data_25254 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the toxin, RhTx ; _BMRB_accession_number 25254 _BMRB_flat_file_name bmr25254.str _Entry_type original _Submission_date 2014-09-30 _Accession_date 2014-09-30 _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 Hong Jing . . 2 Yang Shilong . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 143 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-10-12 original BMRB . stop_ _Original_release_date 2015-10-12 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; 1H assigned chemical shifts for RhTx ; _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 Hong Jing . . 2 Yang Shilong . . stop_ _Journal_abbreviation 'Not known' _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 'toxin, RhTx' _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 2974.468 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 27 _Mol_residue_sequence ; LNNPCNGVTCPSGYRCSIVD KQCIKKE ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 LEU 2 2 ASN 3 3 ASN 4 4 PRO 5 5 CYS 6 6 ASN 7 7 GLY 8 8 VAL 9 9 THR 10 10 CYS 11 11 PRO 12 12 SER 13 13 GLY 14 14 TYR 15 15 ARG 16 16 CYS 17 17 SER 18 18 ILE 19 19 VAL 20 20 ASP 21 21 LYS 22 22 GLN 23 23 CYS 24 24 ILE 25 25 LYS 26 26 LYS 27 27 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-25 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 2MVA "Solution Structure Of The Toxin, Rhtx" 100.00 27 100.00 100.00 1.11e-09 GB AKN58847 "RhTx [Scolopendra mutilans]" 100.00 69 100.00 100.00 4.08e-10 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity centipede 55038 Eukaryota Metazoa Scolopendra subspinipes 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 'purified from the natural source' . . . . . 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 3 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' 'phospate buffer' 20 mM 'natural abundance' NaCl 50 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_ARIA _Saveframe_category software _Name ARIA _Version . loop_ _Vendor _Address _Electronic_address "Linge, O'Donoghue and Nilges" . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ save_ProcheckNMR _Saveframe_category software _Name ProcheckNMR _Version . loop_ _Vendor _Address _Electronic_address 'Laskowski and MacArthur' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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 'ionic strength' 0.025 . M pH 6.5 . 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 water H 1 protons ppm 4.773 internal direct . . . 1.0 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 DQF-COSY' '2D 1H-1H NOESY' '2D 1H-1H TOCSY' 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 LEU HA H 4.015 0.000 1 2 2 2 ASN H H 8.898 0.001 1 3 2 2 ASN HA H 4.761 0.004 1 4 2 2 ASN HB2 H 2.739 0.000 2 5 2 2 ASN HB3 H 2.810 0.000 2 6 3 3 ASN H H 8.637 0.002 1 7 3 3 ASN HA H 4.970 0.001 1 8 3 3 ASN HB2 H 2.693 0.001 2 9 3 3 ASN HB3 H 2.897 0.006 2 10 4 4 PRO HA H 4.504 0.003 1 11 4 4 PRO HB2 H 2.324 0.011 2 12 4 4 PRO HB3 H 2.324 0.011 2 13 4 4 PRO HG2 H 1.902 0.002 2 14 4 4 PRO HG3 H 2.066 0.004 2 15 4 4 PRO HD2 H 3.749 0.000 2 16 4 4 PRO HD3 H 3.843 0.000 2 17 5 5 CYS H H 8.323 0.003 1 18 5 5 CYS HA H 4.546 0.007 1 19 5 5 CYS HB2 H 3.010 0.001 2 20 5 5 CYS HB3 H 3.109 0.004 2 21 6 6 ASN H H 8.195 0.008 1 22 6 6 ASN HA H 4.499 0.003 1 23 6 6 ASN HB2 H 2.766 0.006 2 24 6 6 ASN HB3 H 2.937 0.006 2 25 6 6 ASN HD21 H 6.976 0.001 2 26 7 7 GLY H H 8.623 0.003 1 27 7 7 GLY HA2 H 3.723 0.002 2 28 7 7 GLY HA3 H 4.111 0.002 2 29 8 8 VAL H H 7.642 0.004 1 30 8 8 VAL HA H 4.259 0.002 1 31 8 8 VAL HB H 2.172 0.005 1 32 8 8 VAL HG1 H 0.836 0.008 2 33 8 8 VAL HG2 