data_15992 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of Vm24 synthetic scorpion toxin. ; _BMRB_accession_number 15992 _BMRB_flat_file_name bmr15992.str _Entry_type original _Submission_date 2008-10-20 _Accession_date 2008-10-20 _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 'DEL RIO-PORTILLA' FEDERICO . Sr. 2 HERNANDEZ-LOPEZ ROGELIO . Sr. 3 POSSANI-POSTAY LOURIVAL . Sr. 4 GURROLA GEORGINA . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 205 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-07-19 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure of Vm24 synthetic scorpion toxin.' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hernandez-Lopez Rogelio A. . 2 'del Rio-Portilla' Federico . . 3 Possani Lourival D. . 4 Gurrola-Briones Georgina . . 5 'Rodriguez de la Vega' Ricardo C. . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Vm24 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label VM24 $Vm24 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_Vm24 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Vm24 _Molecular_mass 3879.684 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 36 _Mol_residue_sequence ; AAAISCVGSPECPPKCRAQG CKNGKCMNRKCKCYYC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 0 ALA 2 1 ALA 3 2 ALA 4 3 ILE 5 4 SER 6 5 CYS 7 6 VAL 8 7 GLY 9 8 SER 10 9 PRO 11 10 GLU 12 11 CYS 13 12 PRO 14 13 PRO 15 14 LYS 16 15 CYS 17 16 ARG 18 17 ALA 19 18 GLN 20 19 GLY 21 20 CYS 22 21 LYS 23 22 ASN 24 23 GLY 25 24 LYS 26 25 CYS 27 26 MET 28 27 ASN 29 28 ARG 30 29 LYS 31 30 CYS 32 31 LYS 33 32 CYS 34 33 TYR 35 34 TYR 36 35 CYS 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 2K9O "Solution Structure Of Vm24 Synthetic Scorpion Toxin" 100.00 36 100.00 100.00 3.13e-15 SP P0DJ31 "RecName: Full=Potassium channel toxin alpha-KTx 23.1; AltName: Full=Toxin Vm24; AltName: Full=Toxin alpha-KTx 21.1 [Vaejovis sm" 100.00 36 100.00 100.00 3.13e-15 stop_ save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name single disulfide VM24 6 CYS SG VM24 26 CYS SG single disulfide VM24 12 CYS SG VM24 31 CYS SG single disulfide VM24 16 CYS SG VM24 33 CYS SG single disulfide VM24 21 CYS SG VM24 36 CYS SG 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 $Vm24 . . . . . . 'Based on scorpion toxins after analysis of docking' 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 $Vm24 'chemical synthesis' . . . . . 'PEPTIDE OBTAINED FROM SYNTHESIS AFTER MOLECULAR DYNAMIC STUDIES.' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.3 mL 5 mg' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Vm24 1.2 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.7 mL, 5 mg, Cold probe.' