data_19555 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the C-terminally encoded peptide of the plant parasitic nematode Meloidogyne hapla - CEP11 ; _BMRB_accession_number 19555 _BMRB_flat_file_name bmr19555.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" 58 "13C chemical shifts" 26 "15N chemical shifts" 12 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-12-09 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 19556 'C-terminally encoded peptide of the model plant host Medicago truncatula - CEP1' 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 plant parasitic nematode Meloidogyne hapla - CEP11' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label CEP11 $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 1522.660 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence AFRXTAPGHSXGVGH loop_ _Residue_seq_code _Residue_label 1 ALA 2 PHE 3 ARG 4 HYP 5 THR 6 ALA 7 PRO 8 GLY 9 HIS 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 'Northern root-knot nematode' 6305 Eukaryota Metazoa Meloidogyne hapla 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' D2O 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 CEP11 _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 4.0143 0.0000 1 2 1 1 ALA HB H 1.4735 0.0000 1 3 1 1 ALA H H 8.0816 0.0000 1 4 1 1 ALA CA C 51.7346 0.0000 1 5 1 1 ALA CB C 19.4401 0.0000 1 6 2 2 PHE H H 8.6495 0.0000 1 7 2 2 PHE HA H 4.6139 0.0000 1 8 2 2 PHE HB2 H 3.0407 0.0000 2 9 2 2 PHE HD2 H 7.4527 0.0000 3 10 2 2 PHE CA C 57.9478 0.0000 1 11 2 2 PHE CB C 39.7861 0.0000 1 12 2 2 PHE N N 120.5882 0.0000 1 13 3 3 ARG H H 8.2116 0.0000 1 14 3 3 ARG HA H 4.5711 0.0000 1 15 3 3 ARG HB2 H 1.7378 0.0000 2 16 3 3 ARG HG2 H 1.5736 0.0000 2 17 3 3 ARG HG3 H 1.6302 0.0000 2 18 3 3 ARG HD2 H 3.1564 0.0000 2 19 3 3 ARG HH11 H 7.1449 0.0000 9 20 3 3 ARG CA C 53.5223 0.0000 1 21 3 3 ARG CB C 30.6879 0.0000 1 22 3 3 ARG CG C 26.6688 0.0000 1 23 3 3 ARG CD C 43.3806 0.0000 1 24 3 3 ARG N N 124.6625 0.0000 1 25 3 3 ARG NH1 N 124.7890 0.0000 2 26 4 4 HYP HA H 4.5891 0.0000 1 27 4 4 HYP HB H 2.3572 0.0000 2 28 4 4 HYP HDA H 3.7563 0.0000 2 29 4 4 HYP HOD1 H 2.0158 0.0000 2 30 5 5 THR H H 8.3942 0.0000 1 31 5 5 THR HA H 4.2333 0.0000 1 32 5 5 THR HB H 4.1331 0.0000 1 33 5 5 THR HG2 H 1.2099 0.0000 1 34 5 5 THR CA C 61.9267 0.0000 1 35 5 5 THR CB C 70.0587 0.0000 1 36 5 5 THR CG2 C 21.7368 0.0000 1 37 5 5 THR N N 116.5400 0.0000 1 38 6 6 ALA H H 8.3560 0.0000 1 39 6 6 ALA HA H 4.6030 0.0000 1 40 6 6 ALA HB H 1.3234 0.0000 1 41 6 6 ALA CA C 50.4652 0.0000 1 42 6 6 ALA CB C 18.2319 0.0000 1 43 6 6 ALA N N 108.1996 0.0000 1 44 7 7 PRO HA H 4.4012 0.0000 1 45 7 7 PRO HB2 H 2.2830 0.0000 2 46 7 7 PRO HG2 H 1.9020 0.0000 2 47 7 7 PRO HG3 H 2.0270 0.0000 2 48 7 7 PRO HD2 H 3.6538 0.0000 2 49 7 7 PRO HD3 H 3.7973 0.0000 2 50 8 8 GLY H H 8.5276 0.0000 1 51 8 8 GLY HA2 H 3.9557 0.0000 2 52 8 8 GLY CA C 45.1427 0.0000 1 53 8 8 GLY N N 109.8161 0.0000 1 54 9 9 HIS H H 8.3296 0.0000 1 55 9 9 HIS HA H 4.7390 0.0000 1 56 9 9 HIS HB2 H 3.1380 0.0000 2 57 9 9 HIS HB3 H 3.2520 0.0000 2 58 9 9 HIS CB C 29.3780 0.0000 1 59 9 9 HIS N N 117.8957 0.0000 1 60 10 10 SER H H 8.5016 0.0000 1 61 10 10 SER HA H 4.7469 0.0000 1 62 10 10 SER HB2 H 3.8376 0.0000 2 63 10 10 SER HB3 H 3.7995 0.0000 2 64 10 10 SER CB C 63.2014 0.0000 1 65 10 10 SER N N 112.5987 0.0000 1 66 11 11 HYP CA C 72.5054 0.0000 1 67 11 11 HYP CB C 39.8307 0.0000 1 68 11 11 HYP CD C 58.3690 0.0000 1 69 11 11 HYP CG C 27.4035 0.0000 1 70 11 11 HYP HA H 4.6103 0.0000 1 71 11 11 HYP HB H 2.3508 0.0000 2 72 11 11 HYP HBA H 2.3424 0.0000 2 73 11 11 HYP HD H 3.8612 0.0000 2 74 11 11 HYP HDA H 3.8667 0.0000 2 75 11 11 HYP HG H 2.0753 0.0000 2 76 12 12 GLY H H 8.4532 0.0000 1 77 12 12 GLY HA2 H 3.8969 0.0000 2 78 12 12 GLY CA C 45.1212 0.0000 1 79 12 12 GLY N N 109.0751 0.0000 1 80 13 13 VAL H H 8.0087 0.0000 1 81 13 13 VAL HA H 4.1286 0.0000 1 82 13 13 VAL HB H 2.0740 0.0000 1 83 13 13 VAL HG1 H 0.8933 0.0000 2 84 13 13 VAL CA C 62.4118 0.0000 1 85 13 13 VAL CB C 32.6848 0.0000 1 86 13 13 VAL CG1 C 20.7055 0.0000 2 87 13 13 VAL N N 119.1792 0.0000 1 88 14 14 GLY H H 8.5040 0.0000 1 89 14 14 GLY N N 119.0640 0.0000 1 90 15 15 HIS H H 7.9625 0.0000 1 91 15 15 HIS HA H 4.5180 0.0000 1 92 15 15 HIS HB2 H 3.1284 0.0000 2 93 15 15 HIS HB3 H 3.2630 0.0000 2 94 15 15 HIS CA C 56.2250 0.0000 1 95 15 15 HIS CB C 29.6390 0.0000 1 96 15 15 HIS N N 121.7596 0.0000 1 stop_ save_