data_18645 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of PawS Derived Peptide 7 (PDP-7) ; _BMRB_accession_number 18645 _BMRB_flat_file_name bmr18645.str _Entry_type original _Submission_date 2012-08-06 _Accession_date 2012-08-06 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Head to tail (Gly-Asp) cyclic peptide' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Elliott Alysha G. . 2 Mylne Joshua S. . 3 Rosengren Johan K. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 80 "13C chemical shifts" 41 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-05-13 update BMRB 'update entry citation' 2013-08-15 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 18641 'PawS derived peptide 11 (PDP-11)' 18643 'PawS Derived Peptide 4 (PDP-4)' 18644 'PawS Derived Peptide 5 (PDP-5)' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Evolutionary Origins of a Bioactive Peptide Buried within Preproalbumin.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24681618 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Elliott Alysha G. . 2 Delay Christina . . 3 Liu Huanle . . 4 Phua Zaiyang . . 5 Rosengren 'K. Johan' . . 6 Benfield Aurelie H. . 7 Panero Jose L. . 8 Colgrave Michelle L. . 9 Jayasena Achala S. . 10 Dunse Kerry M. . 11 Anderson Marilyn A. . 12 Schilling Edward E. . 13 Ortiz-Barrientos Daniel . . 14 Craik David J. . 15 Mylne Joshua S. . stop_ _Journal_abbreviation 'Plant Cell' _Journal_name_full 'The Plant cell' _Journal_volume 26 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 981 _Page_last 995 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'PawS Derived Peptide 7 (PDP-7)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'PawS Derived Peptide 7 (PDP-7)' $PDP-7 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_PDP-7 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PDP-7 _Molecular_mass 1571.825 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence GHCIPTTSGPICLRD loop_ _Residue_seq_code _Residue_label 1 GLY 2 HIS 3 CYS 4 ILE 5 PRO 6 THR 7 THR 8 SER 9 GLY 10 PRO 11 ILE 12 CYS 13 LEU 14 ARG 15 ASP stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-29 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 2LWU "Nmr Solution Structure Of Paws Derived Peptide 7 (pdp-7)" 100.00 15 100.00 100.00 3.87e-01 GB AFQ93661 "preproalbumin PawS1 [Otopappus epaleaceus]" 100.00 167 100.00 100.00 1.37e-01 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Gene_mnemonic $PDP-7 'Otopappus epaleaceus' 243770 Eukaryota Viridiplantae Otopappus epaleaceus Oe_pawS1 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 $PDP-7 '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 $PDP-7 3 mg/mL 'natural abundance' DMSO 10 % 'natural abundance' H2O 80 % '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 $PDP-7 3 mg/mL 'natural abundance' DMSO 10 % 'natural abundance' D2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 3.0 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' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 3.0 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 600 _Details . save_ save_spectrometer_2 _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_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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_ save_2D_1H-1H_ECOSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ECOSY' _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 'ionic strength' 0 . M pH 5.0 . 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 carbon' ppm 0.00 internal direct . . . 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-13C HSQC' 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 'PawS Derived Peptide 7 (PDP-7)' _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 4.200 0.001 . 2 1 1 GLY HA3 H 3.770 0.006 . 