H 0.883 0.006 2 34 9 9 THR H H 8.503 0.002 1 35 9 9 THR HA H 4.427 0.001 1 36 9 9 THR HB H 4.057 0.003 1 37 9 9 THR HG2 H 1.167 0.002 1 38 10 10 CYS H H 8.837 0.004 1 39 10 10 CYS HA H 5.138 0.001 1 40 10 10 CYS HB2 H 2.495 0.002 2 41 10 10 CYS HB3 H 2.844 0.003 2 42 11 11 PRO HA H 4.504 0.003 1 43 11 11 PRO HB2 H 2.287 0.004 2 44 11 11 PRO HB3 H 2.287 0.004 2 45 11 11 PRO HG2 H 1.450 0.003 2 46 11 11 PRO HG3 H 1.744 0.008 2 47 11 11 PRO HD2 H 2.930 0.006 2 48 11 11 PRO HD3 H 3.771 0.003 2 49 12 12 SER H H 8.459 0.001 1 50 12 12 SER HA H 4.306 0.001 1 51 12 12 SER HB2 H 3.899 0.003 2 52 12 12 SER HB3 H 3.899 0.003 2 53 13 13 GLY H H 9.086 0.004 1 54 13 13 GLY HA2 H 3.702 0.002 2 55 13 13 GLY HA3 H 4.374 0.009 2 56 14 14 TYR H H 8.413 0.003 1 57 14 14 TYR HA H 5.142 0.004 1 58 14 14 TYR HB2 H 2.476 0.006 2 59 14 14 TYR HB3 H 3.298 0.005 2 60 14 14 TYR HE1 H 6.737 0.004 3 61 14 14 TYR HE2 H 6.780 0.001 3 62 15 15 ARG H H 9.556 0.003 1 63 15 15 ARG HA H 4.784 0.006 1 64 15 15 ARG HB2 H 1.713 0.004 2 65 15 15 ARG HB3 H 1.808 0.005 2 66 15 15 ARG HG2 H 1.488 0.010 2 67 15 15 ARG HG3 H 1.488 0.010 2 68 15 15 ARG HD2 H 3.159 0.010 2 69 15 15 ARG HD3 H 3.159 0.010 2 70 15 15 ARG HE H 7.404 0.005 1 71 16 16 CYS H H 9.083 0.001 1 72 16 16 CYS HA H 4.570 0.001 1 73 16 16 CYS HB2 H 2.943 0.001 2 74 16 16 CYS HB3 H 3.038 0.001 2 75 17 17 SER H H 8.866 0.002 1 76 17 17 SER HA H 4.206 0.003 1 77 17 17 SER HB2 H 3.905 0.001 2 78 17 17 SER HB3 H 3.905 0.001 2 79 18 18 ILE H H 8.617 0.004 1 80 18 18 ILE HA H 3.905 0.003 1 81 18 18 ILE HB H 1.970 0.002 1 82 18 18 ILE HG12 H 1.516 0.001 2 83 18 18 ILE HG13 H 1.315 0.001 2 84 18 18 ILE HG2 H 1.315 0.001 1 85 18 18 ILE HD1 H 0.972 0.004 1 86 19 19 VAL H H 7.859 0.006 1 87 19 19 VAL HA H 3.822 0.003 1 88 19 19 VAL HB H 1.947 0.010 1 89 19 19 VAL HG1 H 0.983 0.006 2 90 19 19 VAL HG2 H 0.906 0.006 2 91 20 20 ASP H H 7.450 0.003 1 92 20 20 ASP HA H 4.685 0.004 1 93 20 20 ASP HB2 H 2.707 0.005 2 94 20 20 ASP HB3 H 2.707 0.005 2 95 21 21 LYS H H 8.237 0.004 1 96 21 21 LYS HA H 3.878 0.002 1 97 21 21 LYS HB2 H 1.940 0.007 2 98 21 21 LYS HB3 H 2.027 0.000 2 99 21 21 LYS HG2 H 1.347 0.003 2 100 21 21 LYS HG3 H 1.347 0.003 2 101 21 21 LYS HD2 H 1.646 0.000 2 102 21 21 LYS HD3 H 1.716 0.000 2 103 21 21 LYS HE2 H 2.989 0.006 2 104 21 21 LYS HE3 H 2.989 0.006 2 105 22 22 GLN H H 7.484 0.001 1 106 22 22 GLN HA H 4.575 0.005 1 107 22 22 GLN HB2 H 1.893 0.004 2 108 22 22 GLN HB3 H 1.893 0.004 2 109 22 22 GLN HG2 H 2.208 0.003 2 110 22 22 GLN HG3 H 2.086 0.005 2 111 23 23 CYS H H 8.862 0.002 1 112 23 23 CYS HA H 5.076 0.003 1 113 23 23 CYS HB2 H 2.636 0.006 2 114 23 23 CYS HB3 H 2.937 0.006 2 115 24 24 ILE H H 9.498 0.004 1 116 24 24 ILE HA H 4.785 0.007 1 117 24 24 ILE HB H 1.956 0.005 1 118 24 24 ILE HG12 H 1.445 0.008 2 119 24 24 ILE HG13 H 1.203 0.005 2 120 24 24 ILE HG2 H 0.875 0.007 1 121 24 24 ILE HD1 H 0.984 0.004 1 122 25 25 LYS H H 8.720 0.003 1 123 25 25 LYS HA H 3.296 0.002 1 124 25 25 LYS HB2 H 1.438 0.004 2 125 25 25 LYS HB3 H 1.545 0.003 2 126 25 25 LYS HG2 H 0.978 0.009 2 127 25 25 LYS HG3 H 1.082 0.004 2 128 25 25 LYS HD2 H 1.319 0.005 2 129 25 25 LYS HD3 H 1.319 0.005 2 130 26 26 LYS H H 8.167 0.003 1 131 26 26 LYS HA H 4.078 0.001 1 132 26 26 LYS HB2 H 1.718 0.003 2 133 26 26 LYS HB3 H 1.718 0.003 2 134 26 26 LYS HG2 H 1.211 0.000 2 135 26 26 LYS HG3 H 1.292 0.000 2 136 26 26 LYS HD2 H 1.483 0.004 2 137 26 26 LYS HD3 H 1.576 0.000 2 138 26 26 LYS HE2 H 2.898 0.001 2 139 26 26 LYS HE3 H 2.898 0.001 2 140 27 27 GLU HB2 H 1.902 0.000 2 141 27 27 GLU HB3 H 2.067 0.000 2 142 27 27 GLU HG2 H 2.349 0.005 2 143 27 27 GLU HG3 H 2.349 0.005 2 stop_ save_