data_25474 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of Protegrin-3 (PG3) in the presence of DPC micelles ; _BMRB_accession_number 25474 _BMRB_flat_file_name bmr25474.str _Entry_type original _Submission_date 2015-02-06 _Accession_date 2015-02-06 _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 Usachev K. S. . 2 Efimov S. V. . 3 Kolosova O. V. . 4 Klochkova E. A. . 5 Aganov A. V. . 6 Klochkov V. V. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 110 "13C chemical shifts" 56 "15N chemical shifts" 14 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-02-11 update BMRB 'update entry citation' 2015-03-23 original author 'original release' stop_ _Original_release_date 2016-02-11 save_ ############################# # Citation for this entry # ############################# save_Protegrin-3_monomer _Saveframe_category entry_citation _Citation_full . _Citation_title ; Antimicrobial peptide protegrin-3 adopt an antiparallel dimer in the presence of DPC micelles: a high-resolution NMR study ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25786621 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Usachev Konstantin S. . 2 Efimov Sergey V. . 3 Kolosova Olga A. . 4 Klochkova Evelina A. . 5 Aganov Albert V. . 6 Klochkov Vladimir V. . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_volume 62 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 71 _Page_last 79 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Protegrin-3 (PG3)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Protegrin-3 (PG3)' $PG3_monomer 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_PG3_monomer _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PG3_monomer _Molecular_mass 2066.527 _Mol_thiol_state 'all disulfide bond' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence ; RGGGLCYCRRRFCVCVGR ; loop_ _Residue_seq_code _Residue_label 1 ARG 2 GLY 3 GLY 4 GLY 5 LEU 6 CYS 7 TYR 8 CYS 9 ARG 10 ARG 11 ARG 12 PHE 13 CYS 14 VAL 15 CYS 16 VAL 17 GLY 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 $PG3_monomer . . . . . . 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 $PG3_monomer '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 $PG3_monomer 3 mg 'natural abundance' TSP 0.01 % '[U-99% 2H]' DPC 20 mg '[U-99% 2H]' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ 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_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 ; All data were acquired at 700 MHz (Bruker Avance III HD) NMR spectrometer equipped with quadruple resonance (1H, 13C, 15N and 31P) 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_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _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_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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_TSP-d4 _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 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-1H COSY' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-15N HSQC' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $TSP-d4 _Mol_system_component_name 'Protegrin-3 (PG3)' _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 4.028 . . 2 1 1 ARG HB2 H 1.875 . . 3 1 1 ARG HB3 H 1.875 . . 4 1 1 ARG HG2 H 1.624 . . 5 1 1 ARG HG3 H 1.525 . . 6 1 1 ARG HD2 H 3.140 . . 7 1 1 ARG HD3 H 3.140 . . 8 1 1 ARG HE H 7.348 . . 9 1 1 ARG C C 170.168 . . 10 1 1 ARG CA C 52.990 . . 11 1 1 ARG CB C 28.051 . . 12 1 1 ARG CG C 23.563 . . 13 1 1 ARG CD C 40.518 . . 14 2 2 GLY H H 8.943 . . 15 2 2 GLY HA2 H 4.017 . . 16 2 2 GLY HA3 H 4.017 . . 17 2 2 GLY CA C 42.609 . . 18 2 2 GLY N N 111.641 . . 19 3 3 GLY H H 8.482 . . 20 3 3 GLY HA2 H 3.940 . . 21 3 3 GLY HA3 H 3.940 . . 22 3 3 GLY CA C 42.733 . . 23 3 3 GLY N N 108.976 . . 24 4 4 GLY H H 8.824 . . 25 4 4 GLY HA2 H 3.869 . . 26 4 4 GLY HA3 H 3.869 . . 27 4 4 GLY CA C 43.706 . . 28 4 4 GLY N N 110.406 . . 29 5 5 LEU H H 8.661 . . 30 5 5 LEU HA H 4.130 . . 31 5 5 LEU HB2 H 1.672 . . 32 5 5 LEU HB3 H 1.672 . . 33 5 5 LEU HG H 1.541 . . 34 5 5 LEU HD1 H 0.885 . . 35 5 5 LEU HD2 H 0.832 . . 36 5 5 LEU CA C 54.437 . . 37 5 5 LEU CB C 39.029 . . 38 5 5 LEU CG C 24.458 . . 39 5 5 LEU CD1 C 22.409 . . 40 5 5 LEU CD2 C 21.429 . . 41 5 5 LEU N N 122.857 . . 42 6 6 CYS H H 8.313 . . 43 6 6 CYS HA H 4.642 . . 44 6 6 CYS HB2 H 2.870 . . 45 6 6 CYS HB3 H 2.870 . . 46 6 6 CYS CA C 58.782 . . 47 6 6 CYS CB C 24.366 . . 48 6 6 CYS N N 118.749 . . 49 7 7 TYR H H 8.014 . . 50 7 7 TYR HA H 4.233 . . 51 7 7 TYR HB2 H 3.068 . . 52 7 7 TYR HB3 H 3.068 . . 53 7 7 TYR HD1 H 7.052 . . 54 7 7 TYR HD2 H 7.052 . . 55 7 7 TYR HE1 H 6.709 . . 56 7 7 TYR HE2 H 6.709 . . 57 7 7 TYR CA C 57.821 . . 58 7 7 TYR CB C 40.694 . . 59 7 7 TYR CD1 C 130.553 . . 60 7 7 TYR CD2 C 130.553 . . 61 7 7 TYR CE1 C 115.426 . . 62 7 7 TYR CE2 C 115.426 . . 63 7 7 TYR N N 120.140 . . 64 8 8 CYS H H 8.100 . . 65 8 8 CYS HA H 4.032 . . 66 8 8 CYS HB2 H 3.012 . . 67 8 8 CYS HB3 H 2.688 . . 68 8 8 CYS CA C 52.871 . . 69 8 8 CYS CB C 24.840 . . 70 8 8 CYS N N 117.450 . . 71 9 9 ARG H H 8.331 . . 72 9 9 ARG HA H 3.935 . . 73 9 9 ARG HB2 H 1.919 . . 74 9 9 ARG HB3 H 1.759 . . 75 9 9 ARG HG2 H 1.588 . . 76 9 9 ARG HG3 H 1.588 . . 77 9 9 ARG HD2 H 3.096 . . 78 9 9 ARG HE H 7.493 . . 79 9 9 ARG HH21 H 7.139 . . 80 9 9 ARG CA C 56.412 . . 81 9 9 ARG CB C 27.467 . . 82 9 9 ARG CG C 24.681 . . 83 9 9 ARG CD C 40.666 . . 84 9 9 ARG N N 120.000 . . 85 10 10 ARG H H 7.900 . . 86 10 10 ARG HA H 4.036 . . 87 10 10 ARG HB2 H 1.757 . . 88 10 10 ARG HB3 H 1.757 . . 