3 1 1 GLY H H 8.224 0.000 . 4 1 1 GLY CA C 45.384 0.007 . 5 2 2 HIS H H 8.059 0.001 . 6 2 2 HIS HA H 4.770 0.000 . 7 2 2 HIS HB2 H 3.257 0.007 . 8 2 2 HIS HB3 H 3.257 0.007 . 9 2 2 HIS HD1 H 7.168 0.003 . 10 2 2 HIS HD2 H 7.158 0.000 . 11 2 2 HIS HE1 H 8.625 0.000 . 12 2 2 HIS CA C 55.234 0.000 . 13 2 2 HIS CB C 28.980 0.000 . 14 3 3 CYS H H 8.688 0.000 . 15 3 3 CYS HA H 5.479 0.000 . 16 3 3 CYS HB2 H 3.148 0.005 . 17 3 3 CYS HB3 H 2.605 0.001 . 18 3 3 CYS CA C 55.919 0.000 . 19 3 3 CYS CB C 47.425 0.000 . 20 4 4 ILE H H 9.034 0.000 . 21 4 4 ILE HA H 4.677 0.000 . 22 4 4 ILE HB H 1.916 0.000 . 23 4 4 ILE HG12 H 1.507 0.000 . 24 4 4 ILE HG13 H 1.125 0.000 . 25 4 4 ILE HG2 H 0.930 0.004 . 26 4 4 ILE HD1 H 0.879 0.005 . 27 4 4 ILE CA C 58.060 0.000 . 28 4 4 ILE CB C 40.513 0.000 . 29 4 4 ILE CG1 C 26.701 0.003 . 30 4 4 ILE CD1 C 17.745 0.000 . 31 5 5 PRO HA H 4.481 0.000 . 32 5 5 PRO HB2 H 2.214 0.000 . 33 5 5 PRO HB3 H 2.055 0.002 . 34 5 5 PRO HG2 H 2.134 0.001 . 35 5 5 PRO HG3 H 2.003 0.005 . 36 5 5 PRO HD2 H 3.831 0.003 . 37 5 5 PRO HD3 H 3.783 0.006 . 38 5 5 PRO CA C 63.204 0.000 . 39 5 5 PRO CB C 32.291 0.008 . 40 5 5 PRO CG C 27.359 0.009 . 41 5 5 PRO CD C 51.037 0.004 . 42 6 6 THR H H 8.694 0.000 . 43 6 6 THR HA H 4.155 0.000 . 44 6 6 THR HB H 4.363 0.000 . 45 6 6 THR HG2 H 1.322 0.000 . 46 6 6 THR CA C 60.796 0.000 . 47 6 6 THR CB C 73.138 0.000 . 48 6 6 THR CG2 C 21.248 0.000 . 49 7 7 THR H H 8.489 0.006 . 50 7 7 THR HA H 4.198 0.004 . 51 7 7 THR HB H 4.376 0.003 . 52 7 7 THR HG2 H 1.333 0.004 . 53 7 7 THR CA C 64.690 0.000 . 54 7 7 THR CB C 68.928 0.000 . 55 7 7 THR CG2 C 22.225 0.000 . 56 8 8 SER H H 8.258 0.000 . 57 8 8 SER HA H 4.689 0.000 . 58 8 8 SER HB2 H 3.869 0.000 . 59 8 8 SER HB3 H 3.869 0.000 . 60 8 8 SER CA C 60.732 0.000 . 61 8 8 SER CB C 63.765 0.000 . 62 9 9 GLY H H 7.516 0.000 . 63 9 9 GLY HA2 H 4.549 0.000 . 64 9 9 GLY HA3 H 4.000 0.000 . 65 9 9 GLY CA C 43.975 0.007 . 66 10 10 PRO HA H 4.889 0.003 . 67 10 10 PRO HB2 H 2.122 0.004 . 68 10 10 PRO HB3 H 1.809 0.002 . 69 10 10 PRO HG2 H 2.099 0.007 . 70 10 10 PRO HG3 H 2.015 0.005 . 71 10 10 PRO HD2 H 3.648 0.001 . 72 10 10 PRO HD3 H 3.648 0.001 . 73 10 10 PRO CA C 63.365 0.000 . 74 10 10 PRO CB C 32.291 0.008 . 75 10 10 PRO CG C 27.534 0.038 . 76 10 10 PRO CD C 49.668 0.000 . 77 11 11 ILE H H 8.805 0.000 . 78 11 11 ILE HA H 4.368 0.000 . 79 11 11 ILE HB H 1.815 0.000 . 80 11 11 ILE HG12 H 1.512 0.000 . 81 11 11 ILE HG13 H 1.181 0.002 . 82 11 11 ILE HD1 H 0.870 0.003 . 83 11 11 ILE CA C 60.354 0.000 . 84 11 11 ILE CB C 39.675 0.000 . 85 11 11 ILE CG1 C 27.295 0.006 . 86 12 12 CYS H H 8.883 0.000 . 87 12 12 CYS HA H 5.165 0.000 . 88 12 12 CYS HB2 H 2.954 0.000 . 89 12 12 CYS HB3 H 2.831 0.000 . 90 12 12 CYS CA C 55.648 0.000 . 91 12 12 CYS CB C 45.163 0.014 . 92 13 13 LEU H H 8.585 0.000 . 93 13 13 LEU HA H 4.514 0.002 . 94 13 13 LEU HB2 H 1.961 0.000 . 95 13 13 LEU HB3 H 1.743 0.001 . 96 13 13 LEU HG H 1.767 0.000 . 97 13 13 LEU HD1 H 0.958 0.003 . 98 13 13 LEU HD2 H 0.863 0.003 . 99 13 13 LEU CA C 54.596 0.000 . 100 13 13 LEU CB C 42.838 0.005 . 101 13 13 LEU CG C 24.812 2.814 . 102 13 13 LEU CD1 C 25.327 0.000 . 103 14 14 ARG H H 8.560 0.000 . 104 14 14 ARG HA H 4.138 0.000 . 105 14 14 ARG HB2 H 1.866 0.000 . 106 14 14 ARG HB3 H 1.866 0.000 . 107 14 14 ARG HG2 H 1.698 0.002 . 108 14 14 ARG HG3 H 1.698 0.002 . 109 14 14 ARG HD2 H 3.218 0.000 . 110 14 14 ARG HD3 H 3.218 0.000 . 111 14 14 ARG HE H 7.232 0.003 . 112 14 14 ARG CA C 58.045 0.000 . 113 14 14 ARG CB C 30.078 0.008 . 114 14 14 ARG CG C 27.252 0.038 . 115 14 14 ARG CD C 43.304 0.000 . 116 15 15 ASP H H 8.059 0.000 . 117 15 15 ASP HA H 4.514 0.000 . 118 15 15 ASP HB2 H 3.088 0.000 . 119 15 15 ASP HB3 H 2.806 0.000 . 120 15 15 ASP CA C 53.615 0.000 . 121 15 15 ASP CB C 38.480 0.000 . stop_ save_