data_15463 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Spatial Structure and Hydrophobic Organization Determine Membrane Activity of Latarcins, Spider Antimicrobial Peptides ; _BMRB_accession_number 15463 _BMRB_flat_file_name bmr15463.str _Entry_type new _Submission_date 2007-09-10 _Accession_date 2007-09-10 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dubovskii P. V. . 2 Volynsky P. E. . 3 Polyansky A. A. . 4 Chupin V. V. . 5 Efremov R. G. . 6 Arseniev A. S. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 138 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-08 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_title 'Three-dimensional structure/hydrophobicity of latarcins specifies their mode of membrane activity' _Citation_status published _Citation_type journal _PubMed_ID 18293934 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dubovskii P. V. . 2 Volynsky P. E. . 3 Polyansky A. A. . 4 Karpunin D. V. . 5 Chupin V. V. . 6 Efremov R. G. . 7 Arseniev A. S. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 47 _Journal_issue 11 _Page_first 3525 _Page_last 3533 _Year 2008 loop_ _Keyword 'linear antimicrobial peptide' 'model phospholipid membrane' 'detergent micelle' 'NMR spectroscopy' 'Monte Carlo method' 'spatial structure' 'molecular hydrophobicity potential' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Ltc1 loop_ _Mol_system_component_name _Mol_label Latarcin-1 $Latarcin-1 stop_ _System_physical_state native _System_oligomer_state ? _System_paramagnetic no save_ ######################## # Monomeric polymers # ######################## save_Latarcin-1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Latarcin-1 _Mol_thiol_state 'not present' ############################## # Polymer residue sequence # ############################## _Residue_count 26 _Mol_residue_sequence ; SMWSGMWRRKLKKLRNALKK KLKGEK ; loop_ _Residue_seq_code _Residue_label 1 SER 2 MET 3 TRP 4 SER 5 GLY 6 MET 7 TRP 8 ARG 9 ARG 10 LYS 11 LEU 12 LYS 13 LYS 14 LEU 15 ARG 16 ASN 17 ALA 18 LEU 19 LYS 20 LYS 21 LYS 22 LEU 23 LYS 24 GLY 25 GLU 26 LYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-07 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 2PCO "Spatial Structure And Membrane Permeabilization For Latarcin-1, A Spider Antimicrobial Peptide" 100.00 26 100.00 100.00 2.54e-06 EMBL CAJ81660 "latarcin 1 precursor, pLtc 1 [Lachesana tarabaevi]" 100.00 88 100.00 100.00 3.00e-07 SP Q1ELT9 "RecName: Full=M-zodatoxin-Lt1a; Short=M-ZDTX-Lt1a; AltName: Full=Latarcin-1; Short=Ltc-1; Short=Ltc1; Flags: Precursor" 100.00 88 100.00 100.00 3.00e-07 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Latarcin-1 'Lachesana tarabaevi' 379576 Eukaryota Metazoa Lachesana tarabaevi 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 _Details $Latarcin-1 'chemical synthesis' . . . . ? 'The peptide was chemically synthesized. This sequence occurs naturally in spider (Lachesana tarabaevi) venom.' