data_11538 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Tachyplesin I in the presence of lipopolysaccharide ; _BMRB_accession_number 11538 _BMRB_flat_file_name bmr11538.str _Entry_type original _Submission_date 2013-10-25 _Accession_date 2013-10-25 _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 Kushibiki Takahiro . . 2 Kamiya Masakatsu . . 3 Aizawa Tomoyasu . . 4 Kumaki Yasuhiro . . 5 Kikukawa Takashi . . 6 Mizuguchi Mineyuki . . 7 Demura Makoto . . 8 Kawabata Syun-ichiro . . 9 Kawano Keiichi . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 113 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-02-14 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 11539 'Tachyplesin I in water' stop_ _Original_release_date 2014-02-14 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Interaction between tachyplesin I, an antimicrobial peptide derived from horseshoe crab, and lipopolysaccharide.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24389234 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kushibiki Takahiro . . 2 Kamiya Masakatsu . . 3 Aizawa Tomoyasu . . 4 Kumaki Yasuhiro . . 5 Kikukawa Takashi . . 6 Mizuguchi Mineyuki . . 7 Demura Makoto . . 8 Kawabata Syun-ichiro . . 9 Kawano Keiichi . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_name_full 'Biochimica et biophysica acta' _Journal_volume 1844 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 527 _Page_last 534 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name TPI-LPS _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label TPI $Tachyplesin_I stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details 'TP I in the presence of lipopolysaccharide(LPS)' save_ ######################## # Monomeric polymers # ######################## save_Tachyplesin_I _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Tachyplesin_I _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence KWCFRVCYRGICYRRCRX loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 LYS 2 2 TRP 3 3 CYS 4 4 PHE 5 5 ARG 6 6 VAL 7 7 CYS 8 8 TYR 9 9 ARG 10 10 GLY 11 11 ILE 12 12 CYS 13 13 TYR 14 14 ARG 15 15 ARG 16 16 CYS 17 17 ARG 18 18 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-02-06 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 BMRB 1135 "tachyplesin I" 88.89 16 100.00 100.00 3.06e-01 BMRB 11539 Tachyplesin_I 94.44 18 100.00 100.00 9.52e-02 PDB 1MA2 "Tachyplesin I Wild Type Peptide Nmr Structure" 94.44 17 100.00 100.00 9.68e-02 PDB 1MA5 "Tachyplesin I Solution Structure In The Presence Of 300mm Dodecylphosphocholine Micelles" 94.44 17 100.00 100.00 9.68e-02 PDB 1WO0 "Solution Structure Of Tachyplesin I In H2o" 94.44 18 100.00 100.00 9.52e-02 PDB 1WO1 "Tachyplesin I In Dodecylphosphocholine Micelles" 94.44 18 100.00 100.00 9.52e-02 PDB 2MDB "Tachyplesin I In The Presence Of Lipopolysaccharide" 94.44 18 100.00 100.00 9.52e-02 PDB 2RTV "Tachyplesin I In Water" 94.44 18 100.00 100.00 9.52e-02 GB AAA63538 "tachyplesin [Tachypleus tridentatus]" 94.44 77 100.00 100.00 6.16e-03 SP P14213 "RecName: Full=Tachyplesin-1; AltName: Full=Tachyplesin I; Flags: Precursor [Tachypleus tridentatus]" 94.44 77 100.00 100.00 6.16e-03 SP P69135 "RecName: Full=Tachyplesin-1; AltName: Full=Tachyplesin I [Tachypleus gigas]" 94.44 17 100.00 100.00 9.68e-02 SP P69136 "RecName: Full=Tachyplesin-1; AltName: Full=Tachyplesin I [Carcinoscorpius rotundicauda]" 94.44 17 100.00 100.00 9.68e-02 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 HN1 ? ? SING N HN2 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Tachyplesin_I 'Tachypleus tridentatus' 6853 Eukaryota Metazoa Tachypleus tridentatus 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 $Tachyplesin_I 'chemical synthesis' . . . . . 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 $Tachyplesin_I 750 uM 'natural abundance' Lipopolysaccharide 50 uM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' 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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer JEOL _Model ECA _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_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-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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 pH 3.8 . pH temperature 308 . 