.057 0.009 1 32 9 9 ARG HB2 H 1.982 0.011 2 33 9 9 ARG HB3 H 2.122 0.008 2 34 9 9 ARG HG2 H 1.739 0.010 1 35 9 9 ARG HG3 H 1.739 0.010 1 36 9 9 ARG HD2 H 3.240 0.012 1 37 9 9 ARG HD3 H 3.240 0.012 1 38 10 10 LEU H H 8.288 0.008 1 39 10 10 LEU HA H 4.075 0.012 1 40 10 10 LEU HB2 H 1.777 0.012 2 41 10 10 LEU HB3 H 1.838 0.016 2 42 10 10 LEU HG H 1.553 0.010 1 43 10 10 LEU HD1 H 0.872 0.009 2 44 10 10 LEU HD2 H 0.872 0.009 2 45 11 11 PHE H H 9.017 0.009 1 46 11 11 PHE HA H 4.041 0.008 1 47 11 11 PHE HB2 H 2.763 0.013 2 48 11 11 PHE HB3 H 2.899 0.009 2 49 11 11 PHE HD1 H 7.057 0.011 1 50 11 11 PHE HD2 H 7.057 0.011 1 51 11 11 PHE HE1 H 7.186 0.016 1 52 11 11 PHE HE2 H 7.186 0.016 1 53 12 12 ASN H H 8.172 0.010 1 54 12 12 ASN HA H 4.346 0.008 1 55 12 12 ASN HB2 H 2.587 0.010 2 56 12 12 ASN HB3 H 2.769 0.007 2 57 12 12 ASN HD21 H 5.498 0.007 2 58 12 12 ASN HD22 H 6.837 0.007 2 59 13 13 ARG H H 8.385 0.011 1 60 13 13 ARG HA H 4.100 0.015 1 61 13 13 ARG HB3 H 1.988 0.010 2 62 13 13 ARG HG2 H 1.729 0.011 1 63 13 13 ARG HG3 H 1.729 0.011 1 64 13 13 ARG HD2 H 3.235 0.014 1 65 13 13 ARG HD3 H 3.235 0.014 1 66 14 14 SER H H 8.166 0.009 1 67 14 14 SER HA H 4.161 0.001 1 68 14 14 SER HB2 H 3.845 0.003 2 69 14 14 SER HB3 H 3.920 0.001 2 70 15 15 PHE H H 8.098 0.009 1 71 15 15 PHE HA H 4.227 0.011 1 72 15 15 PHE HB2 H 2.829 0.013 2 73 15 15 PHE HB3 H 2.969 0.010 2 74 15 15 PHE HD1 H 7.099 0.043 1 75 15 15 PHE HD2 H 7.099 0.043 1 76 15 15 PHE HE1 H 7.167 0.013 1 77 15 15 PHE HE2 H 7.167 0.013 1 78 16 16 THR H H 7.787 0.012 1 79 16 16 THR HA H 4.296 0.012 1 80 16 16 THR HB H 3.963 0.010 1 81 16 16 THR HG2 H 1.317 0.008 1 82 17 17 GLN H H 7.818 0.010 1 83 17 17 GLN HA H 4.153 0.008 1 84 17 17 GLN HB2 H 2.124 0.014 2 85 17 17 GLN HB3 H 2.160 0.012 2 86 17 17 GLN HG2 H 2.364 0.016 2 87 17 17 GLN HG3 H 2.438 0.012 2 88 17 17 GLN HE21 H 6.049 0.009 2 89 17 17 GLN HE22 H 7.027 0.005 2 90 18 18 ALA H H 7.649 0.009 1 91 18 18 ALA HA H 4.127 0.013 1 92 18 18 ALA HB H 1.409 0.008 1 93 19 19 LEU H H 7.375 0.008 1 94 19 19 LEU HA H 4.195 0.007 1 95 19 19 LEU HB2 H 1.594 0.027 2 96 19 19 LEU HB3 H 1.661 0.011 2 97 19 19 LEU HG H 1.338 0.015 1 98 19 19 LEU HD1 H 0.816 0.008 2 99 19 19 LEU HD2 H 0.816 0.008 2 100 20 20 GLY H H 7.854 0.008 1 101 20 20 GLY HA2 H 3.786 0.004 2 102 20 20 GLY HA3 H 3.927 0.002 2 103 21 21 LYS_NH2 H H 7.379 0.010 1 104 21 21 LYS_NH2 HA H 4.330 0.007 1 105 21 21 LYS_NH2 HB2 H 1.692 0.014 2 106 21 21 LYS_NH2 HB3 H 1.908 0.009 2 107 21 21 LYS_NH2 HG2 H 1.357 0.009 1 108 21 21 LYS_NH2 HG3 H 1.357 0.009 1 109 21 21 LYS_NH2 HD2 H 1.619 0.036 1 110 21 21 LYS_NH2 HD3 H 1.619 0.036 1 111 21 21 LYS_NH2 HE2 H 2.961 0.010 1 112 21 21 LYS_NH2 HE3 H 2.961 0.010 1 stop_ save_