data_18102 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure, Activity and Interactions of the Cysteine Deleted Analog of Tachyplesin-1 with Lipopolysaccharide Micelles ; _BMRB_accession_number 18102 _BMRB_flat_file_name bmr18102.str _Entry_type original _Submission_date 2011-11-25 _Accession_date 2011-11-25 _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 Joshi Mangesh . . 2 Bhattacharjya Surajit . . 3 Saravanan Rathi . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 84 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-03-25 update BMRB 'update entry citation' 2012-04-23 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure, activity and interactions of the cysteine deleted analog of tachyplesin-1 with lipopolysaccharide micelle: Mechanistic insights into outer-membrane permeabilization and endotoxin neutralization.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22464970 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Saravanan Rathi . . 2 Mohanram Harini . . 3 Joshi Mangesh . . 4 Domadia Prerna N. . 5 Torres Jaume . . 6 Ruedl Christiane . . 7 Bhattacharjya Surajit . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_name_full 'Biochimica et biophysica acta' _Journal_volume 1818 _Journal_issue 7 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1613 _Page_last 1624 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Cysteine Deleted Analog of Tachyplesin-1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Cysteine Deleted Analog of Tachyplesin-1' $CDT-LPS 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_CDT-LPS _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common CDT-LPS _Molecular_mass 1862.254 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence KWFRVYRGIYRRR loop_ _Residue_seq_code _Residue_label 1 LYS 2 TRP 3 PHE 4 ARG 5 VAL 6 TYR 7 ARG 8 GLY 9 ILE 10 TYR 11 ARG 12 ARG 13 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $CDT-LPS 'horseshoe crab' 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 $CDT-LPS 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelle _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $CDT-LPS 0.5 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _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_NOESY_2 _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 temperature 298 . K pH 4.5 . pH pressure 1 . atm 'ionic strength' 0 . M 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 . . . 1.000000000 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_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 'Cysteine Deleted Analog of Tachyplesin-1' _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 3.944 0.005 1 2 1 1 LYS HB2 H 1.803 0.006 2 3 1 1 LYS HB3 H 1.648 0.002 2 4 1 1 LYS HG2 H 1.314 0.004 2 5 2 2 TRP H H 8.611 0.001 1 6 2 2 TRP HA H 4.667 0.006 1 7 2 2 TRP HB2 H 3.200 0.002 2 8 2 2 TRP HB3 H 2.939 0.002 2 9 2 2 TRP HD1 H 7.227 0.006 1 10 2 2 TRP HE1 H 10.105 0.002 1 11 2 2 TRP HE3 H 7.555 0.001 1 12 2 2 TRP HZ2 H 7.466 0.002 1 13 3 3 PHE H H 7.906 0.003 1 14 3 3 PHE HA H 4.439 0.004 1 15 3 3 PHE HB2 H 2.944 0.004 2 16 3 3 PHE HB3 H 2.826 0.002 2 17 3 3 PHE HD1 H 7.290 0.003 3 18 3 3 PHE HE1 H 7.148 0.005 3 19 4 4 ARG H H 8.009 0.006 1 20 4 4 ARG HA H 4.021 0.006 1 21 4 4 ARG HB2 H 1.599 0.002 2 22 4 4 ARG HB3 H 1.451 0.003 2 23 4 4 ARG HG2 H 1.350 0.005 2 24 4 4 ARG HG3 H 1.350 0.005 2 25 4 4 ARG HD2 H 3.130 0.013 2 26 4 4 ARG HD3 H 3.130 0.013 2 27 5 5 VAL H H 8.076 0.005 1 28 5 5 VAL HA H 4.031 0.006 1 29 5 5 VAL HB H 1.946 0.001 1 30 5 5 VAL HG1 H 0.882 0.006 2 31 5 5 VAL HG1 H 0.826 0.007 2 32 6 6 TYR H H 8.507 0.002 1 33 6 6 TYR HA H 4.566 0.009 1 34 6 6 TYR HB2 H 3.132 0.004 2 35 6 6 TYR HB3 H 2.935 0.001 2 36 6 6 TYR HD2 H 7.100 0.000 3 37 7 7 ARG H H 8.331 0.005 1 38 7 7 ARG HA H 4.292 0.006 1 39 7 7 ARG HB2 H 1.810 0.007 2 40 7 7 ARG HB3 H 1.652 0.007 2 41 7 7 ARG HG2 H 1.549 0.013 2 42 7 7 ARG HG3 H 1.549 0.013 2 43 7 7 ARG HD2 H 3.197 0.002 2 44 7 7 ARG HD3 H 3.197 0.002 2 45 8 8 GLY H H 7.784 0.001 1 46 8 8 GLY HA2 H 3.863 0.001 2 47 8 8 GLY HA3 H 3.863 0.001 2 48 9 9 ILE H H 7.992 0.003 1 49 9 9 ILE HA H 4.140 0.002 1 50 9 9 ILE HB H 1.770 0.007 1 51 9 9 ILE HG12 H 0.876 0.008 2 52 9 9 ILE HG2 H 1.324 0.004 1 53 9 9 ILE HG2 H 1.103 0.002 1 54 9 9 ILE HD1 H 0.823 0.004 1 55 10 10 TYR H H 8.359 0.006 1 56 10 10 TYR HA H 4.573 0.004 1 57 10 10 TYR HB2 H 3.138 0.019 2 58 10 10 TYR HB3 H 2.946 0.005 2 59 10 10 TYR HD1 H 7.094 0.006 3 60 11 11 ARG H H 8.137 0.002 1 61 11 11 ARG HA H 4.273 0.008 1 62 11 11 ARG HB2 H 1.738 0.000 2 63 11 11 ARG HB3 H 1.650 0.005 2 64 11 11 ARG HG2 H 1.533 0.003 2 65 11 11 ARG HG3 H 1.533 0.003 2 66 11 11 ARG HD2 H 3.137 0.001 2 67 11 11 ARG HD3 H 3.137 0.001 2 68 11 11 ARG HH11 H 7.135 0.000 2 69 12 12 ARG H H 8.329 0.005 1 70 12 12 ARG HA H 4.227 0.009 1 71 12 12 ARG HB2 H 1.743 0.000 2 72 12 12 ARG HB3 H 1.637 0.007 2 73 12 12 ARG HG2 H 1.541 0.010 2 74 12 12 ARG HG3 H 1.541 0.010 2 75 13 13 ARG H H 8.439 0.001 1 76 13 13 ARG HA H 4.281 0.004 1 77 13 13 ARG HB2 H 1.821 0.012 2 78 13 13 ARG HB3 H 1.751 0.004 2 79 13 13 ARG HG2 H 1.632 0.002 2 80 13 13 ARG HG3 H 1.632 0.002 2 81 13 13 ARG HD2 H 3.188 0.006 2 82 13 13 ARG HD3 H 3.188 0.006 2 83 13 13 ARG HH11 H 7.668 0.001 2 84 13 13 ARG HH12 H 7.668 0.001 2 stop_ save_