data_11535 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of navitoxin ; _BMRB_accession_number 11535 _BMRB_flat_file_name bmr11535.str _Entry_type original _Submission_date 2013-10-16 _Accession_date 2013-10-16 _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 Umetsu Yoshitaka . . 2 Ohki Shinya . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 169 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-04-22 original author . stop_ _Original_release_date 2014-04-22 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Experimental conversion of a defensin into a neurotoxin: implications for origin of toxic function' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24425781 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhu Shunyi . . 2 Peigneur Steve . . 3 Gao Bin . . 4 Umetsu Yoshitaka . . 5 Ohki Shinya . . 6 Tytgat Jan . . stop_ _Journal_abbreviation 'Mol. Biol. Evol.' _Journal_volume 31 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 546 _Page_last 559 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Navitoxin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 3280.877 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; FSCDHSACAVRCLAQRRKGG KCKNGDCVCR ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 PHE 2 2 SER 3 3 CYS 4 4 ASP 5 5 HIS 6 6 SER 7 7 ALA 8 8 CYS 9 9 ALA 10 10 VAL 11 11 ARG 12 12 CYS 13 13 LEU 14 14 ALA 15 15 GLN 16 16 ARG 17 17 ARG 18 18 LYS 19 19 GLY 20 20 GLY 21 21 LYS 22 22 CYS 23 23 LYS 24 24 ASN 25 25 GLY 26 26 ASP 27 27 CYS 28 28 VAL 29 29 CYS 30 30 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-11-10 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 2RTY "Solution Structure Of Navitoxin" 100.00 30 100.00 100.00 4.73e-11 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $entity 'jewel wasp' 7425 Eukaryota Metazoa Nasonia vitripennis 'Navitoxin is a designed peptide from navidefensin2-2 of the parasitic wasp Nasonia vitripennis.' 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 $entity '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 $entity 1 mM 'natural abundance' H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _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 pH 3.0 . pH 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 . . . 