data_15050 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; piscidin solution structure in presence of DPC micelles ; _BMRB_accession_number 15050 _BMRB_flat_file_name bmr15050.str _Entry_type original _Submission_date 2006-11-22 _Accession_date 2006-11-22 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'NMR_star and NMR-derived constraints' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Campagna Sylvie . . 2 Saint Nathalie . . 3 Molle Gerard . . 4 Aumelas Andre . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 128 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-11-16 original BMRB . stop_ _Original_release_date 2015-11-16 save_ ############################# # Citation for this entry # ############################# save_citation-1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure and mechanism of action of the antimicrobial peptide piscidin ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17253775 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Campagna Sylvie . . 2 Saint Nathalie . . 3 Molle Gerard . . 4 Aumelas Andre . . stop_ _Journal_abbreviation Biochemistry _Journal_volume 46 _Journal_issue 7 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1771 _Page_last 1778 _Year 2007 _Details . loop_ _Keyword 'DPC micelles' NMR alpha-helix 'antimicrobial peptide' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name piscidin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label piscidin-1 $piscidin-1 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_piscidin-1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common piscidin-1 _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function 'Antimicrobial peptide' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 23 _Mol_residue_sequence ; FFHHIFRGIVHVGKTIHRLV TGX ; loop_ _Residue_seq_code _Residue_label 1 PHE 2 PHE 3 HIS 4 HIS 5 ILE 6 PHE 7 ARG 8 GLY 9 ILE 10 VAL 11 HIS 12 VAL 13 GLY 14 LYS 15 THR 16 ILE 17 HIS 18 ARG 19 LEU 20 VAL 21 THR 22 GLY 23 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-18 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 19454 Moronecidin 95.65 23 100.00 100.00 2.41e-04 BMRB 19455 Moronecidin 95.65 23 100.00 100.00 2.41e-04 PDB 2JOS "Solution Structure Of Piscidin In Presence Of Dpc Micelles" 95.65 22 100.00 100.00 2.42e-04 PDB 2MCU "Solid-state Nmr Structure Of Piscidin 1 In Aligned 3:1 Phosphatidylcholine/phosphoglycerol Lipid Bilayers" 95.65 23 100.00 100.00 2.41e-04 PDB 2MCV "Solid-state Nmr Structure Of Piscidin 1 In Aligned 1:1 Phosphatidylethanolamine/phosphoglycerol Lipid Bilayers" 95.65 23 100.00 100.00 2.41e-04 PDB 2OJM "Solution Structure And Cell Selectivity Of Piscidin 1 And Its Analogues" 95.65 22 100.00 100.00 2.42e-04 GB AAL49496 "moronecidin precursor [Morone saxatilis]" 95.65 79 100.00 100.00 6.63e-06 GB AAL57319 "moronecidin precursor [Morone saxatilis]" 95.65 79 100.00 100.00 6.63e-06 SP Q8UUG0 "RecName: Full=Moronecidin; AltName: Full=Piscidin-1; Flags: Precursor" 95.65 79 100.00 100.00 6.63e-06 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'AMINO GROUP' _BMRB_code . _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Oct 4 21:38:37 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 HN1 ? ? SING N HN2 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $piscidin-1 'striped bass' 34816 Eukaryota Metazoa Morone saxatilis 'The peptide has been isolated from the mast cells of striped bass. We have studied the synthetic peptide.' 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 $piscidin-1 'chemical synthesis' . . . . . 'The peptide has been synthesized' 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 $piscidin-1 1 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details 'Piscidin is in presence of 39 mM of DPC' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $piscidin-1 1 mM 'natural abundance' DPC 39 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 'chemical shift assignment' collection processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details Cryoprobe save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.0 0.01 pH pressure 1 0.01 atm temperature 300 0.01 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 'Chemical shifts were measure for the sample 2 in presence od DPC micelles' 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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label DSS H 1 'methyl protons' ppm 0 internal direct . . . 1.0 $citation-1 $citation-1 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-1H COSY' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name piscidin-1 _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 PHE HA H 4.14 0.01 1 2 1 1 PHE HB2 H 3.22 0.01 2 3 1 1 PHE HB3 H 3.06 0.01 2 4 1 1 PHE HD1 H 7.30 0.01 1 5 1 1 PHE HD2 H 7.30 0.01 1 6 1 1 PHE HE1 H 7.10 0.01 3 7 1 1 PHE HE2 H 7.30 0.01 3 8 1 1 PHE HZ H 7.10 0.01 1 9 2 2 PHE HA H 4.31 0.01 1 10 2 2 PHE HB2 H 3.09 0.01 2 11 2 2 PHE HB3 H 2.88 0.01 2 12 2 2 PHE HD1 H 7.40 0.01 1 13 2 2 PHE HD2 H 7.40 0.01 1 14 2 2 PHE HE1 H 7.40 0.01 1 15 2 2 PHE HE2 H 7.40 0.01 1 16 2 2 PHE HZ H 7.20 0.01 1 17 3 3 HIS HA H 4.42 0.01 1 18 3 3 HIS HB2 H 3.13 0.01 1 19 3 3 HIS HB3 H 3.13 0.01 1 20 4 4 HIS H H 8.29 0.01 1 21 4 4 HIS HA H 4.56 0.01 1 22 4 4 HIS HB2 H 3.26 0.01 1 23 4 4 HIS HB3 H 3.26 0.01 1 24 5 5 ILE H H 8.10 0.01 1 25 5 5 ILE HA H 3.91 0.01 1 26 5 5 ILE HB H 1.91 0.01 1 27 5 5 ILE HG12 H 1.42 0.01 2 28 5 5 ILE HG13 H 1.10 0.01 2 29 5 5 ILE HG2 H 0.80 0.01 1 30 5 5 ILE HD1 H 0.80 0.01 1 31 6 6 PHE H H 8.47 0.01 1 32 6 6 PHE HA H 4.33 0.01 1 33 6 6 PHE HB2 H 3.18 0.01 1 34 6 6 PHE HB3 H 3.18 0.01 1 35 6 6 PHE HD1 H 7.40 0.01 1 36 6 6 