data_18644 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of PawS Derived Peptide 5 (PDP-5) ; _BMRB_accession_number 18644 _BMRB_flat_file_name bmr18644.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" 118 "13C chemical shifts" 45 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)' 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 5 (PDP-5)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'PawS Derived Peptide 5 (PDP-5)' $PDP-5 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-5 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PDP-5 _Molecular_mass 2262.706 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence GRYRRCIPGMFRAYCYMD loop_ _Residue_seq_code _Residue_label 1 GLY 2 ARG 3 TYR 4 ARG 5 ARG 6 CYS 7 ILE 8 PRO 9 GLY 10 MET 11 PHE 12 ARG 13 ALA 14 TYR 15 CYS 16 TYR 17 MET 18 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 2LWT "Nmr Solution Structure Of Paws Derived Peptide 5 (pdp-5)" 100.00 18 100.00 100.00 2.91e-03 GB AFQ93657 "preproalbumin PawS1 [Heliopsis helianthoides var. scabra]" 100.00 148 100.00 100.00 1.75e-04 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain _Gene_mnemonic $PDP-5 Ox-eye 192637 Eukaryota Viridiplantae Heliopsis helianthoides scabra Hsc_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-5 '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-5 2 mg/mL 'natural abundance' 'Sodium phosphate' 20 mM '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-5 2 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 6.1 . 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 5 (PDP-5)' _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 4.001 0.000 . 2 1 1 GLY HA3 H 3.513 0.000 . 3 1 1 GLY H H 8.375 0.000 . 4 1 1 GLY CA C 46.450 0.000 . 5 2 2 ARG H H 8.439 0.001 . 6 2 2 ARG HA H 4.080 0.000 . 7 2 2 ARG HB2 H 1.522 0.000 . 8 2 2 ARG HB3 H 1.340 0.000 . 9 2 2 ARG HG2 H 1.309 0.000 . 10 2 2 ARG HG3 H 1.169 0.000 . 11 2 2 ARG HD2 H 2.938 0.000 . 12 2 2 ARG HD3 H 2.938 0.000 . 13 2 2 ARG HE H 6.969 0.000 . 14 2 2 ARG CA C 55.903 0.000 . 15 2 2 ARG CB C 30.356 0.000 . 16 2 2 ARG CG C 26.581 0.000 . 17 3 3 TYR H H 7.729 0.000 . 18 3 3 TYR HA H 4.560 0.000 . 19 3 3 TYR HB2 H 2.893 0.000 . 20 3 3 TYR HB3 H 2.791 0.000 . 21 3 3 TYR HD1 H 7.060 0.000 . 22 3 3 TYR HD2 H 7.060 0.000 . 23 3 3 TYR HE1 H 6.715 0.000 . 24 3 3 TYR HE2 H 6.715 0.000 . 25 3 3 TYR CA C 56.937 0.000 . 26 3 3 TYR CB C 39.850 0.000 . 27 4 4 ARG H H 8.414 0.000 . 28 4 4 ARG HA H 4.522 0.000 . 29 4 4 ARG HB2 H 1.645 0.000 . 30 4 4 ARG HB3 H 1.454 0.000 . 31 4 4 ARG HG2 H 1.257 0.000 . 32 4 4 ARG HG3 H 1.257 0.000 . 33 4 4 ARG HD2 H 2.955 0.000 . 34 4 4 ARG HD3 H 2.955 0.000 . 35 4 4 ARG HE H 7.051 0.000 . 36 4 4 ARG CA C 55.663 0.000 . 37 4 4 ARG CB C 31.104 0.000 . 38 4 4 ARG CG C 27.641 0.000 . 39 5 5 ARG H H 8.698 0.000 . 40 5 5 ARG HA H 4.353 0.000 . 41 5 5 ARG HB2 H 1.352 0.000 . 42 5 5 ARG HB3 H 1.164 0.000 . 43 5 5 ARG HG2 H 1.436 0.000 . 44 5 5 ARG HG3 H 1.350 0.000 . 45 5 5 ARG HD2 H 3.069 0.000 . 46 5 5 ARG HD3 H 3.001 0.000 . 47 5 5 ARG HE H 7.633 0.000 . 48 5 5 ARG CA C 54.612 0.000 . 49 5 5 ARG CB C 31.884 0.000 . 50 5 5 ARG CG C 27.142 0.000 . 51 6 6 CYS H H 8.388 0.000 . 52 6 6 CYS HA H 5.598 0.000 . 53 6 6 CYS HB2 H 2.763 0.000 . 54 6 6 CYS HB3 H 2.635 0.000 . 55 6 6 CYS CA C 54.999 0.000 . 56 7 7 ILE H H 9.018 0.000 . 57 7 7 ILE HA H 4.606 0.000 . 58 7 7 ILE HB H 2.029 0.000 . 59 7 7 ILE HG12 H 1.597 0.000 . 