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Vm24 1.2 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'P.GUNTERT ET AL.' . . stop_ loop_ _Task refinement 'chemical shift assignment' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 9 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ save_XEASY _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unity _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _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_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_2 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'These samples usually do not need a specific media to be structured' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.5 . pH pressure 1 . atm temperature 297 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 'Referenced with DSS' 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_ _Software_label $XEASY stop_ loop_ _Experiment_label 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 VM24 _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 2 2 ALA H H 8.621 0.020 1 2 2 2 ALA HA H 4.358 0.020 1 3 2 2 ALA HB H 1.405 0.020 1 4 3 3 ALA H H 8.472 0.020 1 5 3 3 ALA HA H 4.359 0.020 1 6 3 3 ALA HB H 1.402 0.020 1 7 4 4 ILE H H 8.912 0.020 1 8 4 4 ILE HA H 4.212 0.020 1 9 4 4 ILE HB H 1.640 0.020 1 10 4 4 ILE HD1 H 0.796 0.020 1 11 4 4 ILE HG12 H 1.077 0.020 2 12 4 4 ILE HG13 H 1.615 0.020 2 13 4 4 ILE HG2 H 0.934 0.020 1 14 5 5 SER H H 8.547 0.020 1 15 5 5 SER HA H 4.864 0.020 1 16 5 5 SER HB2 H 3.934 0.020 2 17 5 5 SER HB3 H 3.934 0.020 2 18 6 6 CYS H H 8.064 0.020 1 19 6 6 CYS HA H 4.873 0.020 1 20 6 6 CYS HB2 H 3.078 0.020 2 21 6 6 CYS HB3 H 3.078 0.020 2 22 7 7 VAL H H 8.500 0.020 1 23 7 7 VAL HA H 4.215 0.020 1 24 7 7 VAL HB H 2.156 0.020 1 25 7 7 VAL HG1 H 0.979 0.020 2 26 7 7 VAL HG2 H 0.979 0.020 2 27 8 8 GLY H H 7.941 0.020 1 28 8 8 GLY HA2 H 4.443 0.020 2 29 8 8 GLY HA3 H 4.075 0.020 2 30 9 9 SER H H 8.793 0.020 1 31 9 9 SER HA H 4.356 0.020 1 32 9 9 SER HB2 H 2.602 0.020 2 33 9 9 SER HB3 H 2.602 0.020 2 34 10 10 PRO HA H 4.456 0.020 1 35 10 10 PRO HB2 H 1.887 0.020 2 36 10 10 PRO HB3 H 2.433 0.020 2 37 10 10 PRO HD2 H 3.666 0.020 2 38 10 10 PRO HD3 H 3.860 0.020 2 39 10 10 PRO HG2 H 2.013 0.020 2 40 10 10 PRO HG3 H 2.158 0.020 2 41 11 11 GLU H H 7.475 0.020 1 42 11 11 GLU HA H 4.316 0.020 1 43 11 11 GLU HB2 H 2.247 0.020 2 44 11 11 GLU HB3 H 2.153 0.020 2 45 11 11 GLU HG2 H 2.623 0.020 2 46 11 11 GLU HG3 H 2.394 0.020 2 47 12 12 CYS H H 8.423 0.020 1 48 12 12 CYS HA H 4.779 0.020 1 49 12 12 CYS HB2 