PHE HD2 H 7.40 0.01 1 37 6 6 PHE HE1 H 7.40 0.01 1 38 6 6 PHE HE2 H 7.40 0.01 1 39 6 6 PHE HZ H 7.10 0.01 1 40 7 7 ARG H H 8.29 0.01 1 41 7 7 ARG HA H 3.93 0.01 1 42 7 7 ARG HB2 H 1.91 0.01 1 43 7 7 ARG HB3 H 1.91 0.01 1 44 7 7 ARG HG2 H 1.77 0.01 2 45 7 7 ARG HG3 H 1.63 0.01 2 46 7 7 ARG HD2 H 3.17 0.01 1 47 7 7 ARG HD3 H 3.17 0.01 1 48 8 8 GLY H H 8.17 0.01 1 49 8 8 GLY HA2 H 3.98 0.01 2 50 8 8 GLY HA3 H 3.80 0.01 2 51 9 9 ILE H H 8.27 0.01 1 52 9 9 ILE HA H 3.74 0.01 1 53 9 9 ILE HB H 2.03 0.01 1 54 9 9 ILE HG12 H 1.82 0.01 2 55 9 9 ILE HG13 H 1.10 0.01 2 56 9 9 ILE HG2 H 0.79 0.01 1 57 9 9 ILE HD1 H 0.86 0.01 1 58 10 10 VAL H H 8.06 0.01 1 59 10 10 VAL HA H 3.57 0.01 1 60 10 10 VAL HB H 2.04 0.01 1 61 10 10 VAL HG1 H 0.91 0.01 2 62 10 10 VAL HG2 H 0.80 0.01 2 63 11 11 HIS H H 8.14 0.01 1 64 11 11 HIS HA H 4.42 0.01 1 65 11 11 HIS HB2 H 3.45 0.01 2 66 11 11 HIS HB3 H 3.37 0.01 2 67 12 12 VAL H H 8.45 0.01 1 68 12 12 VAL HA H 3.68 0.01 1 69 12 12 VAL HB H 2.29 0.01 1 70 12 12 VAL HG1 H 1.13 0.01 2 71 12 12 VAL HG2 H 0.95 0.01 2 72 13 13 GLY H H 8.85 0.01 1 73 13 13 GLY HA2 H 3.75 0.01 2 74 13 13 GLY HA3 H 3.69 0.01 2 75 14 14 LYS H H 8.59 0.01 1 76 14 14 LYS HA H 4.07 0.01 1 77 14 14 LYS HB2 H 1.92 0.01 1 78 14 14 LYS HB3 H 1.92 0.01 1 79 14 14 LYS HG2 H 1.45 0.01 1 80 14 14 LYS HG3 H 1.45 0.01 1 81 14 14 LYS HD2 H 1.69 0.01 1 82 14 14 LYS HD3 H 1.69 0.01 1 83 14 14 LYS HE2 H 3.00 0.01 1 84 14 14 LYS HE3 H 3.00 0.01 1 85 15 15 THR H H 8.04 0.01 1 86 15 15 THR HA H 3.94 0.01 1 87 15 15 THR HB H 4.36 0.01 1 88 15 15 THR HG2 H 1.24 0.01 1 89 16 16 ILE H H 8.54 0.01 1 90 16 16 ILE HA H 3.65 0.01 1 91 16 16 ILE HB H 1.99 0.01 1 92 16 16 ILE HG12 H 1.85 0.01 2 93 16 16 ILE HG13 H 1.13 0.01 2 94 16 16 ILE HG2 H 0.81 0.01 1 95 16 16 ILE HD1 H 0.96 0.01 1 96 17 17 HIS H H 8.59 0.01 1 97 17 17 HIS HA H 4.13 0.01 1 98 17 17 HIS HB2 H 3.42 0.01 1 99 17 17 HIS HB3 H 3.22 0.01 1 100 18 18 ARG H H 8.08 0.01 1 101 18 18 ARG HA H 3.95 0.01 1 102 18 18 ARG HB2 H 2.05 0.01 2 103 18 18 ARG HB3 H 1.99 0.01 2 104 18 18 ARG HG2 H 1.71 0.01 2 105 18 18 ARG HG3 H 1.63 0.01 2 106 18 18 ARG HD2 H 3.27 0.01 2 107 18 18 ARG HD3 H 3.30 0.01 2 108 19 19 LEU H H 8.08 0.01 1 109 19 19 LEU HA H 4.14 0.01 1 110 19 19 LEU HB2 H 1.95 0.01 1 111 19 19 LEU HB3 H 1.95 0.01 1 112 19 19 LEU HG H 1.57 0.01 1 113 19 19 LEU HD1 H 0.91 0.01 1 114 19 19 LEU HD2 H 0.91 0.01 1 115 20 20 VAL H H 8.08 0.01 1 116 20 20 VAL HA H 3.95 0.01 1 117 20 20 VAL HB H 2.21 0.01 1 118 20 20 VAL HG1 H 1.05 0.01 2 119 20 20 VAL HG2 H 0.96 0.01 2 120 21 21 THR H H 7.73 0.01 1 121 21 21 THR HA H 4.31 0.01 1 122 21 21 THR HB H 4.24 0.01 1 123 21 21 THR HG2 H 1.1 0.01 1 124 22 22 GLY H H 7.99 0.01 1 125 22 22 GLY HA2 H 4.01 0.01 2 126 22 22 GLY HA3 H 3.90 0.01 2 127 23 23 NH2 HN1 H 7.44 0.01 1 128 23 23 NH2 HN2 H 7.27 0.01 1 stop_ save_