data_20013 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Tertiary structure and lipid interactions of short recombinant antimicrobial peptide ; _BMRB_accession_number 20013 _BMRB_flat_file_name bmr20013.str _Entry_type original _Submission_date 2008-03-21 _Accession_date 2008-03-21 _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 Japelj Bostjan . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 76 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-05-23 update BMRB 'coordinate file not annotated' 2012-05-23 update BMRB 'update residue code' 2009-04-23 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 20012 'PFR peptide in SDS micelle' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Expression, purification and structural studies of a short antimicrobial peptide' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19026609 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zorko Mateja . . 2 Japelj Bostjan . . 3 Hafner-Bratkovica Iva . . 4 Jerala Roman . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_volume 1788 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 314 _Page_last 323 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'PFR peptide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'PFR peptide' $PFR_peptide 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_PFR_peptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PFR_peptide _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence PFWRIRIRRX loop_ _Residue_seq_code _Residue_label 1 PRO 2 PHE 3 TRP 4 ARG 5 ILE 6 ARG 7 ILE 8 ARG 9 ARG 10 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons HN1 HN1 H . 0 . ? HN2 HN2 H . 0 . ? N N N . 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 $PFR_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 $PFR_peptide 'recombinant technology' . . . . . 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 $PFR_peptide 1.8 mM 'natural abundance' DPC . mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_DYANA _Saveframe_category software _Name DYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _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 temperature 303 . K pH 5.1 . pH 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 water H 1 protons ppm 4.75 internal direct . . . 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 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 'PFR peptide' _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 PRO HA H 4.274 . . 2 1 1 PRO HB2 H 1.920 . . 3 1 1 PRO HB3 H 2.152 . . 4 1 1 PRO HD2 H 3.263 . . 5 1 1 PRO HD3 H 3.324 . . 6 1 1 PRO HG2 H 1.425 . . 7 1 1 PRO HG3 H 1.717 . . 8 2 2 PHE H H 8.986 . . 9 2 2 PHE HA H 4.438 . . 10 2 2 PHE HB2 H 3.094 . . 11 2 2 PHE HB3 H 3.094 . . 12 2 2 PHE HD1 H 7.241 . . 13 2 2 PHE HD2 H 7.241 . . 14 2 2 PHE HE1 H 7.426 . . 15 2 2 PHE HE2 H 7.426 . . 16 2 2 PHE HZ H 7.425 . . 17 3 3 TRP H H 7.421 . . 18 3 3 TRP HA H 4.480 . . 19 3 3 TRP HB2 H 3.078 . . 20 3 3 TRP HB3 H 3.201 . . 21 3 3 TRP HD1 H 7.177 . . 22 3 3 TRP HE1 H 10.702 . . 23 3 3 TRP HE3 H 7.230 . . 24 3 3 TRP HH2 H 7.122 . . 25 3 3 TRP HZ2 H 7.477 . . 26 3 3 TRP HZ3 H 6.983 . . 27 4 4 ARG H H 7.842 . . 28 4 4 ARG HA H 4.230 . . 29 4 4 ARG HB2 H 1.800 . . 30 4 4 ARG HB3 H 1.800 . . 31 4 4 ARG HD2 H 3.079 . . 32 4 4 ARG HD3 H 3.125 . . 33 4 4 ARG HE H 7.402 . . 34 4 4 ARG HG2 H 1.381 . . 35 4 4 ARG HG3 H 1.547 . . 36 5 5 ILE H H 7.690 . . 37 5 5 ILE HA H 4.116 . . 38 5 5 ILE HB H 1.867 . . 39 5 5 ILE HD1 H 0.890 . . 40 5 5 ILE HG12 H 1.184 . . 41 5 5 ILE HG13 H 1.514 . . 42 5 5 ILE HG2 H 0.907 . . 43 6 6 ARG H H 8.232 . . 44 6 6 ARG HA H 4.436 . . 45 6 6 ARG HB2 H 1.770 . . 46 6 6 ARG HB3 H 1.836 . . 47 6 6 ARG HD2 H 3.189 . . 48 6 6 ARG HD3 H 3.189 . . 49 6 6 ARG HE H 7.398 . . 50 6 6 ARG HG2 H 1.578 . . 51 6 6 ARG HG3 H 1.578 . . 52 7 7 ILE H H 8.217 . . 53 7 7 ILE HA H 4.172 . . 54 7 7 ILE HB H 1.917 . . 55 7 7 ILE HD1 H 0.904 . . 56 7 7 ILE HG12 H 1.221 . . 57 7 7 ILE HG13 H 1.530 . . 58 7 7 ILE HG2 H 0.920 . . 59 8 8 ARG H H 8.235 . . 60 8 8 ARG HA H 4.397 . . 61 8 8 ARG HB2 H 1.805 . . 62 8 8 ARG HB3 H 1.898 . . 63 8 8 ARG HD2 H 3.198 . . 64 8 8 ARG HD3 H 3.198 . . 65 8 8 ARG HE H 7.466 . . 66 8 8 ARG HG2 H 1.646 . . 67 8 8 ARG HG3 H 1.646 . . 68 9 9 ARG H H 8.405 . . 69 9 9 ARG HA H 4.278 . . 70 9 9 ARG HB2 H 1.781 . . 71 9 9 ARG HB3 H 1.901 . . 72 9 9 ARG HD2 H 3.200 . . 73 9 9 ARG HD3 H 3.200 . . 74 9 9 ARG HE H 7.465 . . 75 9 9 ARG HG2 H 1.656 . . 76 9 9 ARG HG3 H 1.656 . . stop_ save_