data_30152 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Calculated solution structure of [D-Trp3]-Contryphan-Vc2 ; _BMRB_accession_number 30152 _BMRB_flat_file_name bmr30152.str _Entry_type original _Submission_date 2016-08-03 _Accession_date 2016-08-03 _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 Drane S. B. . 2 Chhabra S. . . 3 MacRaild C. A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 42 "13C chemical shifts" 26 "15N chemical shifts" 7 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-04-25 update BMRB 'update entry citation' 2017-03-02 original author 'original release' stop_ _Original_release_date 2016-11-11 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure and activity of contryphan-Vc2: Importance of the D-amino acid residue ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28216409 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Drane S. B. . 2 Robinson S. D. . 3 MacRaild C. A. . 4 Chhabra S. . . 5 Chittoor B. . . 6 Morales R. A.V. . 7 Leung E. W.W. . 8 Belgi A. . . 9 Espino S. S. . 10 Olivera B. M. . 11 Robinson A. J. . 12 Chalmers D. K. . 13 Norton R. S. . stop_ _Journal_abbreviation Toxicon _Journal_volume 129 _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 113 _Page_last 122 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name [D-Trp3]-Contryphan-Vc2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common [D-Trp3]-Contryphan-Vc2 _Molecular_mass 863.062 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence ; CRXTPVCX ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 CYS 2 2 ARG 3 3 DTR 4 4 THR 5 5 PRO 6 6 VAL 7 7 CYS 8 8 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DTR _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-TRYPTOPHAN _BMRB_code DTR _PDB_code DTR _Standard_residue_derivative . _Molecular_mass 204.225 _Mol_paramagnetic . _Details . 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 . ? CD1 CD1 C . 0 . ? NE1 NE1 N . 0 . ? CE2 CE2 C . 0 . ? CZ2 CZ2 C . 0 . ? CH2 CH2 C . 0 . ? CZ3 CZ3 C . 0 . ? CE3 CE3 C . 0 . ? CD2 CD2 C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD1 HD1 H . 0 . ? HE1 HE1 H . 0 . ? HZ2 HZ2 H . 0 . ? HH2 HH2 H . 0 . ? HZ3 HZ3 H . 0 . ? HE3 HE3 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 H ? ? SING N HN2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 NE1 ? ? SING CD1 HD1 ? ? SING NE1 CE2 ? ? SING NE1 HE1 ? ? DOUB CE2 CZ2 ? ? SING CE2 CD2 ? ? SING CZ2 CH2 ? ? SING CZ2 HZ2 ? ? DOUB CH2 CZ3 ? ? SING CH2 HH2 ? ? SING CZ3 CE3 ? ? SING CZ3 HZ3 ? ? DOUB CE3 CD2 ? ? SING CE3 HE3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 HN1 ? ? SING N HN2 ? ? 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_1 gastropods 319920 Eukaryota Metazoa Conus victoriae 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_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '2.0 M [D-Trp3]-Contryphan-Vc2, 93% H2O/7% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2.0 M 'natural abundance' H2O 93 % 'natural abundance' D2O 7 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '2.0 M [D-Trp3]-Contryphan-Vc2, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2.0 M 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name Analysis _Version 2.1.5 loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name CYANA _Version 3.0 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version 3.2 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_software_4 _Saveframe_category software _Name 'X-PLOR NIH' _Version 2.4 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 600 _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_ROESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-15N_SOFAST-HMQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N SOFAST-HMQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 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 . M pH 4.0 . pH pressure 1 . atm temperature 278 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 . M pH 4.0 . pH pressure 1 . atm temperature 283 . K stop_ save_ save_sample_conditions_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 . M pH 4.1 . pH pressure 1 . atm temperature 283 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 dioxane C 13 protons ppm 3.75 internal indirect . . . 0.25144953 dioxane H 1 protons ppm 3.75 internal direct . . . 1 dioxane N 15 protons ppm 3.75 internal indirect . . . 0.10132912 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_1 stop_ loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H ROESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_1 _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 CYS HA H 4.332 0.000 1 2 1 1 CYS HB2 H 3.220 0.013 2 3 1 1 CYS HB3 H 3.267 0.001 2 4 1 1 CYS CA C 54.766 0.000 1 5 1 1 CYS CB C 40.867 0.000 1 6 2 2 ARG H H 8.877 0.002 1 7 2 2 ARG HA H 4.519 0.005 1 8 2 2 ARG HB2 H 1.339 0.005 2 9 2 2 ARG HB3 H 1.425 0.002 2 10 2 2 ARG HG3 H 0.993 0.005 1 11 2 2 ARG HD2 H 2.796 0.002 2 12 2 2 ARG HD3 H 2.882 0.003 2 13 2 2 ARG HE H 6.896 0.004 1 14 2 2 ARG CA C 55.454 0.000 1 15 2 2 ARG CB C 31.537 0.021 1 16 2 2 ARG CG C 26.010 0.000 1 17 2 2 ARG CD C 43.264 0.005 1 18 2 2 ARG N N 122.434 0.000 1 19 3 3 DTR H H 8.615 0.003 1 20 3 3 DTR N N 123.691 0.000 1 21 3 3 DTR CA C 57.078 0.000 1 22 3 3 DTR CB C 29.230 0.022 1 23 3 3 DTR CD1 C 127.386 0.000 1 24 3 3 DTR CE3 C 120.892 0.000 1 25 3 3 DTR CH2 C 124.669 0.000 1 26 3 3 DTR CZ2 C 114.524 0.000 1 27 3 3 DTR CZ3 C 121.858 0.000 1 28 3 3 DTR HA H 4.821 0.005 1 29 3 3 DTR HB2 H 3.215 0.002 2 30 3 3 DTR HB3 H 3.411 0.006 2 31 3 3 DTR HD1 H 7.331 0.003 1 32 3 3 DTR HE1 H 10.214 0.004 1 33 3 3 DTR HE3 H 7.613 0.004 1 34 3 3 DTR HH2 H 7.227 0.003 1 35 3 3 DTR HZ2 H 7.469 0.004 1 36 3 3 DTR HZ3 H 7.144 0.006 1 37 3 3 DTR NE1 N 129.402 0.000 1 38 4 4 THR H H 7.221 0.006 1 39 4 4 THR HA H 4.668 0.007 1 40 4 4 THR HB H 4.399 0.005 1 41 4 4 THR HG2 H 1.133 0.005 1 42 4 4 THR CA C 58.653 0.000 1 43 4 4 THR CB C 69.530 0.000 1 44 4 4 THR CG2 C 21.323 0.000 1 45 4 4 THR N N 113.624 0.000 1 46 5 5 PRO HA H 4.233 0.002 1 47 5 5 PRO HB2 H 2.383 0.004 2 48 5 5 PRO HB3 H 1.985 0.004 2 49 5 5 PRO HG3 H 2.064 0.002 1 50 5 5 PRO HD2 H 3.849 0.005 2 51 5 5 PRO HD3 H 3.716 0.004 2 52 5 5 PRO CA C 64.729 0.000 1 53 5 5 PRO CB C 32.033 0.008 1 54 5 5 PRO CG C 27.425 0.000 1 55 5 5 PRO CD C 51.056 0.021 1 56 6 6 VAL H H 7.447 0.003 1 57 6 6 VAL HA H 4.184 0.002 1 58 6 6 VAL HB H 2.074 0.003 1 59 6 6 VAL HG1 H 0.895 0.005 2 60 6 6 VAL HG2 H 0.889 0.000 2 61 6 6 VAL CA C 61.829 0.000 1 62 6 6 VAL CB C 32.677 0.000 1 63 6 6 VAL CG1 C 21.252 0.000 2 64 6 6 VAL CG2 C 20.189 0.000 2 65 6 6 VAL N N 114.598 0.000 1 66 7 7 CYS H H 8.271 0.004 1 67 7 7 CYS HA H 4.572 0.003 1 68 7 7 CYS HB2 H 2.965 0.003 2 69 7 7 CYS HB3 H 3.163 0.008 2 70 7 7 CYS CA C 55.549 0.000 1 71 7 7 CYS CB C 40.036 0.028 1 72 7 7 CYS N N 121.460 0.000 1 73 8 8 NH2 N N 108.052 0.002 1 74 8 8 NH2 HN1 H 7.411 0.001 1 75 8 8 NH2 HN2 H 7.535 0.004 1 stop_ save_