H 2.808 0.020 2 50 12 12 CYS HB3 H 2.536 0.020 2 51 13 13 PRO HB2 H 2.160 0.020 2 52 13 13 PRO HB3 H 2.160 0.020 2 53 13 13 PRO HD2 H 4.056 0.020 2 54 13 13 PRO HD3 H 3.769 0.020 2 55 13 13 PRO HG2 H 2.436 0.020 2 56 13 13 PRO HG3 H 2.436 0.020 2 57 14 14 PRO HA H 4.309 0.020 1 58 14 14 PRO HB2 H 2.437 0.020 2 59 14 14 PRO HB3 H 1.972 0.020 2 60 14 14 PRO HD2 H 3.472 0.020 2 61 14 14 PRO HD3 H 3.635 0.020 2 62 14 14 PRO HG2 H 2.209 0.020 2 63 14 14 PRO HG3 H 2.134 0.020 2 64 15 15 LYS H H 7.681 0.020 1 65 15 15 LYS HA H 3.059 0.020 1 66 15 15 LYS HB2 H 1.737 0.020 2 67 15 15 LYS HB3 H 1.737 0.020 2 68 15 15 LYS HD2 H 2.016 0.020 2 69 15 15 LYS HD3 H 1.952 0.020 2 70 15 15 LYS HE2 H 4.216 0.020 2 71 15 15 LYS HE3 H 4.216 0.020 2 72 15 15 LYS HG2 H 1.637 0.020 2 73 15 15 LYS HG3 H 1.543 0.020 2 74 15 15 LYS HZ H 6.842 0.020 2 75 16 16 CYS H H 9.607 0.020 1 76 16 16 CYS HA H 4.364 0.020 1 77 16 16 CYS HB2 H 3.043 0.020 2 78 16 16 CYS HB3 H 2.764 0.020 2 79 17 17 ARG H H 8.714 0.020 1 80 17 17 ARG HA H 4.680 0.020 1 81 17 17 ARG HB2 H 1.920 0.020 2 82 17 17 ARG HB3 H 1.920 0.020 2 83 17 17 ARG HD2 H 3.278 0.020 2 84 17 17 ARG HD3 H 3.145 0.020 2 85 17 17 ARG HE H 7.287 0.020 1 86 17 17 ARG HG2 H 1.761 0.020 2 87 17 17 ARG HG3 H 1.761 0.020 2 88 18 18 ALA H H 7.496 0.020 1 89 18 18 ALA HA H 4.356 0.020 1 90 18 18 ALA HB H 1.637 0.020 1 91 19 19 GLN H H 7.276 0.020 1 92 19 19 GLN HA H 4.634 0.020 1 93 19 19 GLN HB2 H 2.188 0.020 2 94 19 19 GLN HB3 H 2.188 0.020 2 95 19 19 GLN HE21 H 6.897 0.020 2 96 19 19 GLN HE22 H 6.740 0.020 2 97 19 19 GLN HG2 H 2.529 0.020 2 98 19 19 GLN HG3 H 2.433 0.020 2 99 20 20 GLY H H 7.906 0.020 1 100 20 20 GLY HA2 H 4.342 0.020 2 101 20 20 GLY HA3 H 3.894 0.020 2 102 21 21 CYS H H 7.892 0.020 1 103 21 21 CYS HA H 5.440 0.020 1 104 21 21 CYS HB2 H 3.290 0.020 2 105 21 21 CYS HB3 H 2.812 0.020 2 106 22 22 LYS H H 8.001 0.020 1 107 22 22 LYS HB2 H 2.055 0.020 2 108 22 22 LYS HB3 H 1.967 0.020 2 109 22 22 LYS HD2 H 1.828 0.020 2 110 22 22 LYS HD3 H 1.828 0.020 2 111 22 22 LYS HG2 H 1.595 0.020 2 112 22 22 LYS HG3 H 1.595 0.020 2 113 22 22 LYS HZ H 7.615 0.020 1 114 22 22 LYS HZ H 7.345 0.020 1 115 23 23 ASN H H 7.996 0.020 1 116 23 23 ASN HA H 4.313 0.020 1 117 23 23 ASN HB2 H 2.624 0.020 2 118 23 23 ASN HB3 H 2.485 0.020 2 119 23 23 ASN HD21 H 7.620 0.020 2 120 23 23 ASN HD22 H 6.983 0.020 2 121 24 24 GLY H H 8.566 0.020 1 122 24 24 GLY HA2 H 5.014 0.020 2 123 24 24 GLY HA3 H 4.125 0.020 2 124 25 25 LYS H H 8.659 0.020 1 125 25 25 LYS HA H 4.719 0.020 1 126 25 25 LYS HB2 H 1.968 0.020 2 127 25 25 LYS HB3 H 1.883 0.020 2 128 25 25 LYS HD2 H 