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '2 mM Ltc1, 120 mM perdeuterated SDS, pH 7.1, salt-free, 90% H2O, 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Latarcin-1 2 mM 'natural abundance' 'perdeuterated SDS' 120 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '2 mM Ltc1, 120 mM perdeuterated SDS, pH 7.1, salt-free, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Latarcin-1 2 mM 'natural abundance' 'perdeuterated SDS' 120 mM 'natural abundance' D2O 100 % . stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version 1.0.6. loop_ _Vendor _Address _Electronic_address 'Guentert P.' . . stop_ loop_ _Task refinement stop_ save_ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version 3.1.a loop_ _Vendor _Address _Electronic_address BRUKER . . stop_ loop_ _Task collection stop_ save_ save_XEASY _Saveframe_category software _Name XEASY _Version 40300000 loop_ _Vendor _Address _Electronic_address 'Xia & Bartels' . . stop_ loop_ _Task 'data analysis' stop_ save_ save_FANMEM _Saveframe_category software _Name FANMEM _Version 4.1 loop_ _Vendor _Address _Electronic_address 'Nolde, Arseniev, Vergoten, Efremov' . . stop_ loop_ _Task refinement stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 save_ ############################# # NMR applied experiments # ############################# save_2D_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_2D_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.1 . pH pressure 1 . bar temperature 318 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference 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 4.75 internal direct ? ? ? 1.000 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 loop_ _Software_label $XEASY stop_ loop_ _Experiment_label '2D TOCSY' '2D NOESY' DQF-COSY stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name Latarcin-1 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 2 2 MET HA H 4.30900 0.01 . 2 3 3 TRP H H 7.66811 0.01 . 3 3 3 TRP HA H 4.87900 0.01 . 4 3 3 TRP HB2 H 3.31800 0.01 . 5 3 3 TRP HB3 H 3.49600 0.01 . 6 3 3 TRP HD1 H 7.31100 0.01 . 7 3 3 TRP HE1 H 9.81200 0.01 . 8 3 3 TRP HE3 H 7.42300 0.01 . 9 3 3 TRP HH2 H 7.07600 0.01 . 10 3 3 TRP HZ2 H 7.40100 0.01 . 11 3 3 TRP HZ3 H 7.00700 0.01 . 12 4 4 SER H H 8.19178 0.01 . 13 4 4 SER HA H 4.41151 0.01 . 14 4 4 SER HB2 H 3.99233 0.01 . 15 4 4 SER HB3 H 4.11930 0.01 . 16 5 5 GLY H H 8.26350 0.01 . 17 5 5 GLY HA2 H 3.97096 0.01 . 18 5 5 GLY HA3 H 4.05718 0.01 . 19 6 6 MET H H 7.90305 0.01 . 20 6 6 MET HA H 4.46436 0.01 . 21 6 6 MET HB2 H 1.61422 0.01 . 22 6 6 MET HB3 H 1.61422 0.01 . 23 6 6 MET HG2 H 1.91172 0.01 . 24 6 6 MET HG3 H 1.91172 0.01 . 25 7 7 TRP H H 8.13280 0.01 . 26 7 7 TRP HA H 4.39129 0.01 . 27 7 7 TRP HB2 H 3.29400 0.01 . 28 7 7 TRP HB3 H 3.39300 0.01 . 29 7 7 TRP HD1 H 7.43925 0.01 . 30 7 7 TRP HE1 H 9.79700 0.01 . 31 7 7 TRP HE3 H 7.44900 0.01 . 32 7 7 TRP HH2 H 7.11200 0.01 . 33 7 7 TRP HZ2 H 7.46800 0.01 . 34 7 7 TRP HZ3 H 6.97400 0.01 . 35 8 8 ARG H H 7.83046 0.01 . 36 8 8 ARG HA H 3.88610 0.01 . 37 8 8 ARG HB2 H 1.72133 0.01 . 38 8 8 ARG HB3 H 1.86000 0.01 . 39 8 8 ARG HD2 H 3.17300 0.01 . 40 8 8 ARG HD3 H 3.17300 0.01 . 41 8 8 ARG HE H 7.13200 0.01 . 42 8 8 ARG HG2 H 1.47000 0.01 . 43 8 8 ARG HG3 H 1.47000 0.01 . 44 9 9 ARG H H 7.67203 0.01 . 45 9 9 ARG HA H 4.09754 0.01 . 