data_25212 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; High-resolution NMR structure of the protegrin-2 docked to DPC Micelles ; _BMRB_accession_number 25212 _BMRB_flat_file_name bmr25212.str _Entry_type original _Submission_date 2014-09-10 _Accession_date 2014-09-10 _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 Filippov Andrey V. . 2 Efimov Sergey V. . 3 Klochkov Vladimir V. . 4 Antzutkin Oleg N. . 5 Usachev Konstantin S. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 95 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-09-23 update BMRB 'update entry citation' 2014-12-08 original author 'original release' stop_ _Original_release_date 2016-09-23 save_ ############################# # Citation for this entry # ############################# save_High-resolution_NMR_structure_of_the_antimicrobial_peptide_protegrin-2_docked_to_DPC_Micelles _Saveframe_category entry_citation _Citation_full . _Citation_title ; High-resolution NMR structure of the antimicrobial peptide protegrin-2 docked to DPC Micelles ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25430060 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 A. A. . 4 Filippov Andrey V. . 5 Klochkov Vladimir V. . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_volume 61 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 227 _Page_last 234 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'protegrin-2 docked to DPC Micelles' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label PG-2 $PG-2 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-2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PG-2 _Molecular_mass 1952.423 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence ; RGGRLCYCRRRFCVCV ; 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 ARG 11 11 ARG 12 12 PHE 13 13 CYS 14 14 VAL 15 15 CYS 16 16 VAL 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 $PG-2 Human 9606 Eukaryota Metazoa Homo sapiens 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 $PG-2 'chemical synthesis' . . . . . ; solid-phase peptide synthesis, using amino acids protected by the 9- uorenylmethoxycarbonyl group and with reaction mixture conductivity control. Fmoc-protected amino acids of peptide synthesis grade were purchased from Applied Biosystems, Foster City, CA, USA ; stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_PG-2_sample _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $PG-2 4 mg 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % '[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' 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_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_Molmol _Saveframe_category software _Name Molmol _Version . loop_ _Vendor _Address _Electronic_address 'Koradi, Billeter and Wuthrich' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $PG-2_sample save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $PG-2_sample save_ save_2D_1H-1H_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $PG-2_sample 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 '3-(trimethylsilyl)-propionic-2,2,3,3 2H4 acid' 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-d4 H 1 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_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H COSY' stop_ loop_ _Sample_label $PG-2_sample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $TSP-d4 _Mol_system_component_name PG-2 _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 4.075 0.002 . 