1.000000000 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 entity _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 PHE HA H 4.324 0.02 1 2 1 1 PHE HB2 H 3.295 0.02 2 3 1 1 PHE HB3 H 3.143 0.02 2 4 1 1 PHE HD1 H 7.299 0.02 3 5 1 1 PHE HD2 H 7.299 0.02 3 6 1 1 PHE HE1 H 7.385 0.02 3 7 1 1 PHE HE2 H 7.385 0.02 3 8 2 2 SER H H 8.637 0.02 1 9 2 2 SER HA H 4.516 0.02 1 10 2 2 SER HB2 H 3.801 0.02 1 11 2 2 SER HB3 H 3.801 0.02 1 12 3 3 CYS H H 8.405 0.02 1 13 3 3 CYS HA H 4.445 0.02 1 14 3 3 CYS HB2 H 2.838 0.02 2 15 3 3 CYS HB3 H 2.803 0.02 2 16 4 4 ASP H H 8.473 0.02 1 17 4 4 ASP HA H 4.856 0.02 1 18 4 4 ASP HB2 H 2.801 0.02 2 19 4 4 ASP HB3 H 2.771 0.02 2 20 5 5 HIS H H 9.156 0.02 1 21 5 5 HIS HA H 4.186 0.02 1 22 5 5 HIS HB2 H 3.397 0.02 2 23 5 5 HIS HB3 H 3.339 0.02 2 24 5 5 HIS HD2 H 7.419 0.02 1 25 5 5 HIS HE1 H 8.651 0.02 1 26 6 6 SER H H 8.263 0.02 1 27 6 6 SER HA H 4.184 0.02 1 28 6 6 SER HB2 H 3.882 0.02 1 29 6 6 SER HB3 H 3.882 0.02 1 30 7 7 ALA H H 8.070 0.02 1 31 7 7 ALA HA H 4.129 0.02 1 32 7 7 ALA HB H 1.461 0.02 1 33 8 8 CYS H H 8.460 0.02 1 34 8 8 CYS HA H 4.613 0.02 1 35 8 8 CYS HB2 H 3.188 0.02 2 36 8 8 CYS HB3 H 2.571 0.02 2 37 9 9 ALA H H 7.897 0.02 1 38 9 9 ALA HA H 3.917 0.02 1 39 9 9 ALA HB H 1.487 0.02 1 40 10 10 VAL H H 7.643 0.02 1 41 10 10 VAL HA H 3.618 0.02 1 42 10 10 VAL HB H 2.118 0.02 1 43 10 10 VAL HG1 H 0.964 0.02 2 44 10 10 VAL HG2 H 1.078 0.02 2 45 11 11 ARG H H 8.025 0.02 1 46 11 11 ARG HA H 4.099 0.02 1 47 11 11 ARG HB2 H 1.986 0.02 1 48 11 11 ARG HB3 H 1.986 0.02 1 49 11 11 ARG HG2 H 1.719 0.02 2 50 11 11 ARG HG3 H 1.559 0.02 2 51 11 11 ARG HD2 H 3.116 0.02 1 52 11 11 ARG HD3 H 3.116 0.02 1 53 11 11 ARG HE H 7.193 0.02 1 54 12 12 CYS H H 8.475 0.02 1 55 12 12 CYS HA H 4.306 0.02 1 56 12 12 CYS HB2 H 2.610 0.02 1 57 12 12 CYS HB3 H 2.610 0.02 1 58 13 13 LEU H H 8.312 0.02 1 59 13 13 LEU HA H 4.278 0.02 1 60 13 13 LEU HB2 H 1.700 0.02 2 61 13 13 LEU HB3 H 1.628 0.02 2 62 13 13 LEU HG H 1.842 0.02 1 63 13 13 LEU HD1 H 0.894 0.02 1 64 13 13 LEU HD2 H 0.894 0.02 1 65 14 14 ALA H H 8.035 0.02 1 66 14 14 ALA HA H 4.232 0.02 1 67 14 14 ALA HB H 1.581 0.02 1 68 15 15 GLN H H 7.496 0.02 1 69 15 15 GLN HA H 4.404 0.02 1 70 15 15 GLN HB2 H 2.361 0.02 2 71 15 15 GLN HB3 H 2.100 0.02 2 72 15 15 GLN HG2 H 2.559 0.02 2 73 15 15 GLN HG3 H 2.422 0.02 2 74 15 15 GLN HE21 H 6.737 0.02 2 75 15 15 GLN HE22 H 7.161 0.02 2 76 16 16 ARG H H 8.133 0.02 1 77 16 16 ARG HA H 4.004 0.02 1 78 16 16 ARG HB2 H 2.143 0.02 2 79 16 16 ARG HB3 H 2.049 0.02 2 80 16 16 ARG HG2 H 1.595 0.02 1 81 16 16 ARG HG3 H 1.595 0.02 1 82 16 16 ARG HD2 H 3.223 0.02 1 83 16 16 ARG HD3 H 3.223 0.02 1 84 16 16 ARG HE H 7.186 0.02 1 85 17 17 ARG H H 7.923 0.02 1 86 17 17 ARG HA H 4.679 0.02 1 87 17 17 ARG HB2 H 2.250 0.02 1 88 17 17 ARG HB3 H 2.250 0.02 1 89 17 17 ARG HG2 H 1.631 0.02 1 90 17 17 ARG HG3 H 1.631 0.02 1 91 