46 9 9 ARG HB2 H 1.96002 0.01 . 47 9 9 ARG HB3 H 1.96002 0.01 . 48 9 9 ARG HD2 H 3.22200 0.01 . 49 9 9 ARG HD3 H 3.22200 0.01 . 50 9 9 ARG HE H 7.23800 0.01 . 51 9 9 ARG HG2 H 1.70600 0.01 . 52 9 9 ARG HG3 H 1.81133 0.01 . 53 10 10 LYS H H 7.82050 0.01 . 54 10 10 LYS HA H 4.10378 0.01 . 55 10 10 LYS HB2 H 1.86400 0.01 . 56 10 10 LYS HB3 H 2.05800 0.01 . 57 10 10 LYS HG2 H 1.50800 0.01 . 58 10 10 LYS HG3 H 1.56677 0.01 . 59 11 11 LEU H H 8.19139 0.01 . 60 11 11 LEU HA H 4.16500 0.01 . 61 11 11 LEU HB2 H 1.72622 0.01 . 62 11 11 LEU HB3 H 1.95024 0.01 . 63 11 11 LEU HD1 H 0.97895 0.01 . 64 11 11 LEU HD2 H 1.00821 0.01 . 65 12 12 LYS H H 7.90751 0.01 . 66 12 12 LYS HA H 4.01252 0.01 . 67 12 12 LYS HB2 H 1.95700 0.01 . 68 12 12 LYS HB3 H 1.95700 0.01 . 69 12 12 LYS HG2 H 1.73800 0.01 . 70 12 12 LYS HG3 H 1.73800 0.01 . 71 13 13 LYS H H 7.71330 0.01 . 72 13 13 LYS HA H 4.13556 0.01 . 73 13 13 LYS HB2 H 2.04318 0.01 . 74 13 13 LYS HB3 H 2.04318 0.01 . 75 13 13 LYS HG2 H 1.55700 0.01 . 76 13 13 LYS HG3 H 1.66459 0.01 . 77 14 14 LEU H H 8.00067 0.01 . 78 14 14 LEU HA H 4.12700 0.01 . 79 14 14 LEU HB2 H 1.80100 0.01 . 80 14 14 LEU HB3 H 1.92000 0.01 . 81 14 14 LEU HD1 H 0.95545 0.01 . 82 14 14 LEU HD2 H 1.00400 0.01 . 83 15 15 ARG H H 8.45329 0.01 . 84 15 15 ARG HA H 3.87000 0.01 . 85 15 15 ARG HB2 H 1.93500 0.01 . 86 15 15 ARG HB3 H 2.11400 0.01 . 87 15 15 ARG HG2 H 1.78000 0.01 . 88 15 15 ARG HG3 H 1.88400 0.01 . 89 16 16 ASN H H 8.15548 0.01 . 90 16 16 ASN HA H 4.46614 0.01 . 91 16 16 ASN HB2 H 2.86121 0.01 . 92 16 16 ASN HB3 H 2.97464 0.01 . 93 17 17 ALA H H 8.14996 0.01 . 94 17 17 ALA HA H 4.20737 0.01 . 95 17 17 ALA HB H 1.60003 0.01 . 96 18 18 LEU H H 8.25854 0.01 . 97 18 18 LEU HA H 4.18449 0.01 . 98 18 18 LEU HB2 H 1.65700 0.01 . 99 18 18 LEU HB3 H 1.88100 0.01 . 100 18 18 LEU HD1 H 0.93800 0.01 . 101 18 18 LEU HD2 H 0.93800 0.01 . 102 19 19 LYS H H 8.24100 0.01 . 103 19 19 LYS HA H 3.92169 0.01 . 104 19 19 LYS HB2 H 2.00700 0.01 . 105 19 19 LYS HB3 H 2.00700 0.01 . 106 20 20 LYS H H 7.77096 0.01 . 107 20 20 LYS HA H 4.03400 0.01 . 108 20 20 LYS HB2 H 1.97600 0.01 . 109 20 20 LYS HB3 H 1.97600 0.01 . 110 20 20 LYS HG2 H 1.49000 0.01 . 111 20 20 LYS HG3 H 1.57300 0.01 . 112 21 21 LYS H H 8.14568 0.01 . 113 21 21 LYS HA H 4.19667 0.01 . 114 21 21 LYS HB2 H 1.98867 0.01 . 115 21 21 LYS HB3 H 1.98867 0.01 . 116 21 21 LYS HG2 H 1.64601 0.01 . 117 21 21 LYS HG3 H 1.82992 0.01 . 118 22 22 LEU H H 8.23013 0.01 . 119 22 22 LEU HA H 4.29900 0.01 . 120 22 22 LEU HB2 H 1.83700 0.01 . 121 22 22 LEU HB3 H 1.83700 0.01 . 122 22 22 LEU HD1 H 0.93500 0.01 . 123 22 22 LEU HD2 H 0.93500 0.01 . 124 23 23 LYS H H 7.77540 0.01 . 125 23 23 LYS HA H 4.22203 0.01 . 126 23 23 LYS HB2 H 1.99618 0.01 . 127 23 23 LYS HB3 H 1.99618 0.01 . 128 24 24 GLY H H 7.90243 0.01 . 129 24 24 GLY HA2 H 3.97348 0.01 . 130 24 24 GLY HA3 H 4.07392 0.01 . 131 25 25 GLU H H 8.08282 0.01 . 132 25 25 GLU HA H 4.21003 0.01 . 133 25 25 GLU HB2 H 1.95513 0.01 . 134 25 25 GLU HB3 H 2.04800 0.01 . 135 25 25 GLU HG2 H 2.34500 0.01 . 136 25 25 GLU HG3 H 2.43900 0.01 . 137 26 26 LYS H H 7.72600 0.01 . 138 26 26 LYS HA H 4.15100 0.01 . stop_ save_