data_19678 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the CLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE5 ; _BMRB_accession_number 19678 _BMRB_flat_file_name bmr19678.str _Entry_type original _Submission_date 2013-12-13 _Accession_date 2013-12-13 _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 M. . 3 Bird David Mck . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 61 "13C chemical shifts" 32 "15N chemical shifts" 13 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-12-22 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 19674 'CLAVATA encoded peptide of Arabidopsis thaliana - AtCLE10' 19675 'CLAVATA encoded peptide of Arabidopsis thaliana - AtCLE44' 19677 'CLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE4' 19679 'CLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE6/7' stop_ _Original_release_date 2014-12-22 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Inferring function of CLE peptides from high resolution tertiary structures' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 DiGennaro Peter G. . 2 Bobay Benjamin M. . 3 Bird David Mck . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'CLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE5' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'CLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE5' $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 1328.510 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence RKVPTGSNPQKN loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 ARG 2 2 LYS 3 3 VAL 4 4 PRO 5 5 THR 6 6 GLY 7 7 SER 8 8 ASN 9 9 PRO 10 10 GLN 11 11 LYS 12 12 ASN 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 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_name _Details $entity 'chemical synthesis' . . . . . 'Synthetically made peptide' 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 $entity 4 mg/mL 'natural abundance' 'sodium chloride' 137 mM 'natural abundance' 'potassium chloride' 2.7 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' 'potassium phosphate' 1.8 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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_ 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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . 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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 140 0.1 mM pH 7.0 0.1 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 'CLAVATA-like encoded peptide of Meloidogyne hapla - MhCLE5' _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 ARG HA H 4.0350 0.03 1 2 1 1 ARG HB2 H 1.9010 0.03 2 3 1 1 ARG HG2 H 1.6070 0.03 2 4 1 1 ARG HD2 H 3.1990 0.03 2 5 1 1 ARG H H 7.1990 0.03 1 6 1 1 ARG CA C 55.4850 0.10 1 7 1 1 ARG CB C 30.9960 0.10 1 8 1 1 ARG CG C 26.2740 0.10 1 9 1 1 ARG CD C 43.3220 0.10 1 10 1 1 ARG N N 124.2110 0.10 1 11 2 2 LYS H H 8.7620 0.03 1 12 2 2 LYS HA H 4.4050 0.03 1 13 2 2 LYS HB2 H 1.7340 0.03 