data_30524 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of Database designed and improved anti-Staphylococcal peptide DFT503 bound to micelles ; _BMRB_accession_number 30524 _BMRB_flat_file_name bmr30524.str _Entry_type original _Submission_date 2018-09-25 _Accession_date 2018-09-25 _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 Wang G. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 69 "13C chemical shifts" 14 "15N chemical shifts" 13 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-07-09 update BMRB 'update entry citation' 2019-06-13 original author 'original release' stop_ _Original_release_date 2018-10-18 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Low cationicity is important for systemic in vivo efficacy of database-derived peptides against drug-resistant Gram-positive pathogens ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 31209048 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mishra B. . . 2 Narayana J. L. . 3 Lushnikova T. . . 4 Wang X. . . 5 Wang G. . . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_name_full 'Proceedings of the National Academy of Sciences of the United States of America' _Journal_volume 116 _Journal_issue 27 _Journal_ISSN 1091-6490 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 13517 _Page_last 13522 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Anti-Staphylococcal peptide DFT503' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass 1337.716 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence ; GLSLLLSLGLKLLX ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 LEU 3 SER 4 LEU 5 LEU 6 LEU 7 SER 8 LEU 9 GLY 10 LEU 11 LYS 12 LEU 13 LEU 14 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 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 $entity_1 . 32630 . . synthetic construct 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 $entity_1 'chemical synthesis' . . . . . 'Chemical synthesis' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelle _Details '2 mM DFT503, 122 mM SDS, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2 mM 'natural abundance' SDS 122 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger A. T. et.al.' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name PIPP _Version . loop_ _Vendor _Address _Electronic_address Garrett . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_DQF-COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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 pH 5.5 0.1 pH pressure 1 0.01 atm temperature 298 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Saveframe_category chemical_shift_reference _Details 'Relative to DSS' 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 4.78 external indirect . . . 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_assigned_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D 1H-15N HSQC' '2D 1H-13C HSQC' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_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 GLY HA2 H 4.0460 . . 2 1 1 GLY HA3 H 3.9890 . . 3 1 1 GLY CA C 43.7066 . . 4 2 2 LEU H H 8.6889 . . 5 2 2 LEU HA H 4.3275 . . 6 2 2 LEU HB2 H 1.8220 . . 7 2 2 LEU HB3 H 1.8220 . . 8 2 2 LEU HG H 1.7160 . . 9 2 2 LEU HD1 H 1.0170 . . 10 2 2 LEU HD2 H 0.9620 . . 11 2 2 LEU CA C 56.7473 . . 12 2 2 LEU N N 121.3643 . . 13 3 3 SER H H 8.4800 . . 14 3 3 SER HA H 4.1415 . . 15 3 3 SER HB2 H 4.0230 . . 16 3 3 SER HB3 H 4.0230 . . 17 3 3 SER CA C 61.5810 . . 18 3 3 SER CB C 62.7985 . . 19 3 3 SER N N 114.5444 . . 20 4 4 LEU H H 8.0856 . . 21 4 4 LEU HA H 4.2475 . . 22 4 4 LEU HB2 H 1.8560 . . 23 4 4 LEU HB3 H 1.7190 . . 24 4 4 LEU CA C 55.7954 . . 25 4 4 LEU N N 123.7161 . . 26 5 5 LEU H H 7.7153 . . 27 5 5 LEU HA H 4.0565 . . 28 5 5 LEU HB2 H 1.8530 . . 29 5 5 LEU HB3 H 1.6550 . . 30 5 5 LEU CA C 58.1391 . . 31 5 5 LEU N N 117.9629 . . 32 6 6 LEU H H 7.8267 . . 33 6 6 LEU HA H 4.0955 . . 34 6 6 LEU HB2 H 1.7630 . . 35 6 6 LEU HB3 H 1.7630 . . 36 6 6 LEU HD1 H 0.9720 . . 37 6 6 LEU HD2 H 0.9720 . . 38 6 6 LEU CA C 58.2942 . . 39 6 6 LEU N N 117.6811 . . 40 7 7 SER H H 7.9916 . . 41 7 7 SER HA H 4.1865 . . 42 7 7 SER HB2 H 4.0670 . . 43 7 7 SER HB3 H 4.0670 . . 44 7 7 SER CA C 62.1019 . . 45 7 7 SER N N 113.3354 . . 46 8 8 LEU H H 8.1900 . . 47 8 8 LEU HA H 4.1720 . . 48 8 8 LEU HB2 H 1.8920 . . 49 8 8 LEU HB3 H 1.8920 . . 50 8 8 LEU CA C 57.8193 . . 51 8 8 LEU N N 122.3704 . . 52 9 9 GLY H H 8.5477 . . 53 9 9 GLY HA2 H 3.7005 . . 54 9 9 GLY HA3 H 3.7005 . . 55 9 9 GLY CA C 47.8772 . . 56 9 9 GLY N N 106.7604 . . 57 10 10 LEU H H 8.4026 . . 58 10 10 LEU HA H 4.1005 . . 59 10 10 LEU HB2 H 1.8800 . . 60 10 10 LEU HB3 H 1.8800 . . 61 10 10 LEU CA C 58.4494 . . 62 10 10 LEU N N 119.8174 . . 63 11 11 LYS H H 7.7730 . . 64 11 11 LYS HA H 4.1105 . . 65 11 11 LYS HB2 H 2.0565 . . 66 11 11 LYS HB3 H 2.0565 . . 67 11 11 LYS HG2 H 1.6430 . . 68 11 11 LYS HG3 H 1.4940 . . 69 11 11 LYS HD2 H 1.7340 . . 70 11 11 LYS HD3 H 1.7340 . . 71 11 11 LYS HE2 H 3.0260 . . 72 11 11 LYS HE3 H 3.0260 . . 73 11 11 LYS HZ H 7.4921 . . 74 11 11 LYS CA C 58.2294 . . 75 11 11 LYS N N 119.4055 . . 76 12 12 LEU H H 8.0052 . . 77 12 12 LEU HA H 4.2160 . . 78 12 12 LEU HB2 H 1.9160 . . 79 12 12 LEU HB3 H 1.9160 . . 80 12 12 LEU HG H 1.6210 . . 81 12 12 LEU HD1 H 0.9470 . . 82 12 12 LEU HD2 H 0.9470 . . 83 12 12 LEU CA C 57.1360 . . 84 12 12 LEU N N 118.3065 . . 85 13 13 LEU H H 7.9325 . . 86 13 13 LEU HA H 4.2455 . . 87 13 13 LEU HB2 H 1.8330 . . 88 13 13 LEU HB3 H 1.8330 . . 89 13 13 LEU HG H 1.6490 . . 90 13 13 LEU HD1 H 0.9390 . . 91 13 13 LEU HD2 H 0.9390 . . 92 13 13 LEU CA C 57.8058 . . 93 13 13 LEU N N 118.0258 . . 94 14 14 NH2 N N 104.6423 . . 95 14 14 NH2 HN1 H 7.1830 . . 96 14 14 NH2 HN2 H 6.9760 . . stop_ save_