data_18510 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of Midi peptide designed based on m-conotoxins ; _BMRB_accession_number 18510 _BMRB_flat_file_name bmr18510.str _Entry_type original _Submission_date 2012-06-08 _Accession_date 2012-06-08 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'The structure of Midi peptide, synthetic bioactive compound analogues of m-conotoxins KIIIA from Conus kinoshital and BuIIIC from Conus bullatus' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dyubankova Natalia . . 2 Lescrinier Eveline . . 3 Stevens Marijke . . 4 Tytgat Jan . . 5 Herdewijn Piet . . 6 Peigneur Steve . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 74 "13C chemical shifts" 39 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-20 update BMRB 'update entry citation' 2012-06-26 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citation1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Design of bioactive peptides from naturally occurring -conotoxin structures.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22773842 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Stevens Marijke . . 2 Peigneur Steve . . 3 Dyubankova Natalia . . 4 Lescrinier Eveline . . 5 Herdewijn Piet . . 6 Tytgat Jan . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 287 _Journal_issue 37 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 31382 _Page_last 31392 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name m-conotoxin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label m-conotoxin $m-conotoxin 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_m-conotoxin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common m-conotoxin _Molecular_mass 1700.943 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence CNCSRWARDHSRCC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 CYS 2 2 ASN 3 3 CYS 4 4 SER 5 5 ARG 6 6 TRP 7 7 ALA 8 8 ARG 9 9 ASP 10 10 HIS 11 11 SER 12 12 ARG 13 13 CYS 14 14 CYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . 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 m-conotoxin 1 CYS SG m-conotoxin 13 CYS SG single disulfide m-conotoxin 3 CYS SG m-conotoxin 14 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 $m-conotoxin . . . . . . 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 $m-conotoxin 'chemical synthesis' . . . . . 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 $m-conotoxin 2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 3.851 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details cryoprobe 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_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC-TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC-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 temperature 278 . K pressure 1 . atm 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 4.9745 internal direct . . . 1 water C 13 protons ppm 0 internal indirect . . . 