data_30337 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; PawL-Derived Peptide PLP-12 ; _BMRB_accession_number 30337 _BMRB_flat_file_name bmr30337.str _Entry_type original _Submission_date 2017-09-05 _Accession_date 2017-09-05 _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 Fisher M. . . 2 Mylne J. S. . 3 Howard M. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 spectral_peak_list 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 35 "13C chemical shifts" 19 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-05-08 update BMRB 'update entry citation' 2018-03-01 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 30344 'PawL-Derived Peptide PLP-10 (cis conformer)' stop_ _Original_release_date 2017-10-05 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30417166 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Fisher Mark F. . 2 Zhang Jingjing . . 3 Taylor Nicolas L. . 4 Howard Mark J. . 5 Berkowitz Oliver . . 6 Debowski Aleksandra W. . 7 Behsaz Bahar . . 8 Whelan James . . 9 Pevzner Pavel A. . 10 Mylne Joshua S. . stop_ _Journal_abbreviation 'Plant Direct' _Journal_name_full 'Plant direct' _Journal_volume 2 _Journal_issue 2 _Journal_ISSN 2475-4455 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first e00042 _Page_last e00042 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name PLP-12 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PLP-12 _Molecular_mass 828.867 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence ; FVGGTSFD ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 PHE 2 2 VAL 3 3 GLY 4 4 GLY 5 5 THR 6 6 SER 7 7 PHE 8 8 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 $entity_1 old-man-in-the-Spring 76276 Eukaryota Viridiplantae Senecio Vulgaris 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1.0 mg/mL PLP-12, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.0 mg/mL 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name Analysis _Version 2.4.2 loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name TOPSPIN _Version 3.5 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_software_3 _Saveframe_category software _Name YASARA _Version 16.7.22 loop_ _Vendor _Address _Electronic_address 'Elmar Krieger' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_20_ms_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY 20 ms' _Sample_label $sample_1 save_ save_2D_1H-1H_ROESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _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-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_80_ms_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY 80 ms' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.5 0.5 pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 protons' ppm 0.000 internal indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0.000 