data_26009 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Antimicrobial peptide protegrin PG-5 ; _BMRB_accession_number 26009 _BMRB_flat_file_name bmr26009.str _Entry_type original _Submission_date 2016-03-21 _Accession_date 2016-03-24 _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 Kolosova Olga A. . 2 Klochkova Evelina A. . 3 Aganov Albert V. . 4 Klochkov Vladimir V. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 107 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-03-17 update author 'update entry citation' 2017-01-26 update author 'update entry citation' 2016-09-29 original author 'original release' stop_ _Original_release_date 2016-09-29 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Oligomerization of the antimicrobial peptide Protegrin-5 in a membrane-mimicking environment. Structural studies by high-resolution NMR spectroscopy ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27589857 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Usachev Konstantin . . 2 Kolosova Olga . . 3 Klochkova Evelina . . 4 Aganov Albert . . 5 Klochkov Vladimir . . 6 Usachev Konstantin . . 7 Kolosova Olga . . 8 Klochkova Evelina . . 9 Aganov Albert . . 10 Klochkov Vladimir . . stop_ _Journal_abbreviation 'Eur. Biophy. J.' _Journal_name_full 'European Biophysics Journal' _Journal_volume 46 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 293 _Page_last 300 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Antimicrobial peptide protegrin PG-5' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Antimicrobial peptide protegrin PG-5' $PG-5 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_PG-5 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PG-5 _Molecular_mass 2106.591 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence ; RGGRLCYCRPRFCVCVGR ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 ARG 2 2 GLY 3 3 GLY 4 4 ARG 5 5 LEU 6 6 CYS 7 7 TYR 8 8 CYS 9 9 ARG 10 10 PRO 11 11 ARG 12 12 PHE 13 13 CYS 14 14 VAL 15 15 CYS 16 16 VAL 17 17 GLY 18 18 ARG 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 _Details $PG-5 'Sus scrofa' 9823 Eukaryota Metazoa Sus scrofa 'isolated from porcine leukocytes' 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 $PG-5 'chemical synthesis' . . . . . 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 $PG-5 3 mg/mL 'natural abundance' DPC 20 mg/mL '[U-99% 2H]' H2O 450 uL 'natural abundance' D2O 50 uL '[U-99% 2H]' stop_ save_ ############################ # Computer software used # ############################ 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_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'chemical shift calculation' 'peak picking' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' 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_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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 293 . 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 TSP H 1 'methyl protons' ppm 0.000 internal direct . . . 1.000000000 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 DQF-COSY' '2D 1H-1H NOESY' '2D 1H-1H TOCSY' 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 'Antimicrobial peptide protegrin PG-5' _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 3.971 0.000 . 2 1 1 ARG HB2 H 1.826 0.004 . 