0.251449530 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' '2D 1H-13C HSQC' '2D 1H-13C HSQC-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 m-conotoxin _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 4.031 0.020 1 2 1 1 CYS HB2 H 2.627 0.020 1 3 1 1 CYS HB3 H 2.627 0.020 1 4 1 1 CYS CA C 50.68 0.300 1 5 1 1 CYS CB C 40.00 0.300 1 6 2 2 ASN H H 8.461 0.020 1 7 2 2 ASN HA H 4.205 0.020 1 8 2 2 ASN HB2 H 2.287 0.020 2 9 2 2 ASN HB3 H 2.175 0.020 2 10 2 2 ASN HD21 H 6.495 0.020 1 11 2 2 ASN HD22 H 6.495 0.020 1 12 2 2 ASN CA C 49.78 0.300 1 13 2 2 ASN CB C 35.90 0.300 1 14 3 3 CYS H H 8.353 0.020 1 15 3 3 CYS HA H 4.184 0.020 1 16 3 3 CYS HB2 H 2.236 0.020 2 17 3 3 CYS HB3 H 2.627 0.020 2 18 3 3 CYS CA C 51.53 0.300 1 19 3 3 CYS CB C 37.60 0.300 1 20 4 4 SER H H 7.829 0.020 1 21 4 4 SER HA H 3.876 0.020 1 22 4 4 SER HB2 H 3.250 0.020 2 23 4 4 SER HB3 H 3.341 0.020 2 24 4 4 SER CA C 55.10 0.300 1 25 4 4 SER CB C 60.06 0.300 1 26 5 5 ARG H H 8.119 0.020 1 27 5 5 ARG HA H 3.479 0.020 1 28 5 5 ARG HB2 H 0.931 0.020 2 29 5 5 ARG HB3 H 1.002 0.020 2 30 5 5 ARG HG2 H 0.528 0.020 2 31 5 5 ARG HG3 H 0.610 0.020 2 32 5 5 ARG HD2 H 2.349 0.020 1 33 5 5 ARG HD3 H 2.349 0.020 1 34 5 5 ARG CA C 54.40 0.300 1 35 5 5 ARG CB C 27.09 0.300 1 36 5 5 ARG CG C 24.07 0.300 1 37 5 5 ARG CD C 39.97 0.300 1 38 6 6 TRP H H 7.443 0.020 1 39 6 6 TRP HA H 4.114 0.020 1 40 6 6 TRP HB2 H 2.637 0.020 2 41 6 6 TRP HB3 H 2.833 0.020 2 42 6 6 TRP HE3 H 7.018 0.020 1 43 6 6 TRP HZ2 H 6.673 0.020 1 44 6 6 TRP HZ3 H 6.573 0.020 1 45 6 6 TRP CA C 54.22 0.300 1 46 6 6 TRP CB C 40.00 0.300 1 47 6 6 TRP CE3 C 117.7 0.300 1 48 6 6 TRP CZ2 C 114.3 0.300 1 49 6 6 TRP CZ3 C 121.7 0.300 1 50 7 7 ALA H H 7.176 0.020 1 51 7 7 ALA HA H 3.671 0.020 1 52 7 7 ALA HB H 0.795 0.020 1 53 7 7 ALA CA C 49.50 0.300 1 54 7 7 ALA CB C 16.30 0.300 1 55 8 8 ARG H H 7.849 0.020 1 56 8 8 ARG HA H 3.587 0.020 1 57 8 8 ARG HB2 H 1.251 0.020 1 58 8 8 ARG HB3 H 1.251 0.020 1 59 8 8 ARG HG2 H 1.104 0.020 1 60 8 8 ARG HG3 H 1.104 0.020 1 61 8 8 ARG HD2 H 2.631 0.020 1 62 8 8 ARG HD3 H 2.631 0.020 1 63 8 8 ARG CA C 54.30 0.300 1 64 8 8 ARG CB C 27.10 0.300 1 65 8 8 ARG CG C 24.10 0.300 1 66 8 8 ARG CD C 40.00 0.300 1 67 9 9 ASP H H 7.641 0.020 1 68 9 9 ASP HA H 4.003 0.020 1 69 9 9 ASP HB2 H 2.074 0.020 1 70 9 9 ASP HB3 H 2.074 0.020 1 71 9 9 ASP CA C 51.01 0.300 1 72 9 9 ASP CB C 37.80 0.300 1 73 10 10 HIS H H 7.712 0.020 1 74 10 10 HIS HA H 3.989 0.020 1 75 10 10 HIS HB2 H 2.434 0.020 2 76 10 10 HIS HB3 H 2.677 0.020 2 77 10 10 HIS HD1 H 9.673 0.020 1 78 10 10 HIS HD2 H 6.878 0.020 1 79 10 10 HIS HE1 H 6.652 0.020 1 80 10 10 HIS CA C 50.89 0.300 1 81 10 10 HIS CB C 40.10 0.300 1 82 10 10 HIS CD2 C 111.3 0.300 1 83 10 10 HIS CE1 C 125.6 0.300 1 84 11 11 SER H H 7.768 0.020 1 85 11 11 SER HA H 3.867 0.020 1 86 11 11 SER HB2 H 3.394 0.020 2 87 11 11 SER HB3 H 3.434 0.020 2 88 11 11 SER CA C 55.84 0.300 1 89 11 11 SER CB C 60.09 0.300 1 90 12 12 ARG H H 8.180 0.020 1 91 12 12 ARG HA H 3.669 0.020 1 92 12 12 ARG HB2 H 1.292 0.020 2 93 12 12 ARG HB3 H 1.338 0.020 2 94 12 12 ARG HG2 H 1.111 0.020 1 95 12 12 ARG HG3 H 1.111 0.020 1 96 12 12 ARG HD2 H 2.644 0.020 1 97 12 12 ARG HD3 H 2.644 0.020 1 98 12 12 ARG CA C 54.58 0.300 1 99 12 12 ARG CB C 26.90 0.300 1 100 12 12 ARG CG C 24.20 0.300 1 101 12 12 ARG CD C 40.00 0.300 1 102 13 13 CYS H H 7.897 0.020 1 103 13 13 CYS HA H 4.014 0.020 1 104 13 13 CYS HB2 H 2.575 0.020 2 105 13 13 CYS HB3 H 2.677 0.020 2 106 13 13 CYS CA C 53.66 0.300 1 107 13 13 CYS CB C 40.10 0.300 1 108 14 14 CYS H H 7.558 0.020 1 109 14 14 CYS HA H 3.940 0.020 1 110 14 14 CYS HB2 H 2.364 0.020 2 111 14 14 CYS HB3 H 2.653 0.020 2 112 14 14 CYS CA C 52.66 0.300 1 113 14 14 CYS CB C 40.10 0.300 1 stop_ save_