2 1 1 ARG HB2 H 1.924 0.004 . 3 1 1 ARG HB3 H 1.924 0.004 . 4 1 1 ARG HG2 H 1.669 0.004 . 5 1 1 ARG HG3 H 1.669 0.004 . 6 1 1 ARG HD2 H 3.196 0.004 . 7 1 1 ARG HD3 H 3.196 0.004 . 8 1 1 ARG HE H 7.403 0.007 . 9 2 2 GLY H H 8.946 0.005 . 10 2 2 GLY HA2 H 3.995 0.005 . 11 2 2 GLY HA3 H 3.995 0.005 . 12 3 3 GLY H H 8.333 0.006 . 13 3 3 GLY HA2 H 3.861 0.004 . 14 3 3 GLY HA3 H 3.861 0.004 . 15 4 4 ARG H H 8.283 0.008 . 16 4 4 ARG HA H 4.380 0.010 . 17 4 4 ARG HB2 H 1.738 0.004 . 18 4 4 ARG HB3 H 1.738 0.004 . 19 4 4 ARG HG2 H 1.596 0.007 . 20 4 4 ARG HG3 H 1.596 0.007 . 21 4 4 ARG HD2 H 3.105 0.008 . 22 4 4 ARG HD3 H 3.105 0.008 . 23 4 4 ARG HE H 7.266 0.006 . 24 5 5 LEU H H 8.486 0.013 . 25 5 5 LEU HA H 4.550 0.004 . 26 5 5 LEU HB2 H 1.738 0.005 . 27 5 5 LEU HB3 H 1.738 0.005 . 28 5 5 LEU HG H 1.579 0.007 . 29 5 5 LEU HD1 H 0.897 0.027 . 30 5 5 LEU HD2 H 0.897 0.027 . 31 6 6 CYS H H 8.298 0.008 . 32 6 6 CYS HA H 5.694 0.017 . 33 6 6 CYS HB2 H 2.853 0.012 . 34 6 6 CYS HB3 H 2.661 0.006 . 35 7 7 TYR H H 8.184 0.009 . 36 7 7 TYR HA H 4.675 0.005 . 37 7 7 TYR HB2 H 2.837 0.010 . 38 7 7 TYR HB3 H 2.837 0.010 . 39 7 7 TYR HD1 H 7.001 0.004 . 40 7 7 TYR HD2 H 7.001 0.004 . 41 7 7 TYR HE1 H 6.695 0.005 . 42 7 7 TYR HE2 H 6.695 0.005 . 43 8 8 CYS H H 9.155 0.006 . 44 8 8 CYS HA H 5.695 0.012 . 45 8 8 CYS HB2 H 2.858 0.007 . 46 8 8 CYS HB3 H 2.661 0.005 . 47 9 9 ARG H H 9.231 0.012 . 48 9 9 ARG HA H 4.347 0.006 . 49 9 9 ARG HB2 H 1.845 0.006 . 50 9 9 ARG HB3 H 1.845 0.006 . 51 9 9 ARG HG2 H 1.609 0.008 . 52 9 9 ARG HG3 H 1.609 0.008 . 53 9 9 ARG HD2 H 3.300 0.006 . 54 9 9 ARG HD3 H 3.300 0.006 . 55 9 9 ARG HE H 7.754 0.006 . 56 10 10 ARG H H 9.236 0.007 . 57 10 10 ARG HA H 3.774 0.007 . 58 10 10 ARG HB2 H 2.044 0.007 . 59 10 10 ARG HB3 H 2.044 0.007 . 60 10 10 ARG HG2 H 1.655 0.008 . 61 10 10 ARG HG3 H 1.655 0.008 . 62 10 10 ARG HD2 H 3.273 0.008 . 63 10 10 ARG HD3 H 3.273 0.008 . 64 10 10 ARG HE H 7.610 0.003 . 65 11 11 ARG H H 8.125 0.008 . 66 11 11 ARG HA H 3.971 0.014 . 67 11 11 ARG HB2 H 2.031 0.007 . 68 11 11 ARG HB3 H 1.865 0.008 . 69 11 11 ARG HG2 H 1.368 0.009 . 70 11 11 ARG HG3 H 1.368 0.009 . 71 11 11 ARG HD2 H 3.101 0.009 . 72 11 11 ARG HD3 H 3.101 0.009 . 73 11 11 ARG HE H 7.257 0.008 . 74 12 12 PHE H H 8.478 0.007 . 75 12 12 PHE HA H 3.862 0.007 . 76 12 12 PHE HB2 H 2.946 0.004 . 77 12 12 PHE HB3 H 2.675 0.004 . 78 13 13 CYS H H 8.807 0.004 . 79 13 13 CYS HA H 5.674 0.021 . 80 13 13 CYS HB2 H 2.945 0.014 . 81 13 13 CYS HB3 H 2.685 0.006 . 82 14 14 VAL H H 8.945 0.006 . 83 14 14 VAL HA H 4.380 0.007 . 84 14 14 VAL HB H 2.038 0.008 . 85 14 14 VAL HG1 H 1.006 0.011 . 86 14 14 VAL HG2 H 1.006 0.011 . 87 15 15 CYS H H 8.858 0.005 . 88 15 15 CYS HA H 5.565 0.012 . 89 15 15 CYS HB2 H 2.857 0.007 . 90 15 15 CYS HB3 H 2.654 0.006 . 91 16 16 VAL H H 8.813 0.009 . 92 16 16 VAL HA H 4.338 0.007 . 93 16 16 VAL HB H 2.238 0.005 . 94 16 16 VAL HG1 H 0.952 0.009 . 95 16 16 VAL HG2 H 0.952 0.009 . stop_ save_