data_4190 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; BmTX1 Toxin from Scorpion Buthus martensii Karsch ; _BMRB_accession_number 4190 _BMRB_flat_file_name bmr4190.str _Entry_type original _Submission_date 1998-08-25 _Accession_date 1998-08-25 _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 Blanc E. . . 2 Romi-Lebrun R. . . 3 Bornet O. . . 4 Nakajima T. . . 5 Darbon H. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 216 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2000-04-04 original author . stop_ _Original_release_date 2000-04-04 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution Structure of two new Toxins from the Venom of the Chinese Scorpion Buthus martensii Karsch Blockers of Potassium Channels ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 98400946 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Blanc E. . . 2 Romi-Lebrun R. . . 3 Bornet O. . . 4 Nakajima T. . . 5 Darbon H. . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 37 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 12412 _Page_last 12418 _Year 1998 _Details . save_ ####################################### # Cited references within the entry # ####################################### save_citation_one _Saveframe_category citation _Citation_full ; Wishart, D. S., Bigam, C. G., Yao, J., Abildgaard, F., Dyson, H. J., Oldfield, E., Markley, J. L., and Sykes, B. D. J. Biomol. NMR 6, 135-140 (1995). ; _Citation_title '1H, 13C and 15N chemical shift referencing in biomolecular NMR.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8589602 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wishart 'D S' S. . 2 Bigam 'C G' G. . 3 Yao J . . 4 Abildgaard F . . 5 Dyson 'H J' J. . 6 Oldfield E . . 7 Markley 'J L' L. . 8 Sykes 'B D' D. . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 6 _Journal_issue 2 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 135 _Page_last 140 _Year 1995 _Details ; A considerable degree of variability exists in the way that 1H, 13C and 15N chemical shifts are reported and referenced for biomolecules. In this article we explore some of the reasons for this situation and propose guidelines for future chemical shift referencing and for conversion from many common 1H, 13C and 15N chemical shift standards, now used in biomolecular NMR, to those proposed here. ; save_ ################################## # Molecular system description # ################################## save_system_Bmtx1 _Saveframe_category molecular_system _Mol_system_name Bmtx1 _Abbreviation_common Bmtx1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Bmtx1 $Bmtx1 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not reported' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Bmtx1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common ; Toxin One from the venom of the chinese Scorpion