data_6561 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of plantaricin a in dpc micelles, 20 structures ; _BMRB_accession_number 6561 _BMRB_flat_file_name bmr6561.str _Entry_type original _Submission_date 2005-03-18 _Accession_date 2005-03-18 _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 Kristiansen P. E. . 2 Fimland G. . . 3 Mantzilas D. . . 4 Nissen-Meyer J. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 155 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2005-08-22 original author . stop_ _Original_release_date 2005-08-22 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure and mode of action of the membrane-permeabilizing antimicrobial peptide pheromone plantaricin A ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15805109 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kristiansen P. E. . 2 Fimland G. . . 3 Mantzilas D. . . 4 Nissen-Meyer J. . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 280 _Journal_issue 24 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 22945 _Page_last 22950 _Year 2005 _Details . loop_ _Keyword antibiotic pheromone 'amphipathic helix' micelle stop_ save_ ################################## # Molecular system description # ################################## save_system_plnA _Saveframe_category molecular_system _Mol_system_name 'plantaricin A' _Abbreviation_common plnA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'plantaricin A' $plnA stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_plnA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'plantaricin A' _Abbreviation_common plnA _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 26 _Mol_residue_sequence ; KSSAYSLQMGATAIKQVKKL FKKWGW ; loop_ _Residue_seq_code _Residue_label 1 LYS 2 SER 3 SER 4 ALA 5 TYR 6 SER 7 LEU 8 GLN 9 MET 10 GLY 11 ALA 12 THR 13 ALA 14 ILE 15 LYS 16 GLN 17 VAL 18 LYS 19 LYS 20 LEU 21 PHE 22 LYS 23 LYS 24 TRP 25 GLY 26 TRP stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-28 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 1YTR "Nmr Structure Of Plantaricin A In Dpc Micelles, 20 Structures" 100.00 26 100.00 100.00 9.81e-08 DBJ BAI99564 "plantaricin A, partial [Lactobacillus plantarum]" 100.00 48 100.00 100.00 6.84e-08 EMBL CAA53069 "precursor for plantaricin A [Lactobacillus plantarum]" 100.00 48 100.00 100.00 6.84e-08 EMBL CAA64204 "plantaricin A precursor peptide [Lactobacillus plantarum]" 100.00 48 100.00 100.00 6.84e-08 EMBL CCC77922 "plantaricin A precursor peptide, induction factor [Lactobacillus plantarum WCFS1]" 100.00 48 100.00 100.00 6.84e-08 GB ABD15221 "plantaricin A precursor peptide, induction factor [Lactobacillus plantarum]" 100.00 48 100.00 100.00 5.71e-08 GB ACO06045 "plantaricin A precursor peptide [Lactobacillus plantarum]" 100.00 48 100.00 100.00 6.84e-08 GB ADE08251 "PlnA [Lactobacillus plantarum]" 100.00 48 100.00 100.00 6.84e-08 GB ADN97568 "plantaricin A precursor peptide, induction factor [Lactobacillus plantarum subsp. plantarum ST-III]" 100.00 48 100.00 100.00 6.84e-08 GB AEI26312 "plantaricin A precursor peptide induction factor [Lactobacillus plantarum]" 100.00 48 100.00 100.00 5.71e-08 REF WP_003641979 "MULTISPECIES: bacteriocin [Lactobacillus]" 100.00 48 100.00 100.00 6.84e-08 REF YP_003923662 "plantaricin A precursor peptide, induction