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY 20 ms' '2D 1H-1H ROESY' '2D DQF-COSY' '2D 1H-13C HSQC' '2D 1H-1H TOCSY 80 ms' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_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 PHE HA H 4.507 0.002 1 2 1 1 PHE HB2 H 3.199 0.006 1 3 1 1 PHE HB3 H 3.149 0.003 1 4 1 1 PHE HD1 H 7.240 0.001 1 5 1 1 PHE HD2 H 7.240 0.001 1 6 1 1 PHE H H 8.462 0.001 1 7 1 1 PHE CA C 59.760 . 1 8 1 1 PHE CB C 38.846 . 1 9 2 2 VAL H H 8.208 0.002 1 10 2 2 VAL HA H 3.832 0.002 1 11 2 2 VAL HB H 2.119 0.004 1 12 2 2 VAL HG1 H 0.953 0.003 2 13 2 2 VAL HG2 H 0.998 0.004 2 14 2 2 VAL CA C 65.860 . 1 15 2 2 VAL CB C 31.341 . 1 16 2 2 VAL CG1 C 20.778 . 2 17 2 2 VAL CG2 C 21.300 . 2 18 3 3 GLY H H 7.934 0.002 1 19 3 3 GLY HA2 H 3.787 0.005 2 20 3 3 GLY HA3 H 4.075 0.004 2 21 3 3 GLY CA C 44.976 . 1 22 4 4 GLY H H 8.002 0.001 1 23 4 4 GLY HA2 H 3.926 0.006 2 24 4 4 GLY HA3 H 4.017 0.004 2 25 4 4 GLY CA C 45.542 . 1 26 5 5 THR H H 7.918 0.005 1 27 5 5 THR HA H 4.674 0.003 1 28 5 5 THR HB H 4.387 0.002 1 29 5 5 THR HG2 H 1.129 0.002 1 30 5 5 THR CA C 59.816 . 1 31 5 5 THR CB C 71.311 . 1 32 5 5 THR CG2 C 21.087 . 1 33 6 6 SER H H 8.477 0.001 1 34 6 6 SER HA H 4.196 0.003 1 35 6 6 SER HB2 H 3.721 0.001 1 36 6 6 SER CA C 59.740 . 1 37 6 6 SER CB C 63.121 . 1 38 7 7 PHE H H 7.700 0.002 1 39 7 7 PHE HA H 4.597 0.003 1 40 7 7 PHE HB2 H 3.003 0.002 1 41 7 7 PHE HB3 H 3.142 0.002 1 42 7 7 PHE HD1 H 7.255 0.001 1 43 7 7 PHE HD2 H 7.255 0.001 1 44 7 7 PHE HZ H 7.247 0.001 1 45 7 7 PHE CA C 57.112 . 1 46 7 7 PHE CB C 39.058 0.047 1 47 7 7 PHE CD1 C 131.892 . 1 48 7 7 PHE CD2 C 131.892 . 1 49 8 8 ASP H H 7.627 0.003 1 50 8 8 ASP HA H 4.604 0.001 1 51 8 8 ASP HB2 H 2.585 0.002 2 52 8 8 ASP HB3 H 2.750 0.004 2 53 8 8 ASP CA C 52.570 . 1 54 8 8 ASP CB C 38.936 . 1 stop_ save_ save_spectral_peak_list_1 _Saveframe_category spectral_peak_list _Details . _Experiment_label '2D 1H-1H ROESY' _Number_of_spectral_dimensions 2 loop_ _Expt_dimension_ID _Atom_type _Spectral_region 1 H H 2 H H stop_ _Sample_label $sample_1 _Sample_conditions_label $sample_conditions_1 _Text_data_format "NMR-STAR v3" _Text_data ; >>save_spectral_peak_list_1 >> _Spectral_peak_list.Sf_category spectral_peak_list >> _Spectral_peak_list.Sf_framecode spectral_peak_list_1 >> _Spectral_peak_list.Entry_ID 30337 >> _Spectral_peak_list.ID 1 >> _Spectral_peak_list.Sample_ID 1 >> _Spectral_peak_list.Sample_label $sample_1 >> _Spectral_peak_list.Sample_condition_list_ID 1 >> _Spectral_peak_list.Sample_condition_list_label $sample_conditions_1 >> _Spectral_peak_list.Experiment_ID 2 >> _Spectral_peak_list.Experiment_name '2D 1H-1H ROESY' >> _Spectral_peak_list.Experiment_class . >> _Spectral_peak_list.Experiment_type . >> _Spectral_peak_list.Number_of_spectral_dimensions 