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 external direct . . . 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' 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 TPI _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 LYS HA H 4.161 0.001 1 2 1 1 LYS HB2 H 1.865 0.001 2 3 1 1 LYS HB3 H 1.865 0.001 2 4 1 1 LYS HD2 H 1.640 0.000 2 5 1 1 LYS HD3 H 1.640 0.000 2 6 1 1 LYS HE2 H 2.959 0.000 2 7 1 1 LYS HE3 H 2.959 0.000 2 8 1 1 LYS HG2 H 1.434 0.002 2 9 1 1 LYS HG3 H 1.434 0.002 2 10 2 2 TRP H H 8.913 0.006 1 11 2 2 TRP HA H 4.962 0.001 1 12 2 2 TRP HB2 H 3.326 0.001 2 13 2 2 TRP HB3 H 3.326 0.001 2 14 2 2 TRP HD1 H 7.264 0.000 1 15 2 2 TRP HE1 H 10.110 0.000 1 16 2 2 TRP HE3 H 7.679 0.000 1 17 2 2 TRP HZ2 H 7.451 0.000 1 18 3 3 CYS H H 8.306 0.000 1 19 3 3 CYS HA H 5.461 0.001 1 20 3 3 CYS HB2 H 2.570 0.001 2 21 3 3 CYS HB3 H 2.979 0.001 2 22 4 4 PHE H H 8.736 0.000 1 23 4 4 PHE HA H 4.766 0.000 1 24 4 4 PHE HB2 H 2.996 0.001 2 25 4 4 PHE HB3 H 2.996 0.001 2 26 4 4 PHE HD1 H 6.872 0.000 3 27 4 4 PHE HD2 H 6.872 0.000 3 28 4 4 PHE HE1 H 7.092 0.000 3 29 4 4 PHE HE2 H 7.092 0.000 3 30 4 4 PHE HZ H 7.159 0.000 1 31 5 5 ARG H H 8.544 0.000 1 32 5 5 ARG HA H 4.963 0.001 1 33 5 5 ARG HB2 H 1.638 0.000 2 34 5 5 ARG HB3 H 1.733 0.000 2 35 5 5 ARG HD2 H 3.112 0.003 2 36 5 5 ARG HD3 H 3.112 0.003 2 37 5 5 ARG HE H 7.157 0.000 1 38 5 5 ARG HG2 H 1.488 0.001 2 39 5 5 ARG HG3 H 1.488 0.001 2 40 6 6 VAL H H 8.843 0.000 1 41 6 6 VAL HA H 4.366 0.000 1 42 6 6 VAL HB H 1.722 0.000 1 43 6 6 VAL HG1 H 0.905 0.000 2 44 6 6 VAL HG2 H 0.905 0.000 2 45 7 7 CYS H H 8.623 0.000 1 46 7 7 CYS HA H 5.639 0.001 1 47 7 7 CYS HB2 H 2.663 0.003 2 48 7 7 CYS HB3 H 3.042 0.003 2 49 8 8 TYR H H 9.113 0.000 1 50 8 8 TYR HA H 4.750 0.001 1 51 8 8 TYR HB2 H 3.039 0.000 1 52 8 8 TYR HB3 H 3.039 0.000 1 53 8 8 TYR HD1 H 7.236 0.001 3 54 8 8 TYR HD2 H 7.236 0.001 3 55 8 8 TYR HE1 H 6.847 0.001 3 56 8 8 TYR HE2 H 6.847 0.001 3 57 9 9 ARG H H 9.213 0.001 1 58 9 9 ARG HA H 3.731 0.000 1 59 9 9 ARG HB2 H 1.626 0.000 2 60 9 9 ARG HB3 H 1.937 0.000 2 61 9 9 ARG HD2 H 3.048 0.000 2 62 9 9 ARG HD3 H 3.048 0.000 2 63 9 9 ARG HG2 H 0.993 0.001 2 64 9 9 ARG HG3 H 1.271 0.001 2 65 10 10 GLY H H 8.529 0.001 1 66 10 10 GLY HA2 H 3.576 0.000 2 67 10 10 GLY HA3 H 4.165 0.000 2 68 11 11 ILE H H 7.792 0.000 1 69 11 11 ILE HA H 4.314 0.001 1 70 11 11 ILE HB H 2.011 0.000 1 71 11 11 ILE HD1 H 0.890 0.001 4 72 11 11 ILE HG12 H 1.163 0.000 2 73 11 11 ILE HG13 H 1.514 0.000 2 74 11 11 ILE HG2 H 0.774 0.003 4 75 12 12 CYS H H 8.532 0.002 1 76 12 12 CYS HA H 5.682 0.001 1 77 12 12 CYS HB2 H 2.553 0.000 2 78 12 12 CYS HB3 H 2.955 0.002 2 79 13 13 TYR H H 9.164 0.001 1 80 13 13 TYR HA H 4.767 0.000 1 81 13 13 TYR HB2 H 2.850 0.000 2 82 13 13 TYR HB3 H 3.054 0.001 2 83 13 13 TYR HD1 H 7.036 0.001 3 84 13 13 TYR HD2 H 7.036 0.001 3 85 13 13 TYR HE1 H 6.734 0.003 3 86 13 13 TYR HE2 H 6.734 0.003 3 87 14 14 ARG H H 8.637 0.001 1 88 14 14 ARG HA H 4.809 0.001 1 89 14 14 ARG HB2 H 1.697 0.000 2 90 14 14 ARG HB3 H 1.697 0.000 2 91 14 14 ARG HG2 H 1.346 0.000 2 92 14 14 ARG HG3 H 1.462 0.000 2 93 15 15 ARG H H 8.710 0.000 1 94 15 15 ARG HA H 4.561 0.001 1 95 15 15 ARG HB2 H 1.460 0.001 2 96 15 15 ARG HB3 H 1.460 0.001 2 97 15 15 ARG HE H 7.155 0.000 1 98 15 15 ARG HG2 H 1.242 0.000 2 99 15 15 ARG HG3 H 1.242 0.000 2 100 16 16 CYS H H 8.622 0.000 1 101 16 16 CYS HA H 5.458 0.001 1 102 16 16 CYS HB2 H 2.775 0.001 2 103 16 16 CYS HB3 H 2.995 0.000 2 104 17 17 ARG H H 8.919 0.000 1 105 17 17 ARG HA H 4.567 0.001 1 106 17 17 ARG HB2 H 1.996 0.001 2 107 17 17 ARG HB3 H 1.996 0.001 2 108 17 17 ARG HD2 H 3.233 0.000 2 109 17 17 ARG HD3 H 3.233 0.000 2 110 17 17 ARG HG2 H 1.827 0.000 2 111 17 17 ARG HG3 H 1.827 0.000 2 112 18 18 NH2 HN1 H 7.870 0.000 2 113 18 18 NH2 HN2 H 7.284 0.000 2 stop_ loop_ _Atom_shift_assign_ID_ambiguity 71 '71,71,74,74,74' stop_ save_