factor [Lactobacillus plantarum subsp. plantarum ST-III]" 100.00 48 100.00 100.00 6.84e-08 REF YP_004888436 "plantaricin A precursor peptide, induction factor [Lactobacillus plantarum WCFS1]" 100.00 48 100.00 100.00 6.84e-08 SP P80214 "RecName: Full=Bacteriocin plantaricin-A; Flags: Precursor [Lactobacillus plantarum WCFS1]" 100.00 48 100.00 100.00 6.84e-08 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $plnA 'Lactobacillus plantarum' 1590 Eubacteria . Lactobascillus Plantarum 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 $plnA 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelles _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $plnA 2.9 mM . stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version 1.1 loop_ _Task refinement 'structure calculation' 'automated assignemnt' 'structure annealing' stop_ _Details 'Guntert P' save_ save_TALOS _Saveframe_category software _Name TALOS _Version 98.040.21.02 loop_ _Task 'Dihedral angle prediction' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label . save_ save_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label . save_ save_DQCOSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQCOSY _Sample_label . save_ save_1H-15N_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N HSQC' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQCOSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N HSQC' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH* 4 1 pH temperature 298 0.5 K 'ionic strength' 0 . M pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 0.0 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_chemical_shift_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label NOESY TOCSY DQCOSY '1H-15N HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'plantaricin A' _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 . 3 SER H H 8.560 0.01 . 2 . 3 SER HA H 4.487 0.01 . 3 . 3 SER HB2 H 3.869 0.01 . 4 . 3 SER HB3 H 3.923 0.01 . 5 . 4 ALA H H 8.415 0.01 . 6 . 4 ALA HA H 4.268 0.01 . 7 . 4 ALA HB H 1.331 0.01 . 8 . 5 TYR H H 7.994 0.01 . 9 . 5 TYR HA H 4.593 0.01 . 10 . 5 TYR HB2 H 2.965 0.01 . 11 . 5 TYR HB3 H 3.035 0.01 . 12 . 5 TYR HD1 H 7.110 0.01 . 13 . 5 TYR HD2 H 7.110 0.01 . 14 . 5 TYR HE1 H 6.829 0.01 . 15 . 5 TYR HE2 H 6.829 0.01 . 16 . 6 SER H H 7.921 0.01 . 17 . 6 SER HA H 4.542 0.01 . 18 . 6 SER HB2 H 3.908 0.01 . 19 . 6 SER HB3 H 4.076 0.01 . 20 . 7 LEU H H 8.576 0.01 . 21 . 7 LEU HA H 4.218 0.01 . 22 . 7 LEU HB2 H 1.818 0.01 . 23 . 7 LEU HB3 H 1.818 0.01 . 24 . 7 LEU HG H 1.681 0.01 . 25 . 7 LEU HD1 H 1.015 0.01 . 26 . 7 LEU HD2 H 0.954 0.01 . 27 . 8 GLN H H 8.307 0.01 . 28 . 8 GLN HA H 4.208 0.01 . 29 . 8 GLN HB2 H 2.139 0.01 . 30 . 8 GLN HB3 H 2.139 0.01 . 31 . 8 GLN HG2 H 2.441 0.01 . 32 . 8 GLN HG3 H 2.441 0.01 . 33 . 8 GLN HE21 H 6.829 0.01 . 34 . 8 GLN HE22 H 7.501 0.01 . 35 . 9 MET H H 8.191 0.01 . 36 . 9 MET HA H 4.365 0.01 . 37 . 9 MET HB2 H 2.135 0.01 . 38 . 9 MET HB3 H 2.224 0.01 . 39 . 9 MET HG2 H 2.587 0.01 . 40 . 9 MET HG3 H 2.674 0.01 . 41 . 10 GLY H H 8.344 0.01 . 42 . 10 GLY HA2 H 3.868 0.01 . 43 . 10 GLY HA3 H 3.778 0.01 . 44 . 11 ALA H H 8.310 0.01 . 45 . 11 ALA HA H 4.120 0.01 . 46 . 11 ALA HB H 1.576 0.01 . 47 . 12 THR H H 8.156 0.01 . 48 . 12 THR HA H 4.363 0.01 . 49 . 12 THR HB H 3.972 0.01 . 50 . 