data_25962 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of PawS Derived Peptide 9 (PDP-9) ; _BMRB_accession_number 25962 _BMRB_flat_file_name bmr25962.str _Entry_type original _Submission_date 2016-01-24 _Accession_date 2016-02-05 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'This plant peptide is naturally head-to-tail cyclic and contains an amide bond between the C- and N-terminal residues.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Armstrong David A . 2 Franke Bastian . . 3 Elliott Alysha G . 4 Mylne Joshua S . 5 Rosengren 'K. Johan' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 95 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-02-16 update BMRB 'update entry citation' 2016-06-27 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 18641 'NMR solution structure of PawS derived peptide 11 (PDP-11)' 18643 'NMR solution structure of PawS Derived Peptide 4 (PDP-4)' 18644 'NMR solution structure of PawS Derived Peptide 5 (PDP-5)' 18645 'NMR solution structure of PawS Derived Peptide 7 (PDP-7)' 18646 'NMR solution structure of PawS Derived Peptide 6 (PDP-6)' 25963 'NMR solution structure of PawS Derived Peptide 10 (PDP-10)' stop_ _Original_release_date 2016-06-27 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Natural Structural Diversity Within a Conserved Cyclic Peptide Scaffold ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27695949 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Elliott Alysha G . 2 Franke Bastian . . 3 Armstrong David A . 4 Craik David J . 5 Mylne Joshua S . 6 Rosengren 'K. Johan' . . stop_ _Journal_abbreviation 'Amino Acids' _Journal_volume 49 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 103 _Page_last 116 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name PDP-9 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $PawS_Derived_Peptide_9_(PDP-9) 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_PawS_Derived_Peptide_9_(PDP-9) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PawS_Derived_Peptide_9_(PDP-9) _Molecular_mass 1938.108 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 17 _Mol_residue_sequence ; GDCYWTSTPPFFTCTPD ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 GLY 2 2 ASP 3 3 CYS 4 4 TYR 5 5 TRP 6 6 THR 7 7 SER 8 8 THR 9 9 PRO 10 10 PRO 11 11 PHE 12 12 PHE 13 13 THR 14 14 CYS 15 15 THR 16 16 PRO 17 17 ASP 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 _Details $PawS_Derived_Peptide_9_(PDP-9) 'Perymenium macrocephalum' 183067 Eukaryota Viridiplantae Perymenium macrocephalum ; Common Name: Perymenium macrocephalum, Taxonomy ID: 183067, Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Perymenium macrocephalum ; 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 _Details $PawS_Derived_Peptide_9_(PDP-9) 'chemical synthesis' . Not applicable . 'Not applicable' 'Solid phase peptide synthesis followed by cyclization through native chemical ligation.' 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 $PawS_Derived_Peptide_9_(PDP-9) 3 mg/mL 'natural abundance' 'methanol (CD3OH)' 100 'v/v %' . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $PawS_Derived_Peptide_9_(PDP-9) 3 mg/mL 'natural abundance' 'methanol (CD3OD)' 100 'v/v %' [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_XEASY _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'data analysis' 'peak picking' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 2.0 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . 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 500 _Details . save_ save_spectrometer_2 _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_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_6 _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 'Peptide was studied in deuterated (CD3OH) methanol.' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH na . pH pressure 1 . atm temperature 288 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details 'Peptide was studied in deuterated (CD3OD) methanol.' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH na . pH pressure 1 . atm temperature 288 . 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 methanol H 1 'methyl protons' ppm 3.31 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' 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 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 GLY HA2 H 4.099 0.01 2 2 1 1 GLY HA3 H 3.640 0.01 2 3 1 1 GLY H H 8.110 0.01 1 4 2 2 ASP H H 7.407 0.01 1 5 2 2 ASP HA H 4.881 0.01 1 6 2 2 ASP HB2 H 2.842 0.01 2 7 2 2 ASP HB3 H 2.771 0.01 2 8 3 3 CYS H H 8.475 0.01 1 9 3 3 CYS HA H 5.600 0.01 1 10 3 3 CYS HB2 H 2.805 0.01 2 11 3 3 CYS HB3 H 2.596 0.01 2 12 4 4 TYR H H 8.657 0.002 1 13 4 4 TYR HA H 4.707 0.005 1 14 4 4 TYR HB2 H 3.093 0.01 2 15 4 4 TYR HB3 H 2.793 0.01 2 16 4 4 TYR HD1 H 6.943 0.001 3 17 4 4 TYR HD2 H 6.943 0.001 3 18 4 4 TYR HE1 H 6.580 0.129 3 19 4 4 TYR HE2 H 6.580 0.129 3 20 5 5 TRP H H 8.332 0.01 1 21 5 5 TRP HA H 5.509 0.002 1 22 5 5 TRP HB2 H 3.429 0.01 2 23 5 5 TRP HB3 H 3.167 0.01 2 24 5 5 TRP HD1 H 7.329 0.01 1 25 5 5 TRP HE1 H 10.260 0.01 1 26 5 5 TRP HE3 H 7.265 1.561 1 27 5 5 TRP HZ2 H 7.198 0.01 1 28 5 5 TRP HZ3 H 6.940 0.01 1 29 5 5 TRP HH2 H 7.200 0.01 1 30 6 6 THR H H 8.528 0.001 1 31 6 6 THR HA H 4.719 0.01 1 32 6 6 THR HB H 4.320 0.003 1 33 6 6 THR HG2 H 1.087 0.003 1 34 7 7 SER H H 8.139 0.01 1 35 7 7 SER HA H 4.566 0.004 1 36 7 7 SER HB2 H 4.115 0.002 2 37 7 7 SER HB3 H 3.933 0.001 2 38 8 8 THR H H 7.506 0.01 1 39 8 8 THR HA H 4.665 0.003 1 40 8 8 THR HB H 3.976 0.01 1 41 8 8 THR HG2 H 1.187 0.01 1 42 9 9 PRO HA H 2.763 0.01 1 43 9 9 PRO HB2 H 1.916 0.01 2 44 9 9 PRO HB3 H 1.564 0.002 2 45 9 9 PRO HG2 H 1.969 0.01 2 46 9 9 PRO HG3 H 1.896 0.01 2 47 9 9 PRO HD2 H 3.666 0.01 1 48 9 9 PRO HD3 H 3.545 0.01 1 49 10 10 PRO HA H 4.078 0.01 1 50 10 10 PRO HB2 H 2.634 0.01 2 51 10 10 PRO HB3 H 1.950 0.01 2 52 10 10 PRO HG2 H 1.735 0.01 2 53 10 10 PRO HG3 H 1.560 0.003 2 54 10 10 PRO HD2 H 3.309 0.007 1 55 10 10 PRO HD3 H 3.309 0.007 1 56 11 11 PHE H H 8.869 0.01 1 57 11 11 PHE HA H 4.561 0.01 1 58 11 11 PHE HB2 H 3.689 0.01 2 59 11 11 PHE HB3 H 3.630 0.01 2 60 11 11 PHE HD1 H 7.292 0.01 3 61 11 11 PHE HD2 H 7.292 0.01 3 62 11 11 PHE HE1 H 7.255 0.01 3 63 11 11 PHE HE2 H 7.255 0.01 3 64 11 11 PHE HZ H 7.191 0.01 1 65 12 12 PHE H H 7.421 0.001 1 66 12 12 PHE HA H 5.365 0.01 1 67 12 12 PHE HB2 H 2.870 0.01 2 68 12 12 PHE HB3 H 2.633 0.002 2 69 12 12 PHE HD1 H 6.723 0.01 3 70 12 12 PHE HD2 H 6.723 0.01 3 71 12 12 PHE HE1 H 6.964 0.01 3 72 12 12 PHE HE2 H 6.964 0.01 3 73 13 13 THR H H 8.331 0.01 1 74 13 13 THR HA H 4.263 0.01 1 75 13 13 THR HB H 3.667 0.01 1 76 13 13 THR HG2 H 0.825 0.01 1 77 14 14 CYS H H 8.160 0.01 1 78 14 14 CYS HA H 5.660 0.003 1 79 14 14 CYS HB2 H 2.785 0.01 1 80 14 14 CYS HB3 H 2.785 0.01 1 81 15 15 THR H H 8.898 0.01 1 82 15 15 THR HA H 4.783 0.006 1 83 15 15 THR HB H 4.642 0.01 1 84 15 15 THR HG2 H 1.486 0.01 1 85 16 16 PRO HA H 4.338 0.01 1 86 16 16 PRO HB2 H 2.377 0.01 2 87 16 16 PRO HB3 H 1.909 0.006 2 88 16 16 PRO HG2 H 2.095 0.01 2 89 16 16 PRO HG3 H 2.003 0.033 2 90 16 16 PRO HD2 H 3.938 0.01 2 91 16 16 PRO HD3 H 3.776 0.01 2 92 17 17 ASP H H 7.625 0.01 1 93 17 17 ASP HA H 4.658 0.01 1 94 17 17 ASP HB2 H 2.907 0.01 1 95 17 17 ASP HB3 H 2.907 0.01 1 stop_ save_