data_5883 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; How C-Terminal Carboxyamidation Alters the Biological Activity of Peptides from the Venom of the Eumenine Solitary WasP ; _BMRB_accession_number 5883 _BMRB_flat_file_name bmr5883.str _Entry_type original _Submission_date 2003-07-28 _Accession_date 2003-07-28 _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 Sforca Mauricio L. . 2 Oyama Sergio . Jr. 3 Canduri Fernanda . . 4 Lorenzi Carla C.B. . 5 Pertinhez Thelma A. . 6 Konno Katsuhiro . . 7 Souza Bibiana M. . 8 Palma Mario S. . 9 Nero Joao R. . 10 Azevedo Walter F. Jr. 11 Spisni Alberto . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 85 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-16 update BMRB 'Updating non-standard residue' stop_ loop_ _Related_BMRB_accession_number _Relationship 5916 'free C-terminal EMP-AF-COOH' stop_ _Original_release_date 2003-07-28 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; How C-Terminal Carboxyamidation Alters the Biological Activity of Peptides from the Venom of the Eumenine Solitary WasP ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15134435 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sforca Mauricio L. . 2 'Oyama Jr.' Sergio . . 3 Canduri Fernanda . . 4 Lorenzi Carla C.B. . 5 Pertinhez Thelma A. . 6 Konno Katsuhiro . . 7 Souza Bibiana M. . 8 Palma Mario S. . 9 Nero Joao R. . 10 'Azevedo Jr.' Walter F. . 11 Spisni Alberto . . stop_ _Journal_abbreviation Biochemistry _Journal_volume 43 _Journal_issue 19 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5608 _Page_last 5617 _Year 2004 _Details . save_ ################################## # Molecular system description # ################################## save_system_EMP-AF _Saveframe_category molecular_system _Mol_system_name 'eumenine mastoparan' _Abbreviation_common EMP-AF _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'empaf, eumenine mastoparan' $EMP-AF stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state peptide _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function 'antimicrobial peptide' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_EMP-AF _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'eumenine mastoparan Antherichium flavourmarginatum micado' _Abbreviation_common EMP-AF _Molecular_mass . _Mol_thiol_state 'not present' _Details 'amidated C-terminal peptide' ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence ; INLLKIAKGIIKSX ; loop_ _Residue_seq_code _Residue_label 1 ILE 2 ASN 3 LEU 4 LEU 5 LYS 6 ILE 7 ALA 8 LYS 9 GLY 10 ILE 11 ILE 12 LYS 13 SER 14 NLW stop_ _Sequence_homology_query_date 2005-11-24 _Sequence_homology_query_revised_last_date 2004-07-01 save_ ###################### # Polymer residues # ###################### save_chem_comp_NLW _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common L-leucinamide _BMRB_code NLW _PDB_code NLW _Standard_residue_derivative . _Molecular_mass 130.188 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CD2 CD2 C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? CB CB C . 0 . ? CA CA C . 0 . ? N N N . 0 . ? C C C . 0 . ? O O O . 0 . ? NH2 NH2 N . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? H7 H7 H . 0 . ? H8 H8 H . 0 . ? H9 H9 H . 0 . ? H10 H10 H . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H14 H14 H . 0 . ? H15 H15 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 CD1 CG ? ? SING CG CD2 ? ? SING CG CB ? ? SING CB CA ? ? SING N CA ? ? SING CA C ? ? SING C NH2 ? ? DOUB C O ? ? SING CD2 H1 ? ? SING CD2 H2 ? ? SING CD2 H3 ? ? SING CG H4 ? ? SING CD1 H5 ? ? SING CD1 H6 ? ? SING CD1 H7 ? ? SING CB H8 ? ? SING CB H9 ? ? SING CA H10 ? ? SING N H11 ? ? SING N H12 ? ? SING NH2 H14 ? ? SING NH2 H15 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $EMP-AF 'Solitary wasp' 329991 Eukaryota Metazoa 'Anterhynchium flavormarginatum micado' flavomarginatum 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 $EMP-AF 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_empaf_contents _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $EMP-AF 1.0 mM . 