data_19595 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of oxytocin ; _BMRB_accession_number 19595 _BMRB_flat_file_name bmr19595.str _Entry_type original _Submission_date 2013-11-01 _Accession_date 2013-11-01 _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 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" 52 "13C chemical shifts" 24 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-02-11 original author . stop_ _Original_release_date 2014-02-11 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 Muttenthaler Margaret . . 3 Miazzo Markus . . 4 Akcan Marion . . 5 Elliott Muharrem . . 6 Daly Alysha G. . 7 Harvey Norelle L. . 8 Arrowsmith Peta J. . 9 Gunasekera Sarah . . 10 Smith Sunithi . . 11 Wray Terry J. . 12 Goransson Susan . . 13 Dawson Ulf . . 14 Craik Philip E. . 15 Freissmuth David J. . 16 Gruber Michael . . 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_CSD . _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 oxytocin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label oxytocin $oxytocin 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_oxytocin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common oxytocin _Molecular_mass 1010.188 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence CYIQNCPLG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 CYS 2 2 TYR 3 3 ILE 4 4 GLN 5 5 ASN 6 6 CYS 7 7 PRO 8 8 LEU 9 9 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $oxytocin human 9606 Eukaryota Metazoa Homo sapiens 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 $oxytocin '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 $oxytocin 2.0 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % '[U-100% 2H]' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $oxytocin 2.0 mM 'natural abundance' D2O 100 % '[U-100% 2H]' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection 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_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_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 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_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_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . 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 3.5 . pH 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 oxytocin _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 4.269 0.003 1 2 1 1 CYS HB2 H 3.456 0.006 2 3 1 1 CYS HB3 H 3.297 0.005 2 4 1 1 CYS CA C 55.013 0.000 1 5 1 1 CYS CB C 42.319 0.000 1 6 2 2 TYR H H 8.991 0.002 1 7 2 2 TYR HA H 4.776 0.002 1 8 2 2 TYR HB2 H 3.012 0.006 2 9 2 2 TYR HB3 H 3.162 0.005 2 10 2 2 TYR HD1 H 7.209 0.002 3 11 2 2 TYR HD2 H 7.209 0.002 3 12 2 2 TYR HE1 H 6.872 0.001 3 13 2 2 TYR HE2 H 6.872 0.001 3 14 2 2 TYR CB C 38.843 0.005 1 15 3 3 ILE H H 7.960 0.001 1 16 3 3 ILE HA H 4.041 0.006 1 17 3 3 ILE HB H 1.918 0.004 1 18 3 3 ILE HG12 H 1.105 0.109 2 19 3 3 ILE HG13 H 1.145 0.100 2 20 3 3 ILE HG2 H 0.872 0.004 1 21 3 3 ILE HD1 H 0.851 0.004 1 22 3 3 ILE CA C 62.672 0.000 1 23 3 3 ILE CB C 38.706 0.000 1 24 3 3 ILE CG1 C 27.261 0.019 1 25 3 3 ILE CG2 C 17.596 0.000 1 26 3 3 ILE CD1 C 13.315 0.000 1 27 4 4 GLN H H 8.229 0.001 1 28 4 4 GLN HA H 4.110 0.002 1 29 4 4 GLN HB2 H 2.070 0.008 2 30 4 4 GLN HB3 H 2.070 0.008 2 31 4 4 GLN HG2 H 2.403 0.005 2 32 4 4 GLN HG3 H 2.403 0.005 2 33 4 4 GLN HE21 H 6.864 0.002 2 34 4 4 GLN HE22 H 7.556 0.001 2 35 4 4 GLN CA C 57.854 0.000 1 36 4 4 GLN CB C 28.542 0.019 1 37 4 4 GLN CG C 33.785 0.015 1 38 5 5 ASN H H 8.339 0.005 1 39 5 5 ASN HA H 4.728 0.003 1 40 5 5 ASN HB2 H 2.852 0.004 2 41 5 5 ASN HB3 H 2.852 0.004 2 42 5 5 ASN HD21 H 6.929 0.002 2 43 5 5 ASN HD22 H 7.608 0.001 2 44 5 5 ASN CA C 53.112 0.021 1 45 5 5 ASN CB C 38.460 0.000 1 46 6 6 CYS H H 8.218 0.002 1 47 6 6 CYS HA H 4.870 0.004 1 48 6 6 CYS HB2 H 2.972 0.004 2 49 6 6 CYS HB3 H 3.220 0.009 2 50 6 6 CYS CA C 54.068 0.000 1 51 6 6 CYS CB C 40.983 0.008 1 52 7 7 PRO HA H 4.443 0.002 1 53 7 7 PRO HB2 H 2.292 0.005 2 54 7 7 PRO HB3 H 1.935 0.005 2 55 7 7 PRO HG2 H 2.030 0.004 2 56 7 7 PRO HG3 H 2.030 0.004 2 57 7 7 PRO HD2 H 3.716 0.012 2 58 7 7 PRO HD3 H 3.738 0.013 2 59 7 7 PRO CA C 63.324 0.000 1 60 7 7 PRO CB C 32.010 0.005 1 61 7 7 PRO CG C 27.370 0.011 1 62 7 7 PRO CD C 50.654 0.020 1 63 8 8 LEU H H 8.488 0.002 1 64 8 8 LEU HA H 4.303 0.003 1 65 8 8 LEU HB2 H 1.622 0.017 2 66 8 8 LEU HB3 H 1.673 0.007 2 67 8 8 LEU HD1 H 0.937 0.010 2 68 8 8 LEU HD2 H 0.896 0.010 2 69 8 8 LEU CA C 55.409 0.000 1 70 8 8 LEU CB C 42.037 0.007 1 71 8 8 LEU CD1 C 24.851 0.000 2 72 8 8 LEU CD2 C 23.417 0.000 2 73 9 9 GLY H H 8.394 0.003 1 74 9 9 GLY HA2 H 3.910 0.007 2 75 9 9 GLY HA3 H 3.910 0.007 2 76 9 9 GLY CA C 44.856 0.000 1 stop_ save_