data_19556 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the C-terminally encoded peptide of the model plant host Medicago truncatula - CEP1 ; _BMRB_accession_number 19556 _BMRB_flat_file_name bmr19556.str _Entry_type original _Submission_date 2013-10-14 _Accession_date 2013-10-14 _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 Bobay Benjamin G. . 2 DiGennaro Peter . . 3 'McK. Bird' David . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 67 "13C chemical shifts" 25 "15N chemical shifts" 14 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-12-09 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 19555 'C-terminally encoded peptide of the plant parasitic nematode Meloidogyne hapla - CEP11' stop_ _Original_release_date 2013-12-09 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution NMR studies of the plant peptide hormone CEP inform function' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24211833 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bobay Benjamin G. . 2 DiGennaro Peter . . 3 Scholl Elizabeth . . 4 Imin Nijat . . 5 Djordjevic Michael A. . 6 'McK. Bird' David . . stop_ _Journal_abbreviation 'FEBS Lett.' _Journal_volume 587 _Journal_issue 24 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3979 _Page_last 3985 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'C-terminally encoded peptide of the model plant host Medicago truncatula - CEP1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label CEP1 $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 1499.576 _Mol_thiol_state 'not preset' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence AFQXTTPGNSXGVGH loop_ _Residue_seq_code _Residue_label 1 ALA 2 PHE 3 GLN 4 HYP 5 THR 6 THR 7 PRO 8 GLY 9 ASN 10 SER 11 HYP 12 GLY 13 VAL 14 GLY 15 HIS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_HYP _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 4-HYDROXYPROLINE _BMRB_code HYP _PDB_code HYP _Standard_residue_derivative . _Molecular_mass 131.130 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? OD1 OD1 O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG HG H . 0 . ? HD22 HD22 H . 0 . ? HD23 HD23 H . 0 . ? HD1 HD1 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N CD ? ? SING N H ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG OD1 ? ? SING CG HG ? ? SING CD HD22 ? ? SING CD HD23 ? ? SING OD1 HD1 ? ? SING OXT HXT ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity 'Barrel medic' . Eukaryota Viridiplantae Medicago truncatula stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name _Details $entity 'chemical synthesis' . synthetic synthetic . N/A N/A 'Synthetic peptide with modification of hydroxy-proline at positions 4 and 11' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'Peptides (4 mg/ml) were dissolved in 90% H2O, 10% D2O (v/v). DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid) was used as an internal standard' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 4 mg/mL 'natural abundance' DSS 10 uM 'natural abundance' H2O 90 % 'natural abundance' D20 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_ARIA _Saveframe_category software _Name ARIA _Version . loop_ _Vendor _Address _Electronic_address 'Linge, O'Donoghue and Nilges' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details 'Equipped with a TCI probe' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'Peptides (4 mg/ml) were dissolved in 90% H2O, 10% D2O (v/v). DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid) was used as an internal standard' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 0 M pH 7.0 . pH pressure 1 . atm temperature 273 . 