2 >> _Spectral_peak_list.Chemical_shift_list . >> _Spectral_peak_list.Assigned_chem_shift_list_ID . >> _Spectral_peak_list.Assigned_chem_shift_list_label . >> _Spectral_peak_list.Details . >> _Spectral_peak_list.Text_data_format text >> _Spectral_peak_list.Text_data >>; >># Number of dimensions 2 >># INAME 1 H >># INAME 2 H >># CYANAFORMAT HH >> 1 7.699 7.240 1 T -6.423e+05 0.00e+00 a 0 - - >> 2 8.002 7.915 1 T -1.171e+06 0.00e+00 a 0 - - >> 3 8.477 7.916 1 T -5.070e+05 0.00e+00 a 0 - - >> 4 7.701 3.721 1 T -5.502e+05 0.00e+00 a 0 - - >> 5 8.209 0.953 1 T -8.150e+05 0.00e+00 a 0 - - >> 7 3.165 2.995 1 T -6.619e+06 0.00e+00 a 0 - - >> 8 8.478 7.696 1 T -4.022e+05 0.00e+00 a 0 - - >> 9 8.464 7.254 1 T -3.577e+05 0.00e+00 a 0 - - >> 10 8.207 7.255 1 T -3.465e+05 0.00e+00 a 0 - - >> 11 7.384 7.240 1 T -9.635e+06 0.00e+00 a 0 - - >> 12 7.428 7.240 1 T -1.741e+06 0.00e+00 a 0 - - >> 13 7.339 7.240 1 T -3.554e+06 0.00e+00 a 0 - - >> 14 7.255 7.196 1 T 6.632e+06 0.00e+00 a 0 - - >> 15 7.255 7.105 1 T 3.810e+05 0.00e+00 a 0 - - >> 16 7.246 7.153 1 T 1.291e+05 0.00e+00 a 0 - - >> 17 8.210 7.934 1 T -6.404e+05 0.00e+00 a 0 - - >> 18 8.463 8.209 1 T -4.959e+05 0.00e+00 a 0 - - >> 19 8.463 4.603 1 T -1.569e+06 0.00e+00 a 0 - - >> 20 8.478 4.679 1 T -1.833e+06 0.00e+00 a 0 - - >> 21 8.463 4.508 1 T -6.626e+05 0.00e+00 a 0 - - >> 22 8.478 4.386 1 T -2.755e+06 0.00e+00 a 0 - - >> 23 8.478 4.195 1 T -1.203e+06 0.00e+00 a 0 - - >> 24 8.478 3.721 1 T -2.166e+06 0.00e+00 a 0 - - >> 25 8.463 3.205 1 T -8.600e+05 0.00e+00 a 0 - - >> 26 8.463 3.149 1 T -6.675e+05 0.00e+00 a 0 - - >> 27 8.209 3.147 1 T -7.637e+05 0.00e+00 a 0 - - >> 28 7.701 3.001 1 T -7.709e+05 0.00e+00 a 0 - - >> 29 7.701 3.142 1 T -4.368e+05 0.00e+00 a 0 - - >> 30 8.211 2.115 1 T -1.858e+06 0.00e+00 a 0 - - >> 31 7.934 2.119 1 T -4.178e+05 0.00e+00 a 0 - - >> 32 7.919 1.127 1 T -1.028e+06 0.00e+00 a 0 - - >> 33 8.211 0.999 1 T -2.142e+06 0.00e+00 a 0 - - >> 34 7.256 0.999 1 T -5.552e+05 0.00e+00 a 0 - - >> 35 7.240 2.581 1 T -6.108e+05 0.00e+00 a 0 - - >> 36 7.240 3.000 1 T -3.076e+06 0.00e+00 a 0 - - >> 37 7.246 3.142 1 T -4.506e+06 0.00e+00 a 0 - - >> 38 7.256 3.205 1 T -2.510e+06 0.00e+00 a 0 - - >> 39 7.254 3.142 1 T -3.834e+06 0.00e+00 a 0 - - >> 40 7.240 3.721 1 T -4.784e+05 0.00e+00 a 0 - - >> 41 7.934 3.829 1 T -1.221e+06 0.00e+00 a 0 - - >> 42 7.934 3.786 1 T -1.221e+06 0.00e+00 a 0 - - >> 43 8.001 3.781 1 T -4.439e+05 0.00e+00 a 0 - - >> 44 8.001 3.924 1 T -2.154e+06 0.00e+00 a 0 - - >> 45 8.001 4.018 1 T -7.802e+05 0.00e+00 a 0 - - >> 46 8.001 4.071 1 T -5.782e+05 0.00e+00 a 0 - - >> 47 7.924 3.929 1 T -3.941e+05 0.00e+00 a 0 - - >> 48 7.924 4.027 1 T -6.236e+05 0.00e+00 a 0 - - >> 49 7.701 4.198 1 T -8.456e+05 0.00e+00 a 0 - - >> 50 7.935 4.071 1 T -4.684e+05 0.00e+00 a 0 - - >> 51 7.924 4.389 