data_30168 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Initial Topology of the globular isomer of PnID ; _BMRB_accession_number 30168 _BMRB_flat_file_name bmr30168.str _Entry_type original _Submission_date 2016-09-01 _Accession_date 2016-09-01 _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 Bingham J. P. . 2 Espiritu M. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 64 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-08-31 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 30167 'Reverse topology of the globular isoform of PnID' stop_ _Original_release_date 2016-11-11 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; PnID, A novel chi conotoxin which exists as native isomers and is capable of forming unique globular topologies ; _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 Espiritu M. J. . 2 Sugai C. K. . 3 Thapa P. . . 4 Niemczura W. P. . 5 Baoanan Z. G. . 6 Baumann M. H. . 7 Bingham J. P. . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _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 'Chi-conotoxin-like PnMRCL-013' _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 'Chi-conotoxin-like PnMRCL-013' _Molecular_mass 1321.636 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence ; STCCGYRMCVPCX ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 SER 2 2 THR 3 3 CYS 4 4 CYS 5 5 GLY 6 6 TYR 7 7 ARG 8 8 MET 9 9 CYS 10 10 VAL 11 11 PRO 12 12 CYS 13 13 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### 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 'Feathered cone' 37335 Eukaryota Metazoa Conus pennaceus 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 '4 mM SER-THR-CYS-CYS-GLY-TYR-ARG-MET-CYS-VAL-PRO-CYS, 0.1 mM None HCl, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling HCl 0.1 mM None $entity_1 4 mM None H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name YASARA _Version 15.10.18 loop_ _Vendor _Address _Electronic_address 'Elmar Krieger' . . 'Elmar, Kreiger' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UNITY _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H 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_1D_DPFG_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1D DPFG' _Sample_label $sample_1 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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' 0.1 . mM pH 3.1 . pH pressure 1 . atm temperature 293 . 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 Methionine H 1 'methyl protons' ppm 2.078 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_2 stop_ loop_ _Experiment_label '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 $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 SER HA H 4.589 0.013 1 2 1 1 SER HB2 H 3.854 0.001 2 3 1 1 SER HB3 H 3.854 0.001 2 4 2 2 THR HA H 4.149 0.029 1 5 2 2 THR HB H 3.913 0.039 1 6 2 2 THR HG2 H 1.292 0.024 2 7 3 3 CYS H H 8.578 0.004 2 8 3 3 CYS HA H 4.821 0.011 1 9 3 3 CYS HB2 H 3.211 0.005 1 10 3 3 CYS HB3 H 2.999 0.017 1 11 4 4 CYS H H 9.185 0.002 1 12 4 4 CYS HA H 4.879 0.008 1 13 4 4 CYS HB2 H 3.197 0.008 1 14 4 4 CYS HB3 H 2.872 0.003 1 15 5 5 GLY H H 8.229 0.003 1 16 5 5 GLY HA2 H 4.441 0.010 1 17 5 5 GLY HA3 H 3.641 0.009 1 18 6 6 TYR H H 8.392 0.025 1 19 6 6 TYR HA H 4.651 0.001 1 20 6 6 TYR HB2 H 2.966 0.003 2 21 6 6 TYR HB3 H 2.966 0.003 2 22 6 6 TYR HD1 H 7.133 0.006 3 23 6 6 TYR HD2 H 7.133 0.006 3 24 6 6 TYR HE1 H 6.807 0.023 3 25 6 6 TYR HE2 H 6.807 0.023 3 26 7 7 ARG H H 8.604 0.009 1 27 7 7 ARG HA H 4.663 0.003 1 28 7 7 ARG HB2 H 1.792 0.005 2 29 7 7 ARG HB3 H 1.792 0.005 2 30 7 7 ARG HG2 H 1.662 0.002 2 31 7 7 ARG HG3 H 1.662 0.002 2 32 7 7 ARG HD2 H 3.833 0.000 2 33 7 7 ARG HD3 H 3.833 0.000 2 34 7 7 ARG HH11 H 7.767 0.060 2 35 7 7 ARG HH12 H 7.767 0.060 2 36 7 7 ARG HH21 H 7.248 0.001 2 37 7 7 ARG HH22 H 7.248 0.001 2 38 8 8 MET H H 7.628 0.002 1 39 8 8 MET HA H 4.432 0.004 1 40 8 8 MET HB2 H 1.904 0.013 2 41 8 8 MET HB3 H 1.904 0.013 2 42 8 8 MET HG2 H 2.389 0.005 2 43 8 8 MET HG3 H 2.389 0.005 2 44 8 8 MET HE H 2.074 0.009 2 45 9 9 CYS H H 8.671 0.012 1 46 9 9 CYS HA H 4.738 0.007 1 47 9 9 CYS HB2 H 3.367 0.003 1 48 9 9 CYS HB3 H 2.833 0.018 1 49 10 10 VAL H H 8.604 0.006 1 50 10 10 VAL HA H 4.668 0.010 1 51 10 10 VAL HB H 2.099 0.011 1 52 10 10 VAL HG1 H 0.929 0.006 2 53 10 10 VAL HG2 H 0.789 0.006 2 54 11 11 PRO HA H 4.503 0.000 1 55 11 11 PRO HB2 H 2.326 0.006 1 56 11 11 PRO HB3 H 1.833 0.012 1 57 11 11 PRO HG2 H 2.109 0.008 1 58 11 11 PRO HG3 H 1.957 0.010 1 59 11 11 PRO HD2 H 3.858 0.007 1 60 11 11 PRO HD3 H 3.622 0.005 1 61 12 12 CYS H H 8.753 0.082 1 62 12 12 CYS HA H 4.499 0.009 1 63 12 12 CYS HB2 H 3.170 0.010 1 64 12 12 CYS HB3 H 2.881 0.004 1 stop_ save_