2 14 2 2 LYS HB3 H 1.7240 0.03 2 15 2 2 LYS HG2 H 1.3910 0.03 2 16 2 2 LYS HG3 H 1.3600 0.03 2 17 2 2 LYS HD2 H 1.6620 0.03 2 18 2 2 LYS HE2 H 2.9730 0.03 2 19 2 2 LYS CA C 56.3310 0.10 1 20 2 2 LYS CB C 33.2070 0.10 1 21 2 2 LYS CG C 24.7820 0.10 1 22 2 2 LYS CD C 29.1780 0.10 1 23 2 2 LYS CE C 42.1980 0.10 1 24 2 2 LYS N N 125.0400 0.10 1 25 3 3 VAL H H 8.3850 0.03 1 26 3 3 VAL HA H 4.4100 0.03 1 27 3 3 VAL HB H 2.0790 0.03 1 28 3 3 VAL HG1 H 0.9620 0.03 2 29 3 3 VAL HG2 H 0.9330 0.03 2 30 3 3 VAL CA C 59.9660 0.10 1 31 3 3 VAL CB C 32.6660 0.10 1 32 3 3 VAL CG1 C 21.0670 0.10 2 33 3 3 VAL CG2 C 20.2550 0.10 2 34 3 3 VAL N N 124.4490 0.10 1 35 4 4 PRO HA H 4.3910 0.03 1 36 4 4 PRO HB2 H 2.2580 0.03 2 37 4 4 PRO HG2 H 1.9950 0.03 2 38 4 4 PRO HG3 H 1.9230 0.03 2 39 4 4 PRO HD2 H 3.7780 0.03 2 40 4 4 PRO CA C 63.5550 0.10 1 41 4 4 PRO CD C 50.7570 0.10 1 42 5 5 THR H H 8.2680 0.03 1 43 5 5 THR HA H 4.3040 0.03 1 44 5 5 THR HB H 4.2080 0.03 1 45 5 5 THR HG2 H 1.2310 0.03 1 46 5 5 THR CA C 62.2220 0.10 1 47 5 5 THR CB C 69.9450 0.10 1 48 5 5 THR CG2 C 21.6470 0.10 1 49 5 5 THR N N 115.0210 0.10 1 50 6 6 GLY H H 8.4440 0.03 1 51 6 6 GLY HA2 H 3.9990 0.03 2 52 6 6 GLY CA C 45.2920 0.10 1 53 6 6 GLY N N 111.4950 0.10 1 54 7 7 SER H H 8.2060 0.03 1 55 7 7 SER HA H 4.4380 0.03 1 56 7 7 SER HB2 H 3.8160 0.03 2 57 7 7 SER CA C 58.2810 0.10 1 58 7 7 SER CB C 64.0410 0.10 1 59 7 7 SER N N 115.4430 0.10 1 60 8 8 ASN H H 8.5110 0.03 1 61 8 8 ASN HA H 4.9720 0.03 1 62 8 8 ASN HB2 H 2.8270 0.03 2 63 8 8 ASN HB3 H 2.6680 0.03 2 64 8 8 ASN HD21 H 7.5360 0.03 2 65 8 8 ASN CA C 51.5170 0.10 1 66 8 8 ASN CB C 38.9480 0.10 1 67 8 8 ASN N N 121.3860 0.10 1 68 8 8 ASN ND2 N 112.7700 0.10 1 69 9 9 PRO HA H 4.4820 0.03 1 70 9 9 PRO HB2 H 2.3040 0.03 2 71 9 9 PRO HG2 H 2.0500 0.03 2 72 9 9 PRO HD2 H 3.8690 0.03 2 73 9 9 PRO CA C 63.2740 0.10 1 74 9 9 PRO CD C 50.7575 0.10 1 75 10 10 GLN H H 8.3770 0.03 1 76 10 10 GLN HA H 4.2760 0.03 1 77 10 10 GLN HB2 H 1.9710 0.03 2 78 10 10 GLN HB3 H 2.0850 0.03 2 79 10 10 GLN HG2 H 2.3630 0.03 2 80 10 10 GLN HE21 H 7.5060 0.03 2 81 10 10 GLN HE22 H 6.8100 0.03 2 82 10 10 GLN CA C 55.8590 0.10 1 83 10 10 GLN CB C 29.5180 0.10 1 84 10 10 GLN CG C 33.9890 0.10 1 85 10 10 GLN N N 120.2250 0.10 1 86 10 10 GLN NE2 N 112.5820 0.10 1 87 11 11 LYS H H 8.2700 0.03 1 88 11 11 LYS HA H 4.3090 0.03 1 89 11 11 LYS HB2 H 1.8440 0.03 2 90 11 11 LYS HB3 H 1.7260 0.03 2 91 11 11 LYS HG2 H 1.4120 0.03 2 92 11 11 LYS HD2 H 1.6760 0.03 2 93 11 11 LYS HE2 H 2.9770 0.03 2 94 11 11 LYS CA C 56.2780 0.10 1 95 11 11 LYS CB C 33.2120 0.10 1 96 11 11 LYS N N 122.9700 0.10 1 97 12 12 ASN H H 8.1380 0.03 1 98 12 12 ASN HA H 4.5210 0.03 1 99 12 12 ASN HB2 H 2.6920 0.03 2 100 12 12 ASN HB3 H 2.7790 0.03 2 101 12 12 ASN HD21 H 7.6010 0.03 2 102 12 12 ASN HD22 H 6.9460 0.03 2 103 12 12 ASN CA C 54.1130 0.10 1 104 12 12 ASN CB C 40.0680 0.10 1 105 12 12 ASN N N 124.6190 0.10 1 106 12 12 ASN ND2 N 113.0880 0.10 1 stop_ save_