Buthus martensii Karsch ; _Abbreviation_common Bmtx1 _Molecular_mass . _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 37 _Mol_residue_sequence ; XFTDVKCTGSKQCWPVCKQM FGKPNGKCMNGKCRCYS ; loop_ _Residue_seq_code _Residue_label 1 PCA 2 PHE 3 THR 4 ASP 5 VAL 6 LYS 7 CYS 8 THR 9 GLY 10 SER 11 LYS 12 GLN 13 CYS 14 TRP 15 PRO 16 VAL 17 CYS 18 LYS 19 GLN 20 MET 21 PHE 22 GLY 23 LYS 24 PRO 25 ASN 26 GLY 27 LYS 28 CYS 29 MET 30 ASN 31 GLY 32 LYS 33 CYS 34 ARG 35 CYS 36 TYR 37 SER stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-13 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 1BIG "Scorpion Toxin Bmtx1 From Buthus Martensii Karsch, Nmr, 25 Structures" 54.55 37 100.00 100.00 7.28e-17 GB AAF63971 "neurotoxin TX1 precursor [Mesobuthus martensii]" 54.55 57 100.00 100.00 1.55e-17 GB AAZ65851 "potassium-channel toxin protein [Mesobuthus martensii]" 54.55 57 100.00 100.00 1.55e-17 GB AFR43615 "toxin BmTX1 [Mesobuthus martensii]" 54.55 57 100.00 100.00 1.55e-17 GB AFR43617 "toxin BmTX4 [Mesobuthus martensii]" 54.55 57 97.22 97.22 6.62e-17 SP Q9NII6 "RecName: Full=Potassium channel toxin alpha-KTx 1.5; AltName: Full=BmTX1; AltName: Full=Neurotoxin TX1; Flags: Precursor" 54.55 57 100.00 100.00 1.55e-17 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_PCA _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 'PYROGLUTAMIC ACID' _BMRB_code . _PDB_code PCA _Standard_residue_derivative . _Molecular_mass 129.114 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jul 14 13:52:53 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? OE OE O . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N CD ? ? SING N H ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? DOUB CD OE ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Organ _Secretion $Bmtx1 . 34649 Eukaryota Metazoa Buthus martensi telson venom 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 $Bmtx1 . . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details 'Both toxin spectra were recorded in H2O/D2O 90/10 (v/v)' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Bmtx1 2.0 mM . H2O 90 % . D2O 10 % . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_one save_ save_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_one save_ save_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name COSY _Sample_label $sample_one save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3 . n/a temperature 300 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_one _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_citation_label DSS H 1 protons ppm 0.00 . direct . . . $citation_one 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_chemical_shifts_one _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name Bmtx1 _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 PCA H H 7.47 . 1 2 . 1 PCA HA H 4.18 . 1 3 . 1 PCA HB2 H 2.35 . 