1.406 0.020 2 129 25 25 LYS HD3 H 1.406 0.020 2 130 25 25 LYS HG2 H 1.546 0.020 2 131 25 25 LYS HG3 H 1.546 0.020 2 132 26 26 CYS H H 9.113 0.020 1 133 26 26 CYS HA H 4.869 0.020 1 134 26 26 CYS HB2 H 2.951 0.020 2 135 26 26 CYS HB3 H 2.730 0.020 2 136 27 27 MET H H 9.117 0.020 1 137 27 27 MET HA H 4.797 0.020 1 138 27 27 MET HB2 H 2.110 0.020 2 139 27 27 MET HB3 H 1.921 0.020 2 140 27 27 MET HG2 H 2.483 0.020 2 141 27 27 MET HG3 H 2.483 0.020 2 142 28 28 ASN H H 9.465 0.020 1 143 28 28 ASN HA H 4.357 0.020 1 144 28 28 ASN HB2 H 3.046 0.020 2 145 28 28 ASN HB3 H 2.767 0.020 2 146 28 28 ASN HD21 H 7.649 0.020 2 147 28 28 ASN HD22 H 6.975 0.020 2 148 29 29 ARG H H 8.519 0.020 1 149 29 29 ARG HA H 3.996 0.020 1 150 29 29 ARG HB2 H 2.300 0.020 2 151 29 29 ARG HB3 H 2.206 0.020 2 152 29 29 ARG HD2 H 3.286 0.020 2 153 29 29 ARG HD3 H 3.286 0.020 2 154 29 29 ARG HE H 7.211 0.020 1 155 29 29 ARG HG2 H 2.998 0.020 2 156 29 29 ARG HG3 H 1.639 0.020 2 157 30 30 LYS H H 7.769 0.020 1 158 30 30 LYS HA H 5.288 0.020 1 159 30 30 LYS HB2 H 1.734 0.020 2 160 30 30 LYS HB3 H 1.734 0.020 2 161 30 30 LYS HD2 H 1.625 0.020 2 162 30 30 LYS HD3 H 1.625 0.020 2 163 30 30 LYS HE2 H 3.048 0.020 2 164 30 30 LYS HE3 H 3.048 0.020 2 165 30 30 LYS HG2 H 1.473 0.020 2 166 30 30 LYS HG3 H 1.405 0.020 2 167 31 31 CYS H H 9.044 0.020 1 168 31 31 CYS HA H 5.056 0.020 1 169 31 31 CYS HB2 H 2.670 0.020 2 170 31 31 CYS HB3 H 2.573 0.020 2 171 32 32 LYS H H 9.576 0.020 1 172 32 32 LYS HA H 4.550 0.020 1 173 32 32 LYS HB2 H 1.871 0.020 2 174 32 32 LYS HB3 H 1.777 0.020 2 175 32 32 LYS HD2 H 1.700 0.020 2 176 32 32 LYS HD3 H 1.700 0.020 2 177 32 32 LYS HE2 H 2.949 0.020 2 178 32 32 LYS HE3 H 2.949 0.020 2 179 32 32 LYS HG2 H 1.269 0.020 2 180 32 32 LYS HG3 H 1.269 0.020 2 181 32 32 LYS HZ H 7.546 0.020 1 182 33 33 CYS H H 8.713 0.020 1 183 33 33 CYS HA H 5.401 0.020 1 184 33 33 CYS HB2 H 2.713 0.020 2 185 33 33 CYS HB3 H 3.143 0.020 2 186 34 34 TYR H H 8.529 0.020 1 187 34 34 TYR HA H 4.728 0.020 1 188 34 34 TYR HB2 H 2.716 0.020 2 189 34 34 TYR HB3 H 2.486 0.020 2 190 34 34 TYR HD1 H 6.792 0.020 3 191 34 34 TYR HD2 H 6.792 0.020 3 192 34 34 TYR HE1 H 6.587 0.020 3 193 34 34 TYR HE2 H 6.587 0.020 3 194 35 35 TYR H H 8.920 0.020 1 195 35 35 TYR HA H 4.360 0.020 1 196 35 35 TYR HB2 H 3.246 0.020 2 197 35 35 TYR HB3 H 3.246 0.020 2 198 35 35 TYR HD1 H 7.141 0.020 3 199 35 35 TYR HD2 H 7.141 0.020 3 200 35 35 TYR HE1 H 6.945 0.020 3 201 35 35 TYR HE2 H 6.945 0.020 3 202 36 36 CYS H H 8.719 0.020 1 203 36 36 CYS HA H 4.962 0.020 1 204 36 36 CYS HB2 H 3.278 0.020 2 205 36 36 CYS HB3 H 2.996 0.020 2 stop_ save_