data_18643 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of PawS Derived Peptide 4 (PDP-4) ; _BMRB_accession_number 18643 _BMRB_flat_file_name bmr18643.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" 58 "13C chemical shifts" 21 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)' 18644 'PawS Derived Peptide 5 (PDP-5)' 18645 'PawS Derived Peptide 7 (PDP-7)' 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 4 (PDP-4)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'PawS Derived Peptide 4 (PDP-4)' $PDP-4 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-4 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PDP-4 _Molecular_mass 1367.559 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GSCFGAFCFRRD loop_ _Residue_seq_code _Residue_label 1 GLY 2 SER 3 CYS 4 PHE 5 GLY 6 ALA 7 PHE 8 CYS 9 PHE 10 ARG 11 ARG 12 ASP stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . 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 GB JX262725 Ih_a_PawS1 . . . . . 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-4 'Iostephane heterophylla' 1048901 Eukaryota Viridiplantae Iostephane heterophylla Ih_a_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-4 '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-4 5 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-4 5 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 280 . 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 4 (PDP-4)' _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 3.850 0.000 . 2 1 1 GLY HA3 H 3.586 0.000 . 3 1 1 GLY H H 8.201 0.000 . 4 1 1 GLY CA C 45.566 0.013 . 5 2 2 SER H H 7.907 0.000 . 6 2 2 SER HA H 4.104 0.000 . 7 2 2 SER HB2 H 3.597 0.000 . 8 2 2 SER HB3 H 3.534 0.000 . 9 2 2 SER CA C 58.862 0.000 . 10 2 2 SER CB C 63.755 0.001 . 11 3 3 CYS H H 7.682 0.000 . 12 3 3 CYS HA H 4.490 0.000 . 13 3 3 CYS HB2 H 2.870 0.000 . 14 3 3 CYS HB3 H 2.741 0.000 . 15 3 3 CYS CA C 57.531 0.000 . 16 4 4 PHE H H 8.408 0.000 . 17 4 4 PHE HA H 4.462 0.000 . 18 4 4 PHE HB2 H 2.846 0.000 . 19 4 4 PHE HB3 H 2.719 0.000 . 20 4 4 PHE HD1 H 6.931 0.000 . 21 4 4 PHE HD2 H 6.931 0.000 . 22 4 4 PHE CA C 53.147 0.000 . 23 4 4 PHE CB C 41.218 0.007 . 24 5 5 GLY H H 8.116 0.000 . 25 5 5 GLY HA2 H 3.901 0.000 . 26 5 5 GLY HA3 H 3.413 0.000 . 27 5 5 GLY CA C 44.623 0.011 . 28 6 6 ALA H H 8.151 0.000 . 29 6 6 ALA HA H 3.658 0.000 . 30 6 6 ALA HB H 0.764 0.000 . 31 6 6 ALA CA C 53.685 0.000 . 32 6 6 ALA CB C 18.863 0.000 . 33 7 7 PHE H H 7.994 0.000 . 34 7 7 PHE HA H 4.221 0.000 . 35 7 7 PHE HB2 H 3.004 0.000 . 36 7 7 PHE HB3 H 2.625 0.000 . 37 7 7 PHE HD1 H 6.960 0.010 . 38 7 7 PHE HD2 H 6.960 0.010 . 39 7 7 PHE CA C 56.923 0.000 . 40 7 7 PHE CB C 38.183 0.007 . 41 8 8 CYS H H 7.168 0.000 . 42 8 8 CYS HA H 4.345 0.000 . 43 8 8 CYS HB2 H 2.704 0.000 . 44 8 8 CYS HB3 H 2.444 0.000 . 45 8 8 CYS CA C 57.742 0.000 . 46 8 8 CYS CB C 39.975 0.008 . 47 9 9 PHE H H 8.433 0.000 . 48 9 9 PHE HA H 4.360 0.000 . 49 9 9 PHE HB2 H 2.933 0.000 . 50 9 9 PHE HB3 H 2.720 0.000 . 51 9 9 PHE HD1 H 6.977 0.000 . 52 9 9 PHE HD2 H 6.977 0.000 . 53 9 9 PHE CA C 54.798 0.000 . 54 9 9 PHE CB C 39.224 0.007 . 55 10 10 ARG H H 7.583 0.000 . 56 10 10 ARG HA H 4.019 0.000 . 57 10 10 ARG HB2 H 1.527 0.000 . 58 10 10 ARG HB3 H 1.401 0.000 . 59 10 10 ARG HG2 H 1.221 0.000 . 60 10 10 ARG HD2 H 2.863 0.000 . 61 10 10 ARG HD3 H 2.863 0.000 . 62 10 10 ARG CA C 55.992 0.000 . 63 10 10 ARG CB C 31.746 0.009 . 64 11 11 ARG H H 8.279 0.000 . 65 11 11 ARG HA H 4.168 0.000 . 66 11 11 ARG HB2 H 1.655 0.000 . 67 11 11 ARG HB3 H 1.415 0.000 . 68 11 11 ARG HG2 H 1.330 0.000 . 69 11 11 ARG HG3 H 1.255 0.000 . 70 11 11 ARG HD2 H 2.886 0.000 . 71 11 11 ARG HD3 H 2.886 0.000 . 72 11 11 ARG CA C 55.909 0.000 . 73 11 11 ARG CB C 29.832 0.013 . 74 12 12 ASP H H 7.881 0.000 . 75 12 12 ASP HA H 4.417 0.000 . 76 12 12 ASP HB2 H 2.743 0.000 . 77 12 12 ASP HB3 H 2.548 0.000 . 78 12 12 ASP CA C 58.117 0.000 . 79 12 12 ASP CB C 39.722 0.000 . stop_ save_