1 T -4.802e+05 0.00e+00 a 0 - - >> 52 7.924 4.513 1 T -5.291e+05 0.00e+00 a 0 - - >> 53 7.701 4.596 1 T -5.365e+05 0.00e+00 a 0 - - >> 54 7.924 4.613 1 T -8.133e+05 0.00e+00 a 0 - - >> 55 7.925 4.669 1 T -1.777e+06 0.00e+00 a 0 - - >> 56 7.909 4.693 1 T -1.200e+06 0.00e+00 a 0 - - >> 57 7.625 4.596 1 T -1.130e+06 0.00e+00 a 0 - - >> 58 7.241 4.596 1 T -1.990e+06 0.00e+00 a 0 - - >> 59 7.257 4.505 1 T -2.167e+06 0.00e+00 a 0 - - >> 60 7.908 4.976 1 T -4.709e+05 0.00e+00 a 0 - - >> 61 7.934 0.951 1 T -2.802e+05 0.00e+00 a 0 - - >> 63 8.211 3.206 1 T -2.940e+05 0.00e+00 a 0 - - >> 64 7.356 3.149 1 T -3.489e+05 0.00e+00 a 0 - - >> 65 7.240 4.382 1 T -3.086e+05 0.00e+00 a 0 - - >> 66 7.408 3.143 1 T -2.348e+05 0.00e+00 a 0 - - >> 67 8.210 3.836 1 T -1.128e+06 0.00e+00 a 0 - - >> 68 8.210 4.507 1 T -9.087e+05 0.00e+00 a 0 - - >> 69 7.700 4.387 1 T -3.285e+05 0.00e+00 a 0 - - >> 70 8.470 7.626 1 T -2.907e+05 0.00e+00 a 0 - - >> 72 3.834 1.000 1 T -2.273e+06 0.00e+00 a 0 - - >> 73 3.833 0.956 1 T -2.220e+06 0.00e+00 a 0 - - >> 74 4.404 1.127 1 T -7.376e+05 0.00e+00 a 0 - - >> 75 4.369 1.131 1 T -9.511e+05 0.00e+00 a 0 - - >> 76 3.833 2.118 1 T -2.187e+06 0.00e+00 a 0 - - >> 77 4.192 3.722 1 T -4.331e+06 0.00e+00 a 0 - - >> 78 4.061 3.778 1 T -7.356e+06 0.00e+00 a 0 - - >> 79 4.046 3.913 1 T -3.627e+06 0.00e+00 a 0 - - >> 80 4.005 3.901 1 T -2.301e+06 0.00e+00 a 0 - - >> 81 3.779 0.955 1 T -2.798e+05 0.00e+00 a 0 - - >> 82 2.114 0.950 1 T -2.303e+06 0.00e+00 a 0 - - >> 83 2.114 0.997 1 T -2.066e+06 0.00e+00 a 0 - - >> 84 1.019 0.955 1 T -1.258e+06 0.00e+00 a 0 - - >> 85 2.218 0.482 1 T -3.666e+05 0.00e+00 a 0 - - >> 86 0.009 -0.035 1 T 1.700e+05 0.00e+00 a 0 - - >> 87 -0.002 -0.083 1 T -5.569e+05 0.00e+00 a 0 - - >> 88 -0.009 -0.058 1 T 2.158e+04 0.00e+00 a 0 - - >> 89 0.972 0.506 1 T -3.032e+05 0.00e+00 a 0 - - >> 90 0.972 0.583 1 T -2.934e+05 0.00e+00 a 0 - - >> 91 4.388 1.129 1 T -3.667e+04 0.00e+00 a 0 - - >> 92 1.013 2.115 1 T -3.559e+06 0.00e+00 a 0 - - >> 93 7.254 0.952 1 T -3.840e+05 0.00e+00 a 0 - - >>; >> >> loop_ >> _Spectral_dim.ID >> _Spectral_dim.Axis_code >> _Spectral_dim.Spectrometer_frequency >> _Spectral_dim.Atom_type >> _Spectral_dim.Atom_isotope_number >> _Spectral_dim.Spectral_region >> _Spectral_dim.Magnetization_linkage_ID >> _Spectral_dim.Under_sampling_type >> _Spectral_dim.Sweep_width >> _Spectral_dim.Sweep_width_units >> _Spectral_dim.Value_first_point >> _Spectral_dim.Absolute_peak_positions >> _Spectral_dim.Acquisition >> _Spectral_dim.Center_frequency_offset >> _Spectral_dim.Encoding_code >> _Spectral_dim.Encoded_reduced_dimension_ID >> _Spectral_dim.Entry_ID >> _Spectral_dim.Spectral_peak_list_ID >> >> 1 . . H 1 H . . 12 ppm . . . 4.697 . . 30337 1 >> 2 . . H 1 H . . 12 ppm . . . 4.697 . . 30337 1 >> >> stop_ >> >>save_ >> ; save_