12 THR HG2 H 1.315 0.01 . 51 . 13 ALA H H 8.182 0.01 . 52 . 13 ALA HA H 4.088 0.01 . 53 . 13 ALA HB H 1.545 0.01 . 54 . 14 ILE H H 8.110 0.01 . 55 . 14 ILE HA H 3.686 0.01 . 56 . 14 ILE HB H 2.034 0.01 . 57 . 14 ILE HG12 H 1.278 0.01 . 58 . 14 ILE HG13 H 1.746 0.01 . 59 . 14 ILE HG2 H 0.983 0.01 . 60 . 14 ILE HD1 H 0.891 0.01 . 61 . 15 LYS H H 7.781 0.01 . 62 . 15 LYS HA H 3.949 0.01 . 63 . 15 LYS HB2 H 1.686 0.01 . 64 . 15 LYS HB3 H 1.732 0.01 . 65 . 15 LYS HG2 H 1.477 0.01 . 66 . 15 LYS HG3 H 1.477 0.01 . 67 . 15 LYS HD2 H 1.984 0.01 . 68 . 15 LYS HD3 H 2.040 0.01 . 69 . 15 LYS HE2 H 3.002 0.01 . 70 . 15 LYS HE3 H 3.002 0.01 . 71 . 16 GLN H H 7.957 0.01 . 72 . 16 GLN HA H 4.190 0.01 . 73 . 16 GLN HB2 H 2.173 0.01 . 74 . 16 GLN HB3 H 2.228 0.01 . 75 . 16 GLN HG2 H 2.393 0.01 . 76 . 16 GLN HG3 H 2.581 0.01 . 77 . 16 GLN HE21 H 7.200 0.01 . 78 . 16 GLN HE22 H 6.886 0.01 . 79 . 17 VAL H H 8.224 0.01 . 80 . 17 VAL HA H 3.569 0.01 . 81 . 17 VAL HB H 2.161 0.01 . 82 . 17 VAL HG1 H 1.037 0.01 . 83 . 17 VAL HG2 H 0.802 0.01 . 84 . 18 LYS H H 8.217 0.01 . 85 . 18 LYS HA H 3.835 0.01 . 86 . 18 LYS HB2 H 1.703 0.01 . 87 . 18 LYS HB3 H 1.703 0.01 . 88 . 18 LYS HG2 H 1.357 0.01 . 89 . 18 LYS HG3 H 1.357 0.01 . 90 . 18 LYS HD2 H 1.907 0.01 . 91 . 18 LYS HD3 H 1.907 0.01 . 92 . 18 LYS HE2 H 2.877 0.01 . 93 . 18 LYS HE3 H 2.877 0.01 . 94 . 19 LYS H H 7.574 0.01 . 95 . 19 LYS HA H 3.994 0.01 . 96 . 19 LYS HB2 H 1.655 0.01 . 97 . 19 LYS HB3 H 1.717 0.01 . 98 . 19 LYS HG2 H 1.428 0.01 . 99 . 19 LYS HG3 H 1.428 0.01 . 100 . 19 LYS HD2 H 1.977 0.01 . 101 . 19 LYS HD3 H 1.919 0.01 . 102 . 19 LYS HE2 H 2.987 0.01 . 103 . 19 LYS HE3 H 2.987 0.01 . 104 . 20 LEU H H 7.686 0.01 . 105 . 20 LEU HA H 3.803 0.01 . 106 . 20 LEU HB2 H 1.546 0.01 . 107 . 20 LEU HB3 H 1.546 0.01 . 108 . 20 LEU HG H 1.215 0.01 . 109 . 20 LEU HD1 H 0.729 0.01 . 110 . 20 LEU HD2 H 0.692 0.01 . 111 . 21 PHE H H 8.056 0.01 . 112 . 21 PHE HA H 4.204 0.01 . 113 . 21 PHE HB2 H 3.255 0.01 . 114 . 21 PHE HB3 H 3.196 0.01 . 115 . 21 PHE HD1 H 7.143 0.01 . 116 . 21 PHE HD2 H 7.143 0.01 . 117 . 21 PHE HZ H 7.147 0.01 . 118 . 22 LYS H H 7.900 0.01 . 119 . 22 LYS HA H 4.316 0.01 . 120 . 22 LYS HB2 H 1.631 0.01 . 121 . 22 LYS HB3 H 1.596 0.01 . 122 . 22 LYS HD2 H 1.784 0.01 . 123 . 22 LYS HD3 H 1.991 0.01 . 124 . 22 LYS HE2 H 3.026 0.01 . 125 . 22 LYS HE3 H 3.026 0.01 . 126 . 23 LYS H H 7.905 0.01 . 127 . 23 LYS HA H 4.111 0.01 . 128 . 23 LYS HB2 H 1.596 0.01 . 129 . 23 LYS HB3 H 1.632 0.01 . 130 . 23 LYS HG2 H 1.594 0.01 . 131 . 23 LYS HG3 H 1.683 0.01 . 132 . 23 LYS HE2 H 2.931 0.01 . 133 . 23 LYS HE3 H 2.931 0.01 . 134 . 24 TRP H H 7.902 0.01 . 135 . 24 TRP HA H 4.733 0.01 . 136 . 24 TRP HB3 H 3.082 0.01 . 137 . 24 TRP HD1 H 7.050 0.01 . 138 . 24 TRP HE1 H 10.378 0.01 . 139 . 24 TRP HE3 H 6.816 0.01 . 140 . 24 TRP HZ2 H 7.381 0.01 . 141 . 24 TRP HZ3 H 6.721 0.01 . 142 . 24 TRP HH2 H 7.014 0.01 . 143 . 25 GLY H H 7.898 0.01 . 144 . 25 GLY HA2 H 3.914 0.01 . 145 . 25 GLY HA3 H 4.170 0.01 . 146 . 26 TRP H H 8.055 0.01 . 147 . 26 TRP HA H 4.704 0.01 . 148 . 26 TRP HB2 H 3.045 0.01 . 149 . 26 TRP HB3 H 3.316 0.01 . 150 . 26 TRP HD1 H 7.177 0.01 . 151 . 26 TRP HE1 H 10.486 0.01 . 152 . 26 TRP HE3 H 7.232 0.01 . 153 . 26 TRP HZ2 H 7.410 0.01 . 154 . 26 TRP HZ3 H 6.885 0.01 . 155 . 26 TRP HH2 H 7.031 0.01 . stop_ save_