89 10 10 ARG HG2 H 1.606 . . 90 10 10 ARG HG3 H 1.522 . . 91 10 10 ARG HD2 H 3.093 . . 92 10 10 ARG HD3 H 3.093 . . 93 10 10 ARG HE H 7.214 . . 94 10 10 ARG HH21 H 7.214 . . 95 10 10 ARG CA C 55.596 . . 96 10 10 ARG CB C 27.475 . . 97 10 10 ARG CG C 23.639 . . 98 10 10 ARG CD C 40.531 . . 99 10 10 ARG NE N 84.825 . . 100 11 11 ARG H H 7.957 . . 101 11 11 ARG HA H 3.994 . . 102 11 11 ARG HB2 H 1.758 . . 103 11 11 ARG HB3 H 1.758 . . 104 11 11 ARG HG2 H 1.526 . . 105 11 11 ARG HG3 H 1.247 . . 106 11 11 ARG HD2 H 2.969 . . 107 11 11 ARG HD3 H 2.874 . . 108 11 11 ARG HE H 7.398 . . 109 11 11 ARG HH11 H 6.709 . . 110 11 11 ARG HH12 H 6.709 . . 111 11 11 ARG HH21 H 6.805 . . 112 11 11 ARG HH22 H 6.805 . . 113 11 11 ARG CA C 54.347 . . 114 11 11 ARG CB C 27.475 . . 115 11 11 ARG CG C 24.055 . . 116 11 11 ARG CD C 39.937 . . 117 11 11 ARG N N 117.419 . . 118 12 12 PHE H H 8.138 . . 119 12 12 PHE HA H 4.348 . . 120 12 12 PHE HB2 H 3.187 . . 121 12 12 PHE HB3 H 2.982 . . 122 12 12 PHE HD1 H 7.054 . . 123 12 12 PHE HD2 H 7.054 . . 124 12 12 PHE HE1 H 7.139 . . 125 12 12 PHE HE2 H 7.139 . . 126 12 12 PHE CA C 58.491 . . 127 12 12 PHE CB C 36.982 . . 128 12 12 PHE CD1 C 126.584 . . 129 12 12 PHE CD2 C 126.584 . . 130 12 12 PHE CE1 C 129.118 . . 131 12 12 PHE CE2 C 129.118 . . 132 13 13 CYS H H 8.047 . . 133 13 13 CYS HA H 4.155 . . 134 13 13 CYS HB2 H 2.961 . . 135 13 13 CYS HB3 H 2.887 . . 136 13 13 CYS CB C 24.426 . . 137 13 13 CYS N N 119.944 . . 138 14 14 VAL H H 7.836 . . 139 14 14 VAL HA H 3.932 . . 140 14 14 VAL HB H 2.059 . . 141 14 14 VAL HG1 H 0.923 . . 142 14 14 VAL HG2 H 0.872 . . 143 14 14 VAL CA C 61.054 . . 144 14 14 VAL CB C 29.860 . . 145 14 14 VAL CG1 C 18.766 . . 146 15 15 CYS H H 8.045 . . 147 15 15 CYS HA H 4.275 . . 148 15 15 CYS HB2 H 2.849 . . 149 15 15 CYS HB3 H 2.809 . . 150 15 15 CYS CA C 57.856 . . 151 15 15 CYS CB C 25.187 . . 152 15 15 CYS N N 117.212 . . 153 16 16 VAL H H 7.743 . . 154 16 16 VAL HA H 4.075 . . 155 16 16 VAL HB H 2.033 . . 156 16 16 VAL HG1 H 0.723 . . 157 16 16 VAL HG2 H 0.723 . . 158 16 16 VAL CA C 59.486 . . 159 16 16 VAL CB C 29.632 . . 160 16 16 VAL CG1 C 18.763 . . 161 16 16 VAL CG2 C 17.658 . . 162 17 17 GLY H H 8.001 . . 163 17 17 GLY HA2 H 3.859 . . 164 17 17 GLY HA3 H 3.859 . . 165 17 17 GLY CA C 42.780 . . 166 17 17 GLY N N 110.355 . . 167 18 18 ARG H H 7.871 . . 168 18 18 ARG HA H 4.244 . . 169 18 18 ARG HB2 H 1.847 . . 170 18 18 ARG HB3 H 1.847 . . 171 18 18 ARG HG2 H 1.596 . . 172 18 18 ARG HG3 H 1.530 . . 173 18 18 ARG HD2 H 3.096 . . 174 18 18 ARG HD3 H 3.096 . . 175 18 18 ARG HE H 7.349 . . 176 18 18 ARG CA C 53.059 . . 177 18 18 ARG CB C 28.539 . . 178 18 18 ARG CG C 24.656 . . 179 18 18 ARG CD C 40.640 . . 180 18 18 ARG N N 121.880 . . stop_ save_