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 protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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-15N HSQC' '2D 1H-13C HSQC' '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 CEP1 _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 ALA HA H 4.0510 0.03 1 2 1 1 ALA HB H 1.1448 0.03 1 3 1 1 ALA H H 8.0238 0.03 1 4 1 1 ALA N N 116.9638 0.10 1 5 2 2 PHE H H 8.6275 0.03 1 6 2 2 PHE HA H 4.6047 0.03 1 7 2 2 PHE HB2 H 3.0366 0.03 2 8 2 2 PHE HB3 H 2.3461 0.03 2 9 2 2 PHE HD2 H 7.2332 0.03 3 10 2 2 PHE HE2 H 7.3442 0.03 3 11 2 2 PHE HZ H 7.2965 0.03 1 12 2 2 PHE CB C 39.8325 0.10 1 13 2 2 PHE CD2 C 131.8458 0.10 1 14 2 2 PHE CE2 C 131.6231 0.10 1 15 2 2 PHE CZ C 130.0700 0.10 1 16 2 2 PHE N N 120.3495 0.10 1 17 3 3 GLN H H 8.2509 0.03 1 18 3 3 GLN HA H 4.6024 0.03 1 19 3 3 GLN HB2 H 2.3076 0.03 2 20 3 3 GLN HG2 H 1.9864 0.03 2 21 3 3 GLN HG3 H 1.8523 0.03 2 22 3 3 GLN HE21 H 7.4719 0.03 2 23 3 3 GLN HE22 H 6.8568 0.03 2 24 3 3 GLN N N 123.8396 0.10 1 25 3 3 GLN NE2 N 112.3450 0.10 1 26 4 4 HYP CD C 50.5803 0.10 1 27 4 4 HYP CG C 27.4256 0.10 1 28 4 4 HYP HA H 4.6001 0.03 1 29 4 4 HYP HB H 2.3700 0.03 2 30 4 4 HYP HD H 3.6429 0.03 2 31 4 4 HYP HDA H 3.7911 0.03 2 32 4 4 HYP HOD1 H 2.0160 0.03 2 33 5 5 THR H H 8.4452 0.03 1 34 5 5 THR HA H 4.3455 0.03 1 35 5 5 THR HB H 4.1863 0.03 1 36 5 5 THR HG2 H 1.2067 0.03 1 37 5 5 THR CG2 C 21.7655 0.10 1 38 5 5 THR N N 115.9803 0.10 1 39 6 6 THR H H 8.2373 0.03 1 40 6 6 THR HA H 4.6072 0.03 1 41 6 6 THR HB H 4.1278 0.03 1 42 6 6 THR HG2 H 1.2144 0.03 1 43 6 6 THR CA C 57.9705 0.10 1 44 6 6 THR CB C 70.0896 0.10 1 45 6 6 THR N N 118.7700 0.10 1 46 7 7 PRO HA H 4.4013 0.03 1 47 7 7 PRO HB2 H 2.2750 0.03 2 48 7 7 PRO HB3 H 1.9052 0.03 2 49 7 7 PRO HG2 H 2.0735 0.03 2 50 7 7 PRO HG3 H 2.0166 0.03 2 51 7 7 PRO HD2 H 3.7528 0.03 2 52 7 7 PRO HD3 H 3.8579 0.03 2 53 7 7 PRO CA C 63.3487 0.10 1 54 7 7 PRO CB C 32.1774 0.10 1 55 7 7 PRO CD C 58.3642 0.10 1 56 8 8 GLY H H 8.5365 0.03 1 57 8 8 GLY HA2 H 3.9513 0.03 2 58 8 8 GLY CA C 45.1722 0.10 1 59 8 8 GLY N N 109.8721 0.10 1 60 9 9 ASN H H 8.2648 0.03 1 61 9 9 ASN HA H 4.7621 0.03 1 62 9 9 ASN HB2 H 2.7871 0.03 2 63 9 9 ASN HB3 H 2.7204 0.03 2 64 9 9 ASN HD21 H 7.5386 0.03 2 65 9 9 ASN HD22 H 6.8910 0.03 2 66 9 9 ASN N N 118.5538 0.10 1 67 9 9 ASN ND2 N 112.7534 0.10 1 68 10 10 SER H H 8.3164 0.03 1 69 10 10 SER HA H 4.7302 0.03 1 70 10 10 SER HB2 H 3.8263 0.03 2 71 10 10 SER HB3 H 3.7786 0.03 2 72 10 10 SER CA C 54.9909 0.10 1 73 10 10 SER CB C 63.2284 0.10 1 74 10 10 SER N N 117.1950 0.10 1 75 11 11 HYP CA C 72.5243 0.10 1 76 11 11 HYP CG C 32.7024 0.10 1 77 11 11 HYP HA H 4.5890 0.03 1 78 11 11 HYP HB H 2.3132 0.03 2 79 11 11 HYP HDA H 3.8507 0.03 2 80 11 11 HYP HOD1 H 2.0681 0.03 2 81 12 12 GLY H H 8.5088 0.03 1 82 12 12 GLY HA2 H 3.8932 0.03 2 83 12 12 GLY CA C 45.1522 0.10 1 84 12 12 GLY N N 112.5638 0.10 1 85 13 13 VAL H H 7.9837 0.03 1 86 13 13 VAL HA H 4.1238 0.03 1 87 13 13 VAL HB H 2.0810 0.03 1 88 13 13 VAL HG1 H 0.8895 0.03 2 89 13 13 VAL CA C 62.4350 0.10 1 90 13 13 VAL CG1 C 20.7363 0.10 2 91 13 13 VAL N N 119.2529 0.10 1 92 14 14 GLY H H 8.4372 0.03 1 93 14 14 GLY HA2 H 3.9341 0.03 2 94 14 14 GLY CA C 45.1722 0.10 1 95 14 14 GLY N N 109.1268 0.10 1 96 15 15 HIS H H 8.0047 0.03 1 97 15 15 HIS HA H 4.5126 0.03 1 98 15 15 HIS HB2 H 3.0945 0.03 2 99 15 15 HIS HB3 H 3.2512 0.03 2 100 15 15 HIS HD2 H 7.1956 0.03 1 101 15 15 HIS HE1 H 8.5549 0.03 1 102 15 15 HIS CA C 56.2802 0.10 1 103 15 15 HIS CB C 29.7363 0.10 1 104 15 15 HIS CD2 C 119.7593 0.10 1 105 15 15 HIS CE1 C 136.3429 0.10 1 106 15 15 HIS N N 121.5006 0.10 1 stop_ save_