data_25486 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Purotoxin-2 NMR structure in water ; _BMRB_accession_number 25486 _BMRB_flat_file_name bmr25486.str _Entry_type original _Submission_date 2015-02-12 _Accession_date 2015-02-12 _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 Nadezhdin Kirill . . 2 Vassilevski Alexander . . 3 Oparin Peter . . 4 Grishin Evgeny . . 5 Arseniev Alexander . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 41 "15N chemical shifts" 41 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-03-29 update BMRB 'update entry citation' 2016-04-12 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 25487 'Purotoxin-2 in DPC micelles' stop_ _Original_release_date 2016-04-12 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure of purotoxin-2 from wolf spider: modular design and membrane-assisted mode of action in arachnid toxins. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27412961 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Oparin Peter B. . 2 Nadezhdin Kirill D. . 3 Berkut Antonina A. . 4 Arseniev Alexander S. . 5 Grishin Eugene V. . 6 Vassilevski Alexander A. . stop_ _Journal_abbreviation 'Biochem. J.' _Journal_name_full 'The Biochemical journal' _Journal_volume 473 _Journal_issue 19 _Journal_ISSN 1470-8728 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3113 _Page_last 3126 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Purotoxin-2 in water' _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 7278.426 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 64 _Mol_residue_sequence ; AKACTPLLHDCSHDRHSCCR GDMFKYVCDCFYPEGEDKTE VCSCQQPKSHKIAEKIIDKA KTTL ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 ALA 2 2 LYS 3 3 ALA 4 4 CYS 5 5 THR 6 6 PRO 7 7 LEU 8 8 LEU 9 9 HIS 10 10 ASP 11 11 CYS 12 12 SER 13 13 HIS 14 14 ASP 15 15 ARG 16 16 HIS 17 17 SER 18 18 CYS 19 19 CYS 20 20 ARG 21 21 GLY 22 22 ASP 23 23 MET 24 24 PHE 25 25 LYS 26 26 TYR 27 27 VAL 28 28 CYS 29 29 ASP 30 30 CYS 31 31 PHE 32 32 TYR 33 33 PRO 34 34 GLU 35 35 GLY 36 36 GLU 37 37 ASP 38 38 LYS 39 39 THR 40 40 GLU 41 41 VAL 42 42 CYS 43 43 SER 44 44 CYS 45 45 GLN 46 46 GLN 47 47 PRO 48 48 LYS 49 49 SER 50 50 HIS 51 51 LYS 52 52 ILE 53 53 ALA 54 54 GLU 55 55 LYS 56 56 ILE 57 57 ILE 58 58 ASP 59 59 LYS 60 60 ALA 61 61 LYS 62 62 THR 63 63 THR 64 64 LEU 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 $entity 'Wolf spiders' 74999 Eukaryota Metazoa Alopecosa . 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 'recombinant technology' . Escherichia coli . pET32b 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 '[U-100% 15N]' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version 3 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection 'data analysis' processing stop_ _Details . save_ save_TALOS _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task 'data analysis' refinement stop_ _Details . save_ save_CARA _Saveframe_category software _Name CARA _Version . loop_ _Vendor _Address _Electronic_address 'Keller and Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' 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-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_3D_HNHA_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNHA' _Sample_label $sample_1 save_ save_3D_HNHB_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNHB' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_3D_1H-15N_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N 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 3.3 . pH pressure 1 . atm temperature 313 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_TSP _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 C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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-15N HSQC' '3D HNHB' '2D 1H-13C HSQC aliphatic' '3D 1H-15N NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $TSP _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 5 5 THR H H 9.086 . . 2 5 5 THR N N 121.275 . . 3 7 7 LEU H H 7.737 . . 4 7 7 LEU N N 119.189 . . 5 9 9 HIS H H 8.183 . . 6 9 9 HIS N N 117.475 . . 7 10 10 ASP H H 8.412 . . 8 10 10 ASP N N 119.603 . . 9 12 12 SER H H 8.878 . . 10 12 12 SER N N 118.626 . . 11 13 13 HIS H H 8.637 . . 12 13 13 HIS N N 117.163 . . 13 14 14 ASP H H 7.361 . . 14 14 14 ASP N N 117.460 . . 15 15 15 ARG H H 9.046 . . 16 15 15 ARG N N 124.164 . . 17 16 16 HIS H H 8.584 . . 18 16 16 HIS N N 116.137 . . 19 17 17 SER H H 7.574 . . 20 17 17 SER N N 112.589 . . 21 19 19 CYS H H 9.009 . . 22 19 19 CYS N N 119.807 . . 23 21 21 GLY H H 7.785 . . 24 21 21 GLY N N 110.508 . . 25 22 22 ASP H H 8.494 . . 26 22 22 ASP N N 119.802 . . 27 23 23 MET H H 8.261 . . 28 23 23 MET N N 115.406 . . 29 24 24 PHE H H 7.299 . . 30 24 24 PHE N N 115.472 . . 31 25 25 LYS H H 8.510 . . 32 25 25 LYS N N 121 . . 33 27 27 VAL H H 9.150 . . 34 27 27 VAL N N 115.590 . . 35 28 28 CYS H H 8.852 . . 36 28 28 CYS N N 123.906 . . 37 30 30 CYS H H 8.580 . . 38 30 30 CYS N N 122.610 . . 39 31 31 PHE H H 9.150 . . 40 31 31 PHE N N 121.139 . . 41 32 32 TYR H H 8.702 . . 42 32 32 TYR N N 119.937 . . 43 34 34 GLU H H 8.568 . . 44 34 34 GLU N N 119.274 . . 45 35 35 GLY H H 8.320 . . 46 35 35 GLY N N 109.929 . . 47 36 36 GLU H H 8.214 . . 48 36 36 GLU N N 119.500 . . 49 37 37 ASP H H 8.375 . . 50 37 37 ASP N N 117.588 . . 51 38 38 LYS H H 8.029 . . 52 38 38 LYS N N 119.463 . . 53 39 39 THR H H 7.991 . . 54 39 39 THR N N 114.995 . . 55 40 40 GLU H H 8.428 . . 56 40 40 GLU N N 124.542 . . 57 43 43 SER H H 8.926 . . 58 43 43 SER N N 117.719 . . 59 44 44 CYS H H 8.020 . . 60 44 44 CYS N N 120.932 . . 61 46 46 GLN H H 8.926 . . 62 46 46 GLN HE21 H 7.432 . . 63 46 46 GLN N N 120.637 . . 64 46 46 GLN NE2 N 110.622 . . 65 49 49 SER H H 8.243 . . 66 49 49 SER N N 116.435 . . 67 50 50 HIS H H 8.551 . . 68 50 50 HIS N N 120.637 . . 69 54 54 GLU H H 8.560 . . 70 54 54 GLU N N 121.083 . . 71 55 55 LYS H H 8.245 . . 72 55 55 LYS N N 120.503 . . 73 58 58 ASP H H 8.451 . . 74 58 58 ASP N N 124.070 . . 75 60 60 ALA H H 8.219 . . 76 60 60 ALA N N 124.605 . . 77 61 61 LYS H H 8.224 . . 78 61 61 LYS N N 120.318 . . 79 62 62 THR H H 8.144 . . 80 62 62 THR N N 115.120 . . 81 63 63 THR H H 8.117 . . 82 63 63 THR N N 116.833 . . stop_ save_