2 4 . 1 PCA HB3 H 1.52 . 2 5 . 1 PCA HG2 H 2.00 . 2 6 . 1 PCA HG3 H 1.22 . 2 7 . 2 PHE H H 8.39 . 1 8 . 2 PHE HA H 4.57 . 1 9 . 2 PHE HB2 H 3.28 . 2 10 . 2 PHE HB3 H 2.99 . 2 11 . 2 PHE HD1 H 7.4 . 3 12 . 3 THR H H 7.85 . 1 13 . 3 THR HA H 4.88 . 1 14 . 3 THR HB H 4.33 . 1 15 . 3 THR HG2 H 1.21 . 1 16 . 4 ASP H H 8.78 . 1 17 . 4 ASP HA H 4.96 . 1 18 . 4 ASP HB2 H 2.98 . 2 19 . 4 ASP HB3 H 2.87 . 2 20 . 5 VAL H H 8.18 . 1 21 . 5 VAL HA H 3.85 . 1 22 . 5 VAL HB H 1.82 . 1 23 . 5 VAL HG1 H 0.97 . 1 24 . 5 VAL HG2 H 0.97 . 1 25 . 6 LYS H H 8.36 . 1 26 . 6 LYS HA H 4.77 . 1 27 . 6 LYS HB2 H 1.79 . 1 28 . 6 LYS HB3 H 1.79 . 1 29 . 6 LYS HG2 H 1.59 . 2 30 . 6 LYS HG3 H 1.41 . 2 31 . 6 LYS HD2 H 1.72 . 1 32 . 6 LYS HD3 H 1.72 . 1 33 . 6 LYS HE2 H 3.00 . 1 34 . 6 LYS HE3 H 3.00 . 1 35 . 7 CYS HA H 4.91 . 1 36 . 7 CYS HB2 H 3.17 . 2 37 . 7 CYS HB3 H 2.87 . 2 38 . 8 THR H H 9.19 . 1 39 . 8 THR HA H 4.41 . 1 40 . 8 THR HB H 4.37 . 1 41 . 8 THR HG2 H 1.17 . 1 42 . 9 GLY H H 7.63 . 1 43 . 9 GLY HA2 H 4.40 . 2 44 . 9 GLY HA3 H 3.94 . 2 45 . 10 SER H H 8.92 . 1 46 . 10 SER HA H 3.93 . 1 47 . 10 SER HB2 H 4.10 . 2 48 . 10 SER HB3 H 4.02 . 2 49 . 11 LYS H H 8.39 . 1 50 . 11 LYS HA H 2.27 . 1 51 . 11 LYS HB2 H 1.36 . 2 52 . 11 LYS HB3 H 1.28 . 2 53 . 11 LYS HG2 H 0.99 . 2 54 . 11 LYS HG3 H 0.79 . 2 55 . 11 LYS HD2 H 1.43 . 1 56 . 11 LYS HD3 H 1.43 . 1 57 . 11 LYS HE2 H 2.85 . 1 58 . 11 LYS HE3 H 2.85 . 1 59 . 12 GLN H H 7.17 . 1 60 . 12 GLN HA H 4.00 . 1 61 . 12 GLN HB2 H 2.26 . 2 62 . 12 GLN HB3 H 2.07 . 2 63 . 12 GLN HG2 H 2.46 . 1 64 . 12 GLN HG3 H 2.46 . 1 65 . 12 GLN HE21 H 7.01 . 2 66 . 12 GLN HE22 H 7.70 . 2 67 . 13 CYS H H 7.71 . 1 68 . 13 CYS HA H 4.67 . 1 69 . 13 CYS HB2 H 2.97 . 2 70 . 13 CYS HB3 H 2.76 . 2 71 . 14 TRP H H 7.48 . 1 72 . 14 TRP HA H 4.85 . 1 73 . 14 TRP HB2 H 3.58 . 2 74 . 14 TRP HB3 H 3.31 . 2 75 . 14 TRP HD1 H 6.88 . 1 76 . 14 TRP HE3 H 7.66 . 1 77 . 14 TRP HE1 H 9.84 . 1 78 . 14 TRP HZ3 H 7.19 . 1 79 . 14 TRP HZ2 H 7.51 . 1 80 . 14 TRP HH2 H 7.26 . 1 81 . 15 PRO HA H 4.40 . 1 82 . 15 PRO HB2 H 2.34 . 2 83 . 15 PRO HB3 H 1.95 . 2 84 . 15 PRO HG2 H 2.06 . 1 85 . 15 PRO HG3 H 2.06 . 1 86 . 15 PRO HD2 H 3.96 . 2 87 . 15 PRO HD3 H 3.83 . 2 88 . 16 VAL H H 6.39 . 1 89 . 16 VAL HA H 3.82 . 1 90 . 16 VAL HB H 2.22 . 1 91 . 16 VAL HG1 H 1.17 . 2 92 . 16 VAL HG2 H 1.03 . 2 93 . 17 CYS H H 8.59 . 1 94 . 17 CYS HA H 4.66 . 1 95 . 17 CYS HB2 H 3.33 . 2 96 . 17 CYS HB3 H 2.92 . 2 97 . 18 LYS H H 8.14 . 1 98 . 18 LYS HA H 3.71 . 1 99 . 18 LYS HB2 H 1.92 . 2 100 . 18 LYS HB3 H 1.63 . 2 101 . 18 LYS HG2 H 1.36 . 2 102 . 18 LYS HG3 H 1.23 . 2 103 . 18 LYS HD2 H 1.54 . 1 104 . 18 LYS HD3 H 1.54 . 1 105 . 18 LYS HE2 H 2.92 . 1 106 . 18 LYS HE3 H 2.92 . 1 107 . 19 GLN H H 8.03 . 1 108 . 19 GLN HA H 3.99 . 1 109 . 19 GLN HB2 H 2.16 . 1 110 . 19 GLN HB3 H 2.16 . 1 111 . 19 GLN HG2 H 2.44 . 2 112 . 19 GLN HG3 H 2.36 . 2 113 . 