17 17 ARG HD2 H 3.183 0.02 2 92 17 17 ARG HD3 H 3.129 0.02 2 93 17 17 ARG HE H 7.347 0.02 1 94 18 18 LYS HA H 4.365 0.02 1 95 18 18 LYS HB2 H 1.829 0.02 2 96 18 18 LYS HB3 H 1.673 0.02 2 97 18 18 LYS HG2 H 1.471 0.02 2 98 18 18 LYS HG3 H 1.399 0.02 2 99 18 18 LYS HD2 H 1.610 0.02 1 100 18 18 LYS HD3 H 1.610 0.02 1 101 18 18 LYS HE2 H 2.971 0.02 1 102 18 18 LYS HE3 H 2.971 0.02 1 103 19 19 GLY H H 7.908 0.02 1 104 19 19 GLY HA2 H 4.004 0.02 2 105 19 19 GLY HA3 H 3.821 0.02 2 106 20 20 GLY H H 8.293 0.02 1 107 20 20 GLY HA2 H 4.566 0.02 2 108 20 20 GLY HA3 H 3.930 0.02 2 109 21 21 LYS H H 8.585 0.02 1 110 21 21 LYS HA H 4.538 0.02 1 111 21 21 LYS HB2 H 1.777 0.02 2 112 21 21 LYS HB3 H 1.691 0.02 2 113 21 21 LYS HG2 H 1.385 0.02 2 114 21 21 LYS HG3 H 1.261 0.02 2 115 21 21 LYS HD2 H 1.617 0.02 1 116 21 21 LYS HD3 H 1.617 0.02 1 117 21 21 LYS HE2 H 2.906 0.02 1 118 21 21 LYS HE3 H 2.906 0.02 1 119 21 21 LYS HZ H 7.547 0.02 1 120 22 22 CYS H H 8.818 0.02 1 121 22 22 CYS HA H 5.223 0.02 1 122 22 22 CYS HB2 H 2.951 0.02 2 123 22 22 CYS HB3 H 2.795 0.02 2 124 23 23 LYS H H 9.394 0.02 1 125 23 23 LYS HA H 4.503 0.02 1 126 23 23 LYS HB2 H 1.791 0.02 2 127 23 23 LYS HB3 H 1.579 0.02 2 128 23 23 LYS HG2 H 1.372 0.02 2 129 23 23 LYS HG3 H 1.254 0.02 2 130 23 23 LYS HD2 H 1.681 0.02 2 131 23 23 LYS HD3 H 1.643 0.02 2 132 23 23 LYS HE2 H 2.946 0.02 1 133 23 23 LYS HE3 H 2.946 0.02 1 134 23 23 LYS HZ H 7.565 0.02 1 135 24 24 ASN H H 9.556 0.02 1 136 24 24 ASN HA H 4.303 0.02 1 137 24 24 ASN HB2 H 3.036 0.02 2 138 24 24 ASN HB3 H 2.790 0.02 2 139 24 24 ASN HD21 H 7.298 0.02 1 140 24 24 ASN HD22 H 7.298 0.02 1 141 25 25 GLY H H 8.553 0.02 1 142 25 25 GLY HA2 H 3.540 0.02 2 143 25 25 GLY HA3 H 4.128 0.02 2 144 26 26 ASP H H 7.819 0.02 1 145 26 26 ASP HA H 4.989 0.02 1 146 26 26 ASP HB2 H 2.775 0.02 2 147 26 26 ASP HB3 H 2.716 0.02 2 148 27 27 CYS H H 8.844 0.02 1 149 27 27 CYS HA H 4.893 0.02 1 150 27 27 CYS HB2 H 2.996 0.02 2 151 27 27 CYS HB3 H 2.650 0.02 2 152 28 28 VAL H H 9.144 0.02 1 153 28 28 VAL HA H 4.333 0.02 1 154 28 28 VAL HB H 2.053 0.02 1 155 28 28 VAL HG1 H 0.937 0.02 1 156 28 28 VAL HG2 H 0.937 0.02 1 157 29 29 CYS H H 8.904 0.02 1 158 29 29 CYS HA H 5.290 0.02 1 159 29 29 CYS HB2 H 2.626 0.02 2 160 29 29 CYS HB3 H 3.156 0.02 2 161 30 30 ARG H H 8.240 0.02 1 162 30 30 ARG HA H 4.234 0.02 1 163 30 30 ARG HB2 H 1.728 0.02 2 164 30 30 ARG HB3 H 1.608 0.02 2 165 30 30 ARG HG2 H 1.489 0.02 1 166 30 30 ARG HG3 H 1.489 0.02 1 167 30 30 ARG HD2 H 3.129 0.02 1 168 30 30 ARG HD3 H 3.129 0.02 1 169 30 30 ARG HE H 7.212 0.02 1 stop_ save_