data_5890 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The NMR-derived Solution Structure of a New Cationic Antimicrobial Peptide from the Skin Secretion of the Anuran Hyla punctata ; _BMRB_accession_number 5890 _BMRB_flat_file_name bmr5890.str _Entry_type original _Submission_date 2003-08-04 _Accession_date 2003-08-04 _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 Prates Maura V. . 2 Regis Wiliam C.B. . 3 Sforca Mauricio L. . 4 Leite Jose R.S.A. . 5 Pertinhez Thelma A. . 6 Araujo Antonio L.T. . 7 Spisni Alberto . . 8 Bloch Carlos . Jr. stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 coupling_constants 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 65 "coupling constants" 12 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2004-02-12 original author . stop_ _Original_release_date 2004-02-12 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; The NMR-derived Solution Structure of a New Cationic Antimicrobial Peptide from the Skin Secretion of the Anuran Hyla punctata ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 14715660 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Prates Maura V. . 2 Regis Wiliam C.B. . 3 Sforca Mauricio L. . 4 Leite Jose R.S.A. . 5 Pertinhez Thelma A. . 6 Araujo Antonio L.T. . 7 Spisni Alberto . . 8 Bloch Carlos . Jr. stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 279 _Journal_issue 13 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 13018 _Page_last 13026 _Year 2004 _Details . save_ ################################## # Molecular system description # ################################## save_system_HSP1 _Saveframe_category molecular_system _Mol_system_name 'Hylaseptin P1' _Abbreviation_common HSP1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'HSP1, Hylaseptin' $HSP1 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function 'antimicrobial peptide' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_HSP1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'Hylaseptin P1' _Abbreviation_common HSP1 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence GILDAIKAIAKAAG loop_ _Residue_seq_code _Residue_label 1 GLY 2 ILE 3 LEU 4 ASP 5 ALA 6 ILE 7 LYS 8 ALA 9 ILE 10 ALA 11 LYS 12 ALA 13 ALA 14 GLY stop_ _Sequence_homology_query_date 2005-11-24 _Sequence_homology_query_revised_last_date 2004-07-01 save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $HSP1 'Polka-dot treefrog' 280006 Eukaryota Metazoa Hypsiboas punctatus 'amphibian skin secretion' 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 $HSP1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_HSP1_sample _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_max_value _Isotopic_labeling $HSP1 . mM 3 . 2,2,2-Trifluorethanol 30 % . . D2O 5 % . . H2O 95 % . . stop_ save_ ############################ # Computer software used # ############################ save_NMRpipe _Saveframe_category software _Name NMRpipe _Version 5.0 loop_ _Task 'semi automated 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_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_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_PROCHECK-NMR _Saveframe_category software _Name ProcheckNMR _Version 3.5.4 loop_ _Task 'analysis of the 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_solve _Saveframe_category software _Name CNSSOLVE _Version 1.1 loop_ _Task 'analysis of the 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 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 $HSP1_sample save_ save_2D_1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H TOCSY' _Sample_label $HSP1_sample save_ save_2D_1H_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H