data_11543 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of [G5,T7,S9]-oxytocin ; _BMRB_accession_number 11543 _BMRB_flat_file_name bmr11543.str _Entry_type original _Submission_date 2013-11-13 _Accession_date 2013-11-18 _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 Harvey Peta J . 2 Craik David J . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 51 "13C chemical shifts" 21 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-10-20 original author . stop_ _Original_release_date 2014-10-20 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Oxytocic plant cyclotides as templates for peptide G protein-coupled receptor ligand design' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24248349 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Koehbach Johannes . . 2 O'Brien Margaret . . 3 Muttenthaler Markus . . 4 Miazzo Marion . . 5 Akcan Muharrem . . 6 Elliott Alysha G . 7 Daly Norelle L . 8 Harvey Peta J . 9 Arrowsmith Sarah . . 10 Gunasekera Sunithi . . 11 Smith Terry J . 12 Wray Susan . . 13 Goransson Ulf . . 14 Dawson Philip E . 15 Craik David J . 16 Freissmuth Michael . . 17 Gruber Christian W . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_name_full 'Proceedings of the National Academy of Sciences of the United States of America' _Journal_volume 110 _Journal_issue 52 _Journal_ASTM PNASA6 _Journal_ISSN 0027-8424 _Journal_CSD 0040 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 21183 _Page_last 21188 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name [G5,T7,S9]-oxytocin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label subunit1 $polypeptide 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_polypeptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common polypeptide _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence CYIQGCTLSX loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 CYS 2 2 TYR 3 3 ILE 4 4 GLN 5 5 GLY 6 6 CYS 7 7 THR 8 8 LEU 9 9 SER 10 10 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 $polypeptide . . . . . . 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 $polypeptide '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 $polypeptide 2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $polypeptide 2 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNSSOLVE _Saveframe_category software _Name CNSSOLVE _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _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_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _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 pH 3.5 . 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 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-13C HSQC aliphatic' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name subunit1 _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 4.267 0.002 1 2 1 1 CYS HB2 H 3.448 0.007 2 3 1 1 CYS HB3 H 3.285 0.008 2 4 1 1 CYS CA C 51.937 0.000 1 5 1 1 CYS CB C 40.010 0.007 1 6 2 2 TYR H H 8.833 0.002 1 7 2 2 TYR HA H 4.793 0.001 1 8 2 2 TYR HB2 H 2.988 0.008 2 9 2 2 TYR HB3 H 3.210 0.005 2 10 2 2 TYR HD1 H 7.184 0.001 3 11 2 2 TYR HD2 H 7.184 0.001 3 12 2 2 TYR HE1 H 6.868 0.000 3 13 2 2 TYR HE2 H 6.868 0.000 3 14 2 2 TYR CA C 55.676 0.000 1 15 2 2 TYR CB C 36.444 0.003 1 16 3 3 ILE H H 7.642 0.002 1 17 3 3 ILE HA H 4.144 0.001 1 18 3 3 ILE HB H 1.852 0.002 1 19 3 3 ILE HG12 H 1.074 0.003 2 20 3 3 ILE HG13 H 1.346 0.005 2 21 3 3 ILE HG2 H 0.912 0.001 4 22 3 3 ILE HD1 H 0.861 0.001 4 23 3 3 ILE CA C 58.724 0.000 1 24 3 3 ILE CB C 36.522 0.002 1 25 4 4 GLN H H 8.532 0.002 1 26 4 4 GLN HA H 4.120 0.000 1 27 4 4 GLN HB2 H 2.075 0.005 2 28 4 4 GLN HB3 H 2.075 0.005 2 29 4 4 GLN HG2 H 2.413 0.005 1 30 4 4 GLN HG3 H 2.413 0.005 1 31 4 4 GLN HE21 H 6.869 0.002 2 32 4 4 GLN HE22 H 7.566 0.000 2 33 4 4 GLN CA C 54.881 0.000 1 34 4 4 GLN CB C 25.495 0.004 1 35 4 4 GLN CG C 30.804 0.005 1 36 5 5 GLY H H 8.706 0.001 1 37 5 5 GLY HA2 H 3.789 0.005 2 38 5 5 GLY HA3 H 4.221 0.005 2 39 5 5 GLY CA C 42.455 0.011 1 40 6 6 CYS H H 8.203 0.001 1 41 6 6 CYS HA H 4.620 0.002 1 42 6 6 CYS HB2 H 3.266 0.002 2 43 6 6 CYS HB3 H 3.380 0.006 2 44 6 6 CYS CA C 54.458 0.000 1 45 6 6 CYS CB C 40.418 0.008 1 46 7 7 THR H H 8.193 0.003 1 47 7 7 THR HA H 4.363 0.005 1 48 7 7 THR HB H 4.236 0.001 1 49 7 7 THR HG2 H 1.224 0.003 1 50 7 7 THR CA C 59.159 0.000 1 51 7 7 THR CB C 66.926 0.014 1 52 7 7 THR CG2 C 18.892 0.000 1 53 8 8 LEU H H 8.288 0.001 1 54 8 8 LEU HA H 4.405 0.003 1 55 8 8 LEU HB2 H 1.651 0.006 2 56 8 8 LEU HB3 H 1.651 0.006 2 57 8 8 LEU HG H 1.642 0.018 1 58 8 8 LEU HD1 H 0.932 0.004 2 59 8 8 LEU HD2 H 0.880 0.003 2 60 8 8 LEU HD2 H 0.880 0.003 1 61 8 8 LEU CA C 52.514 0.000 1 62 8 8 LEU CB C 39.471 0.025 1 63 8 8 LEU CG C 24.277 0.000 1 64 8 8 LEU CD1 C 22.191 0.000 2 65 9 9 SER H H 8.209 0.002 1 66 9 9 SER HA H 4.403 0.005 1 67 9 9 SER HB2 H 3.855 0.007 2 68 9 9 SER HB3 H 3.855 0.007 2 69 9 9 SER CA C 55.241 0.000 1 70 9 9 SER CB C 61.068 0.000 1 71 10 10 NH2 HN1 H 7.539 0.000 2 72 10 10 NH2 HN2 H 7.151 0.000 2 stop_ loop_ _Atom_shift_assign_ID_ambiguity 21 '21,21,22,22,22' stop_ save_