60 7 7 ILE HG13 H 1.361 0.000 . 61 7 7 ILE HG2 H 0.991 0.000 . 62 7 7 ILE HD1 H 0.913 0.000 . 63 7 7 ILE CA C 58.210 0.000 . 64 7 7 ILE CB C 39.448 0.000 . 65 7 7 ILE CG1 C 26.706 0.000 . 66 7 7 ILE CG2 C 17.284 0.000 . 67 7 7 ILE CD1 C 12.857 0.000 . 68 8 8 PRO HA H 4.331 0.000 . 69 8 8 PRO HB2 H 2.226 0.000 . 70 8 8 PRO HB3 H 1.833 0.000 . 71 8 8 PRO HG2 H 2.024 0.000 . 72 8 8 PRO HG3 H 1.891 0.000 . 73 8 8 PRO HD2 H 3.827 0.000 . 74 8 8 PRO HD3 H 3.671 0.000 . 75 8 8 PRO CA C 63.543 0.000 . 76 8 8 PRO CB C 32.165 0.000 . 77 8 8 PRO CG C 27.423 0.000 . 78 8 8 PRO CD C 51.005 0.000 . 79 9 9 GLY H H 8.000 0.000 . 80 9 9 GLY HA2 H 4.126 0.000 . 81 9 9 GLY HA3 H 3.923 0.000 . 82 9 9 GLY CA C 44.422 0.000 . 83 10 10 MET H H 8.239 0.000 . 84 10 10 MET HA H 4.105 0.000 . 85 10 10 MET HB2 H 1.791 0.000 . 86 10 10 MET HB3 H 1.654 0.000 . 87 10 10 MET HG2 H 2.141 0.000 . 88 10 10 MET HG3 H 2.017 0.000 . 89 10 10 MET HE H 1.927 0.000 . 90 10 10 MET CA C 56.848 0.000 . 91 10 10 MET CB C 32.540 0.000 . 92 10 10 MET CG C 31.572 0.000 . 93 10 10 MET CE C 16.722 0.000 . 94 11 11 PHE H H 8.500 0.000 . 95 11 11 PHE HA H 4.574 0.000 . 96 11 11 PHE HB2 H 3.179 0.000 . 97 11 11 PHE HB3 H 2.924 0.000 . 98 11 11 PHE HD1 H 7.182 0.000 . 99 11 11 PHE HD2 H 7.182 0.000 . 100 11 11 PHE HE1 H 7.269 0.000 . 101 11 11 PHE HE2 H 7.269 0.000 . 102 11 11 PHE HZ H 7.222 0.000 . 103 11 11 PHE CA C 58.122 0.000 . 104 11 11 PHE CB C 39.555 0.000 . 105 12 12 ARG H H 7.721 0.000 . 106 12 12 ARG HA H 4.349 0.000 . 107 12 12 ARG HB2 H 1.904 0.000 . 108 12 12 ARG HB3 H 1.693 0.000 . 109 12 12 ARG HG2 H 1.477 0.000 . 110 12 12 ARG HG3 H 1.370 0.000 . 111 12 12 ARG HD2 H 3.077 0.000 . 112 12 12 ARG HD3 H 3.077 0.000 . 113 12 12 ARG HE H 7.079 0.000 . 114 12 12 ARG CA C 55.153 0.000 . 115 12 12 ARG CB C 31.385 0.000 . 116 12 12 ARG CG C 26.019 0.000 . 117 13 13 ALA H H 8.230 0.000 . 118 13 13 ALA HA H 4.385 0.000 . 119 13 13 ALA HB H 1.214 0.000 . 120 13 13 ALA CA C 52.345 0.000 . 121 13 13 ALA CB C 19.530 0.000 . 122 14 14 TYR H H 8.483 0.000 . 123 14 14 TYR HA H 4.738 0.000 . 124 14 14 TYR HB2 H 2.876 0.000 . 125 14 14 TYR HB3 H 2.876 0.000 . 126 14 14 TYR HD1 H 7.004 0.000 . 127 14 14 TYR HD2 H 7.004 0.000 . 128 14 14 TYR HE1 H 6.611 0.000 . 129 14 14 TYR HE2 H 6.611 0.000 . 130 14 14 TYR CA C 57.025 0.000 . 131 14 14 TYR CB C 39.871 0.000 . 132 15 15 CYS H H 8.230 0.000 . 133 15 15 CYS HA H 5.359 0.000 . 134 15 15 CYS HB2 H 2.864 0.000 . 135 15 15 CYS HB3 H 2.473 0.000 . 136 15 15 CYS CA C 54.922 0.000 . 137 16 16 TYR H H 8.902 0.000 . 138 16 16 TYR HA H 4.638 0.000 . 139 16 16 TYR HB2 H 2.853 0.000 . 140 16 16 TYR HB3 H 2.776 0.000 . 141 16 16 TYR HD1 H 6.715 0.000 . 142 16 16 TYR HD2 H 6.715 0.000 . 143 16 16 TYR HE1 H 6.566 0.000 . 144 16 16 TYR HE2 H 6.566 0.000 . 145 16 16 TYR CA C 55.796 0.000 . 146 16 16 TYR CB C 39.930 0.000 . 147 17 17 MET H H 8.443 0.000 . 148 17 17 MET HA H 4.745 0.000 . 149 17 17 MET HB2 H 1.918 0.000 . 150 17 17 MET HB3 H 1.918 0.000 . 151 17 17 MET HG2 H 2.509 0.000 . 152 17 17 MET HG3 H 2.355 0.000 . 153 17 17 MET HE H 1.776 0.000 . 154 17 17 MET CA C 53.382 0.000 . 155 17 17 MET CB C 30.824 0.000 . 156 17 17 MET CG C 31.354 0.000 . 157 17 17 MET CE C 15.256 0.000 . 158 18 18 ASP H H 8.828 0.000 . 159 18 18 ASP HA H 4.764 0.000 . 160 18 18 ASP HB2 H 2.901 0.000 . 161 18 18 ASP HB3 H 2.380 0.000 . 162 18 18 ASP CA C 51.839 0.000 . 163 18 18 ASP CB C 39.682 0.000 . stop_ save_