COSY' _Sample_label $HSP1_sample save_ save_2D_1H_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H DQF-COSY' _Sample_label $HSP1_sample save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H DQF-COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_HSP1_cond _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4 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_HSP1_CS _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $HSP1_sample stop_ _Sample_conditions_label $HSP1_cond _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'HSP1, Hylaseptin' _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 GLY HA2 H 3.972 0.002 2 2 . 2 ILE H H 8.800 0.002 1 3 . 2 ILE HA H 4.080 0.002 1 4 . 2 ILE HB H 1.888 0.002 1 5 . 2 ILE HG12 H 1.584 0.002 1 6 . 2 ILE HG13 H 1.341 0.002 1 7 . 2 ILE HG2 H 1.013 0.002 1 8 . 2 ILE HD1 H 0.962 0.002 1 9 . 3 LEU H H 8.391 0.002 1 10 . 3 LEU HA H 4.191 0.002 1 11 . 3 LEU HB2 H 1.735 0.002 2 12 . 3 LEU HB3 H 1.595 0.002 2 13 . 3 LEU HD1 H 0.977 0.002 2 14 . 3 LEU HD2 H 0.915 0.002 2 15 . 4 ASP H H 7.465 0.002 1 16 . 4 ASP HA H 4.338 0.002 1 17 . 4 ASP HB2 H 2.835 0.002 2 18 . 4 ASP HB3 H 2.749 0.002 2 19 . 5 ALA H H 7.662 0.002 1 20 . 5 ALA HA H 4.197 0.002 1 21 . 5 ALA HB H 1.550 0.002 1 22 . 6 ILE H H 8.148 0.002 1 23 . 6 ILE HA H 3.723 0.002 1 24 . 6 ILE HB H 1.984 0.002 1 25 . 6 ILE HG12 H 1.778 0.002 1 26 . 6 ILE HG13 H 1.228 0.002 1 27 . 6 ILE HG2 H 1.144 0.002 1 28 . 6 ILE HD1 H 0.930 0.002 1 29 . 7 LYS H H 8.068 0.002 1 30 . 7 LYS HA H 3.957 0.002 1 31 . 7 LYS HB2 H 1.953 0.002 2 32 . 7 LYS HB3 H 1.907 0.002 2 33 . 7 LYS HG2 H 1.449 0.002 2 34 . 7 LYS HD2 H 1.731 0.002 2 35 . 7 LYS HE2 H 2.941 0.002 2 36 . 7 LYS HZ H 7.678 0.002 1 37 . 8 ALA H H 7.721 0.002 1 38 . 8 ALA HA H 4.173 0.002 1 39 . 8 ALA HB H 1.586 0.002 1 40 . 9 ILE H H 8.342 0.002 1 41 . 9 ILE HA H 3.731 0.002 1 42 . 9 ILE HB H 1.982 0.002 1 43 . 9 ILE HG12 H 1.841 0.002 1 44 . 9 ILE HG13 H 1.100 0.002 1 45 . 9 ILE HG2 H 1.144 0.002 1 46 . 9 ILE HD1 H 0.850 0.002 1 47 . 10 ALA H H 7.966 0.002 1 48 . 10 ALA HA H 4.220 0.002 1 49 . 10 ALA HB H 1.552 0.002 1 50 . 11 LYS H H 8.013 0.002 1 51 . 11 LYS HA H 4.115 0.002 1 52 . 11 LYS HB2 H 1.995 0.002 2 53 . 11 LYS HB3 H 1.750 0.002 2 54 . 11 LYS HG2 H 1.504 0.002 2 55 . 11 LYS HD2 H 1.596 0.002 2 56 . 11 LYS HE2 H 3.019 0.002 2 57 . 11 LYS HZ H 7.648 0.002 1 58 . 12 ALA H H 8.578 0.002 1 59 . 12 ALA HA H 4.057 0.002 1 60 . 12 ALA HB H 1.491 0.002 1 61 . 13 ALA H H 8.373 0.002 1 62 . 13 ALA HA H 4.268 0.002 1 63 . 13 ALA HB H 1.493 0.002 1 64 . 14 GLY H H 7.911 0.002 1 65 . 14 GLY HA2 H 3.958 0.002 2 stop_ save_ ######################## # Coupling constants # ######################## save_empaf_Jcoupling _Saveframe_category coupling_constants _Details . loop_ _Sample_label $HSP1_sample stop_ _Sample_conditions_label $HSP1_cond _Spectrometer_frequency_1H 500 _Mol_system_component_name 'HSP1, Hylaseptin' _Text_data_format . _Text_data . loop_ _Coupling_constant_ID _Coupling_constant_code _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_name _Coupling_constant_value _Coupling_constant_min_value _Coupling_constant_max_value _Coupling_constant_value_error 1 3JHNHA 2 ILE H 2 ILE HA 8.5 . . 0.2 2 3JHNHA 3 LEU H 3 LEU HA 7.8 . . 0.2 3 3JHNHA 4 ASP H 4 ASP HA 6.0 . . 0.2 4 3JHNHA 5 ALA H 5 ALA HA 6.8 . . 0.2 5 3JHNHA 6 ILE H 6 ILE HA 5.8 . . 0.2 6 3JHNHA 7 LYS H 7 LYS HA 6.4 . . 0.2 7 3JHNHA 8 ALA H 8 ALA HA 5.8 . . 0.2 8 3JHNHA 9 ILE H 9 ILE HA 6.5 . . 0.2 9 3JHNHA 10 ALA H 10 ALA HA 6.1 . . 0.2 10 3JHNHA 11 LYS H 11 LYS HA 5.9 . . 0.2 11 3JHNHA 12 ALA H 12 ALA HA 6.5 . . 0.2 12 3JHNHA 13 ALA H 13 ALA HA 6.1 . . 0.2 stop_ save_