2,2,2-Trifluorethanol 30 % . stop_ save_ ############################ # Computer software used # ############################ save_NMRpipe _Saveframe_category software _Name NMRpipe _Version 5.0 loop_ _Task 'semi automated peak assignments' stop_ _Details ; Delaglio, F., Grzesiek S., Vuister G. W., Zhu G., Pfeifer J. and Bax A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR. 6, 277-293 ; save_ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 2000 loop_ _Task 'energy minimization' stop_ _Details 'INSIGHT II User Guide Version 95 (1995) Accelrys Inc., San Diego, CA' save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Task annealing stop_ _Details ; Guntert, P., Mumenthaler, C. and Wuthrich, K. (1997) Torsion Angle Dynamics for NMR Structure Calculation with the New Program Dyana. J. Mol. Biol., 273, 283-298. ; save_ save_PROCHECK-NMR _Saveframe_category software _Name ProcheckNMR _Version 3.5.4 loop_ _Task 'analysis of NMR restraints violations' stop_ _Details ; Laskowsky, R.A., Rullmann, J.A., MacArthur, M.W., Kaptein, R., and Thorton, J.M. (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477-486 ; save_ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Task 'analysis of NMR restraints violations' stop_ _Details ; Brunger, A. T., Adams, P. D., Clore, G. M., Delano, W. L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J-S., Kuszewski, J., Nilges, N., Pannu, N. S., Read, R. J., Rice, L.M., Simonson, T. and Warren, G. L. (1998) Crystallography and nmr system (cns): a new software system for macromolecular structure determination. Acta Cryst. D. 54, 905-921. ; save_ save_NMRview _Saveframe_category software _Name NMRview _Version 5.0 loop_ _Task 'semi automated peak assignments' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H NOESY' _Sample_label $empaf_contents save_ save_2D_1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H TOCSY' _Sample_label $empaf_contents save_ save_2D_1H_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H COSY' _Sample_label $empaf_contents save_ save_2D_1H_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H DQF-COSY' _Sample_label $empaf_contents save_ ####################### # Sample conditions # ####################### save_empaf_cond _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.5 0.2 n/a temperature 293 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 H 1 'methyl protons' ppm 0.0 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_empaf_cs _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $empaf_contents stop_ _Sample_conditions_label $empaf_cond _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'empaf, eumenine mastoparan' _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 ILE HA H 3.89 0.01 1 2 . 1 ILE HB H 1.94 0.01 1 3 . 1 ILE HG12 H 1.20 0.01 2 4 . 1 ILE HG13 H 1.52 0.01 2 5 . 1 ILE HD1 H 0.99 0.01 1 6 . 2 ASN H H 8.49 0.01 1 7 . 2 ASN HA H 4.90 0.01 1 8 . 2 ASN HB2 H 2.81 0.01 2 9 . 2 ASN HB3 H 3.06 0.01 2 10 . 2 ASN HD21 H 7.74 0.01 2 11 . 2 ASN HD22 H 6.73 0.01 2 12 . 3 LEU H H 8.39 0.01 1 13 . 3 LEU HA H 4.10 0.01 1 14 . 3 LEU HB2 H 1.44 0.01 2 15 . 3 LEU HB3 H 1.68 0.01 2 16 . 3 LEU HG H 1.21 0.01 1 17 . 3 LEU HD1 H 0.96 0.01 1 18 . 3 LEU HD2 H 0.89 0.01 1 19 . 4 LEU H H 7.89 0.01 1 20 . 4 LEU HA H 4.13 0.01 1 21 . 4 LEU HB2 H 1.68 0.01 2 22 . 4 LEU HB3 H 1.78 0.01 2 23 . 4 LEU HG H 1.09 0.01 1 24 . 4 LEU HD1 H 0.98 0.01 1 25 . 4 LEU HD2 H 0.92 0.01 1 26 . 5 LYS H H 7.52 0.01 1 27 . 5 LYS HA H 3.98 0.01 1 28 . 5 LYS HB2 H 1.73 0.01 2 29 . 5 LYS HB3 H 1.84 0.01 2 30 . 5 LYS HG3 H 1.42 0.01 1 31 . 5 LYS HD3 H 1.52 0.01 1 32 . 5 LYS HE3 H 3.01 0.01 1 33 . 6 ILE H H 7.45 0.01 1 34 . 6 ILE HA H 3.86 0.01 1 35 . 6 ILE HB H 2.05 0.01 1 36 . 6 ILE HG12 H 1.22 0.01 2 37 . 6 ILE HG13 H 1.66 0.01 2 38 . 6 ILE HG2 H 0.93 0.01 1 39 . 6 ILE HD1 H 0.86 0.01 1 40 . 7 ALA H H 8.44 0.01 1 41 . 7 ALA HA H 4.03 0.01 1 42 . 7 ALA HB H 1.50 0.01 1 43 . 8 LYS H H 8.26 0.01 1 44 . 8 LYS HA H 3.96 0.01 1 45 . 8 LYS HB2 H 1.70 0.01 2 46 . 8 LYS HB3 H 1.84 0.01 2 47 . 8 LYS HG3 H 1.44 0.01 1 48 . 8 LYS HD3 H 1.52 0.01 1 49 . 8 LYS HE3 H 2.94 0.01 2 50 . 9 GLY H H 7.89 0.01 1 51 . 9 GLY HA2 H 3.91 0.01 2 52 . 10 ILE H H 8.22 0.01 1 53 . 10 ILE HA H 3.78 0.01 1 54 . 10 ILE HB H 2.058 0.01 1 55 . 10 ILE HG12 H 1.09 0.01 2 56 . 10 ILE HG13 H 1.78 0.01 2 57 . 10 ILE HG2 H 0.89 0.01 1 58 . 10 ILE HD1 H 0.83 0.01 1 59 . 11 ILE H H 8.38 0.01 1 60 . 11 ILE HA H 3.71 0.01 1 61 . 11 ILE HB H 1.93 0.01 1 62 . 11 ILE HG12 H 1.20 0.01 2 63 . 11 ILE HG13 H 1.73 0.01 2 64 . 11 ILE HG2 H 0.93 0.01 1 65 . 11 ILE HD1 H 0.83 0.01 1 66 . 12 LYS H H 8.18 0.01 1 67 . 12 LYS HA H 4.11 0.01 1 68 . 12 LYS HB2 H 1.77 0.01 2 69 . 12 LYS HB3 H 1.99 0.01 2 70 . 12 LYS HG3 H 1.55 0.01 1 71 . 12 LYS HD3 H 1.68 0.01 1 72 . 12 LYS HE3 H 3.02 0.01 2 73 . 13 SER H H 7.93 0.01 1 74 . 13 SER HA H 4.34 0.01 1 75 . 13 SER HB2 H 3.99 0.01 2 76 . 13 SER HB3 H 4.08 0.01 2 77 . 14 NLW H H 7.89 0.01 1 78 . 14 NLW HA H 4.28 0.01 1 79 . 14 NLW HB2 H 1.59 0.01 2 80 . 14 NLW HB3 H 1.88 0.01 2 81 . 14 NLW HG H 1.43 0.01 1 82 . 14 NLW HD1 H 0.86 0.01 2 83 . 14 NLW HD2 H 0.88 0.01 2 84 . 14 NLW HT1 H 7.22 0.01 2 85 . 14 NLW HT2 H 6.97 0.01 2 stop_ save_