3 1 1 ARG HB3 H 1.826 0.004 . 4 1 1 ARG HD2 H 3.095 0.003 . 5 1 1 ARG HD3 H 3.095 0.003 . 6 1 1 ARG HE H 7.380 0.048 . 7 2 2 GLY H H 8.978 0.001 . 8 2 2 GLY HA2 H 3.894 0.000 . 9 2 2 GLY HA3 H 3.894 0.000 . 10 3 3 GLY H H 8.455 0.052 . 11 3 3 GLY HA2 H 3.894 0.037 . 12 3 3 GLY HA3 H 3.894 0.037 . 13 4 4 ARG H H 8.647 0.002 . 14 4 4 ARG HA H 4.202 0.058 . 15 4 4 ARG HB2 H 1.711 0.001 . 16 4 4 ARG HB3 H 1.711 0.001 . 17 4 4 ARG HG2 H 1.531 0.000 . 18 4 4 ARG HG3 H 1.531 0.000 . 19 4 4 ARG HD2 H 3.042 0.000 . 20 4 4 ARG HD3 H 3.042 0.000 . 21 4 4 ARG HE H 7.518 0.046 . 22 5 5 LEU H H 8.543 0.031 . 23 5 5 LEU HA H 4.214 0.059 . 24 5 5 LEU HB2 H 1.616 0.059 . 25 5 5 LEU HB3 H 1.616 0.059 . 26 5 5 LEU HG H 1.507 0.059 . 27 5 5 LEU HD1 H 0.769 0.001 . 28 5 5 LEU HD2 H 0.825 0.003 . 29 6 6 CYS H H 8.010 0.055 . 30 6 6 CYS HA H 4.279 0.040 . 31 6 6 CYS HB2 H 2.730 0.001 . 32 6 6 CYS HB3 H 2.730 0.001 . 33 7 7 TYR H H 8.073 0.002 . 34 7 7 TYR HA H 4.433 0.052 . 35 7 7 TYR HB2 H 2.818 0.004 . 36 7 7 TYR HB3 H 2.967 0.001 . 37 7 7 TYR HD1 H 7.046 0.055 . 38 7 7 TYR HD2 H 7.046 0.055 . 39 7 7 TYR HE1 H 6.739 0.057 . 40 7 7 TYR HE2 H 6.739 0.057 . 41 8 8 CYS H H 7.876 0.044 . 42 8 8 CYS HA H 4.349 0.003 . 43 8 8 CYS HB2 H 2.742 0.003 . 44 8 8 CYS HB3 H 2.742 0.003 . 45 9 9 ARG H H 8.402 0.002 . 46 9 9 ARG HA H 4.245 0.037 . 47 9 9 ARG HB2 H 1.636 0.000 . 48 9 9 ARG HB3 H 1.745 0.000 . 49 9 9 ARG HG2 H 1.519 0.000 . 50 9 9 ARG HG3 H 1.519 0.000 . 51 9 9 ARG HD2 H 3.027 0.001 . 52 9 9 ARG HD3 H 3.027 0.001 . 53 9 9 ARG HE H 7.525 0.048 . 54 10 10 PRO HA H 4.280 0.000 . 55 10 10 PRO HB2 H 1.930 0.000 . 56 10 10 PRO HB3 H 1.930 0.000 . 57 10 10 PRO HG2 H 1.643 0.001 . 58 10 10 PRO HG3 H 1.643 0.001 . 59 10 10 PRO HD2 H 3.458 0.002 . 60 10 10 PRO HD3 H 3.771 0.046 . 61 11 11 ARG H H 8.198 0.001 . 62 11 11 ARG HA H 4.069 0.004 . 63 11 11 ARG HB2 H 1.532 0.002 . 64 11 11 ARG HB3 H 1.667 0.000 . 65 11 11 ARG HG2 H 1.468 0.000 . 66 11 11 ARG HG3 H 1.468 0.000 . 67 11 11 ARG HD2 H 3.004 0.000 . 68 11 11 ARG HD3 H 3.004 0.000 . 69 11 11 ARG HE H 7.420 0.000 . 70 12 12 PHE H H 7.999 0.058 . 71 12 12 PHE HA H 4.454 0.001 . 72 12 12 PHE HB2 H 3.000 0.000 . 73 12 12 PHE HB3 H 3.060 0.000 . 74 12 12 PHE HD1 H 7.218 0.050 . 75 12 12 PHE HD2 H 7.218 0.050 . 76 12 12 PHE HE1 H 7.146 0.008 . 77 12 12 PHE HE2 H 7.146 0.008 . 78 13 13 CYS H H 8.197 0.001 . 79 13 13 CYS HA H 4.280 0.005 . 80 13 13 CYS HB2 H 2.777 0.002 . 81 13 13 CYS HB3 H 2.777 0.002 . 82 14 14 VAL H H 7.908 0.055 . 83 14 14 VAL HA H 4.018 0.051 . 84 14 14 VAL HB H 2.045 0.040 . 85 14 14 VAL HG1 H 0.845 0.003 . 86 14 14 VAL HG2 H 0.845 0.003 . 87 15 15 CYS H H 8.286 0.002 . 88 15 15 CYS HA H 4.350 0.002 . 89 15 15 CYS HB2 H 2.796 0.000 . 90 15 15 CYS HB3 H 2.796 0.000 . 91 16 16 VAL H H 7.947 0.057 . 92 16 16 VAL HA H 4.086 0.052 . 93 16 16 VAL HB H 2.052 0.049 . 94 16 16 VAL HG1 H 0.792 0.005 . 95 16 16 VAL HG2 H 0.792 0.005 . 96 17 17 GLY H H 8.327 0.002 . 97 17 17 GLY HA2 H 3.866 0.055 . 98 17 17 GLY HA3 H 3.866 0.055 . 99 18 18 ARG H H 8.015 0.044 . 100 18 18 ARG HA H 4.168 0.004 . 101 18 18 ARG HB2 H 1.790 0.004 . 102 18 18 ARG HB3 H 1.790 0.004 . 103 18 18 ARG HG2 H 1.500 0.000 . 104 18 18 ARG HG3 H 1.600 0.002 . 105 18 18 ARG HD2 H 3.053 0.001 . 106 18 18 ARG HD3 H 3.053 0.001 . 107 18 18 ARG HE H 7.419 0.042 . stop_ save_