20 MET H H 8.39 . 1 114 . 20 MET HA H 3.92 . 1 115 . 20 MET HB2 H 1.56 . 2 116 . 20 MET HB3 H 0.98 . 2 117 . 20 MET HG2 H 2.52 . 2 118 . 20 MET HG3 H 2.03 . 2 119 . 21 PHE H H 7.77 . 1 120 . 21 PHE HA H 5.04 . 1 121 . 21 PHE HB2 H 3.56 . 2 122 . 21 PHE HB3 H 2.88 . 2 123 . 21 PHE HD1 H 7.4 . 3 124 . 21 PHE HE1 H 7.2 . 3 125 . 21 PHE HZ H 7.31 . 1 126 . 22 GLY H H 7.79 . 1 127 . 22 GLY HA2 H 4.29 . 2 128 . 22 GLY HA3 H 3.97 . 2 129 . 23 LYS H H 7.33 . 1 130 . 23 LYS HA H 4.90 . 1 131 . 23 LYS HB2 H 1.88 . 2 132 . 23 LYS HB3 H 1.59 . 2 133 . 23 LYS HG2 H 1.49 . 2 134 . 23 LYS HG3 H 1.38 . 2 135 . 23 LYS HD2 H 1.66 . 1 136 . 23 LYS HD3 H 1.66 . 1 137 . 23 LYS HE2 H 2.98 . 1 138 . 23 LYS HE3 H 2.98 . 1 139 . 24 PRO HA H 4.59 . 1 140 . 24 PRO HB2 H 1.87 . 1 141 . 24 PRO HB3 H 1.87 . 1 142 . 24 PRO HG2 H 2.01 . 2 143 . 24 PRO HG3 H 1.81 . 2 144 . 24 PRO HD2 H 3.74 . 2 145 . 24 PRO HD3 H 3.62 . 2 146 . 25 ASN H H 7.40 . 1 147 . 25 ASN HA H 4.49 . 1 148 . 25 ASN HB2 H 2.44 . 2 149 . 25 ASN HB3 H 2.38 . 2 150 . 26 GLY H H 7.80 . 1 151 . 26 GLY HA2 H 4.84 . 2 152 . 26 GLY HA3 H 4.11 . 2 153 . 27 LYS H H 9.18 . 1 154 . 27 LYS HA H 4.82 . 1 155 . 27 LYS HB2 H 1.84 . 1 156 . 27 LYS HB3 H 1.84 . 1 157 . 27 LYS HG2 H 1.43 . 1 158 . 27 LYS HG3 H 1.43 . 1 159 . 27 LYS HD2 H 1.73 . 2 160 . 27 LYS HD3 H 1.68 . 2 161 . 27 LYS HE2 H 2.91 . 1 162 . 27 LYS HE3 H 2.91 . 1 163 . 28 CYS H H 8.67 . 1 164 . 28 CYS HA H 4.81 . 1 165 . 28 CYS HB2 H 2.79 . 2 166 . 28 CYS HB3 H 2.47 . 2 167 . 29 MET H H 8.93 . 1 168 . 29 MET HA H 4.80 . 1 169 . 29 MET HB2 H 1.83 . 1 170 . 29 MET HB3 H 1.83 . 1 171 . 29 MET HG2 H 2.45 . 2 172 . 29 MET HG3 H 2.13 . 2 173 . 30 ASN H H 9.45 . 1 174 . 30 ASN HA H 4.34 . 1 175 . 30 ASN HB2 H 3.07 . 2 176 . 30 ASN HB3 H 2.82 . 2 177 . 31 GLY H H 8.33 . 1 178 . 31 GLY HA2 H 4.10 . 2 179 . 31 GLY HA3 H 3.90 . 2 180 . 32 LYS H H 7.65 . 1 181 . 32 LYS HA H 5.43 . 1 182 . 32 LYS HB2 H 1.83 . 2 183 . 32 LYS HB3 H 1.72 . 2 184 . 32 LYS HG2 H 1.48 . 2 185 . 32 LYS HG3 H 1.24 . 2 186 . 32 LYS HD2 H 1.61 . 1 187 . 32 LYS HD3 H 1.61 . 1 188 . 32 LYS HE2 H 2.98 . 1 189 . 32 LYS HE3 H 2.98 . 1 190 . 33 CYS H H 8.61 . 1 191 . 33 CYS HA H 4.99 . 1 192 . 33 CYS HB2 H 2.91 . 2 193 . 33 CYS HB3 H 2.56 . 2 194 . 34 ARG H H 9.50 . 1 195 . 34 ARG HA H 4.90 . 1 196 . 34 ARG HB2 H 1.74 . 2 197 . 34 ARG HB3 H 1.62 . 2 198 . 34 ARG HG2 H 1.16 . 2 199 . 34 ARG HG3 H 1.04 . 2 200 . 34 ARG HD2 H 2.65 . 1 201 . 34 ARG HD3 H 2.65 . 1 202 . 34 ARG HE H 6.82 . 1 203 . 35 CYS H H 8.63 . 1 204 . 35 CYS HA H 5.44 . 1 205 . 35 CYS HB2 H 3.32 . 2 206 . 35 CYS HB3 H 2.46 . 2 207 . 36 TYR H H 8.30 . 1 208 . 36 TYR HA H 4.79 . 1 209 . 36 TYR HB2 H 3.10 . 2 210 . 36 TYR HB3 H 2.63 . 2 211 . 36 TYR HD1 H 6.9 . 3 212 . 36 TYR HE1 H 6.6 . 3 213 . 37 SER H H 8.21 . 1 214 . 37 SER HA H 4.28 . 1 215 . 37 SER HB2 H 3.87 . 1 216 . 37 SER HB3 H 3.87 . 1 stop_ save_