data_25963 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of PawS Derived Peptide 10 (PDP-10) ; _BMRB_accession_number 25963 _BMRB_flat_file_name bmr25963.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 . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Franke Bastian G . 2 Elliott Alysha G . 3 Mylne Joshua S . 4 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" 94 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)' 25962 'NMR solution structure of PawS Derived Peptide 9 (PDP-9)' 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-10 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $PawS_Derived_Peptide_10_(PDP-10) 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_10_(PDP-10) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PawS_Derived_Peptide_10_(PDP-10) _Molecular_mass 1817.059 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence ; GCYPVPYPPFFTCDPN ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 GLY 2 2 CYS 3 3 TYR 4 4 PRO 5 5 VAL 6 6 PRO 7 7 TYR 8 8 PRO 9 9 PRO 10 10 PHE 11 11 PHE 12 12 THR 13 13 CYS 14 14 ASP 15 15 PRO 16 16 ASN 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_10_(PDP-10) 'Galinsoga quadriradiata' 183030 Eukaryota Viridiplantae Galinsoga quadriradiata ; Common Name: Peruvian daisy, Taxonomy ID: 183030, Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Galinsoga quadriradiata ; 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_10_(PDP-10) 'chemical synthesis' . . . . . 'Solid phase peptide 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 $PawS_Derived_Peptide_10_(PDP-10) 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_10_(PDP-10) 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 . 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 3.889 0.01 2 2 1 1 GLY HA3 H 3.889 0.01 2 3 2 2 CYS H H 8.923 0.01 1 4 2 2 CYS HA H 5.812 0.01 1 5 2 2 CYS HB2 H 2.909 0.01 2 6 2 2 CYS HB3 H 2.868 0.003 2 7 3 3 TYR H H 8.944 0.01 1 8 3 3 TYR HA H 5.108 0.01 1 9 3 3 TYR HB2 H 3.105 0.01 2 10 3 3 TYR HB3 H 2.829 0.01 2 11 3 3 TYR HD1 H 7.004 0.01 3 12 3 3 TYR HD2 H 7.004 0.01 3 13 3 3 TYR HE1 H 6.602 0.001 3 14 3 3 TYR HE2 H 6.602 0.001 3 15 4 4 PRO HA H 5.208 0.01 1 16 4 4 PRO HB2 H 2.379 0.01 2 17 4 4 PRO HB3 H 1.932 0.01 2 18 4 4 PRO HG2 H 2.193 0.01 2 19 4 4 PRO HG3 H 2.087 0.01 2 20 4 4 PRO HD2 H 3.880 0.01 2 21 4 4 PRO HD3 H 3.833 0.01 2 22 5 5 VAL H H 7.546 0.01 1 23 5 5 VAL HA H 4.687 0.002 1 24 5 5 VAL HB H 1.616 0.01 1 25 5 5 VAL HG1 H 0.940 0.01 2 26 5 5 VAL HG2 H 0.340 0.01 2 27 6 6 PRO HA H 4.711 0.01 1 28 6 6 PRO HB2 H 2.286 0.01 2 29 6 6 PRO HB3 H 1.897 0.01 2 30 6 6 PRO HG2 H 2.046 0.01 2 31 6 6 PRO HG3 H 1.897 0.01 2 32 6 6 PRO HD2 H 3.610 0.003 2 33 6 6 PRO HD3 H 3.469 0.001 2 34 7 7 TYR H H 6.572 0.01 1 35 7 7 TYR HA H 4.897 0.005 1 36 7 7 TYR HB2 H 2.927 0.01 2 37 7 7 TYR HB3 H 2.816 0.01 2 38 7 7 TYR HD1 H 6.926 0.01 3 39 7 7 TYR HD2 H 6.926 0.01 3 40 7 7 TYR HE1 H 6.625 0.002 3 41 7 7 TYR HE2 H 6.625 0.002 3 42 8 8 PRO HA H 2.852 0.01 1 43 8 8 PRO HB2 H 1.999 0.01 2 44 8 8 PRO HB3 H 1.647 0.01 2 45 8 8 PRO HG2 H 2.036 0.01 2 46 8 8 PRO HG3 H 1.913 0.001 2 47 8 8 PRO HD2 H 3.656 0.01 2 48 8 8 PRO HD3 H 3.569 0.01 2 49 9 9 PRO HA H 4.199 0.01 1 50 9 9 PRO HB2 H 2.609 0.003 2 51 9 9 PRO HB3 H 1.973 0.01 2 52 9 9 PRO HG2 H 1.730 0.006 2 53 9 9 PRO HG3 H 1.626 0.01 2 54 9 9 PRO HD2 H 3.402 0.01 2 55 9 9 PRO HD3 H 3.314 0.01 2 56 10 10 PHE H H 9.132 0.01 1 57 10 10 PHE HA H 4.688 0.01 1 58 10 10 PHE HB2 H 3.658 0.001 2 59 10 10 PHE HB3 H 3.439 0.01 2 60 10 10 PHE HD1 H 7.242 0.01 3 61 10 10 PHE HD2 H 7.242 0.01 3 62 10 10 PHE HE1 H 7.547 0.01 3 63 10 10 PHE HE2 H 7.547 0.01 3 64 11 11 PHE H H 7.353 0.01 1 65 11 11 PHE HA H 5.450 0.002 1 66 11 11 PHE HB2 H 3.078 0.005 2 67 11 11 PHE HB3 H 2.747 0.002 2 68 11 11 PHE HD1 H 7.100 0.002 3 69 11 11 PHE HD2 H 7.100 0.002 3 70 11 11 PHE HE1 H 7.197 0.001 3 71 11 11 PHE HE2 H 7.197 0.001 3 72 12 12 THR H H 8.617 0.01 1 73 12 12 THR HA H 4.423 0.01 1 74 12 12 THR HB H 3.789 0.004 1 75 12 12 THR HG2 H 0.951 0.01 1 76 13 13 CYS H H 8.473 0.01 1 77 13 13 CYS HA H 5.564 0.001 1 78 13 13 CYS HB2 H 2.923 0.001 2 79 13 13 CYS HB3 H 2.887 0.002 2 80 14 14 ASP H H 8.792 0.01 1 81 14 14 ASP HA H 5.179 0.004 1 82 14 14 ASP HB2 H 3.094 0.01 2 83 14 14 ASP HB3 H 2.861 0.01 2 84 15 15 PRO HA H 4.500 0.01 1 85 15 15 PRO HB2 H 2.247 0.01 2 86 15 15 PRO HB3 H 2.029 0.01 2 87 15 15 PRO HG2 H 2.093 0.01 2 88 15 15 PRO HG3 H 2.093 0.01 2 89 15 15 PRO HD2 H 3.850 0.001 2 90 15 15 PRO HD3 H 3.850 0.001 2 91 16 16 ASN H H 8.263 0.01 1 92 16 16 ASN HA H 4.741 0.01 1 93 16 16 ASN HB2 H 2.855 0.01 2 94 16 16 ASN HB3 H 2.743 0.003 2 stop_ save_