data_25751 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Disulphide linked homodimer of designed antimicrobial peptide VG16KRKP ; _BMRB_accession_number 25751 _BMRB_flat_file_name bmr25751.str _Entry_type original _Submission_date 2015-08-12 _Accession_date 2015-08-25 _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 Datta Aritreyee . . 2 Bhunia Anirban . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 92 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-03-21 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 25749 'VG16KRKP monomer' stop_ _Original_release_date 2016-03-21 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Designing potent antimicrobial peptides by disulphide linked dimerization and N-terminal lipidation to increase antimicrobial activity and membrane perturbation: Structural insights into lipopolysaccharide binding ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26407061 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Datta Aritreyee . . 2 Kundu Pallob . . 3 Bhunia Anirban . . stop_ _Journal_abbreviation 'J. Colloid. Interface Sci.' _Journal_volume 461 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 335 _Page_last 345 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name VG16KRKP_DIMER _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity entity_2 $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 1765.171 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence ; VARGWKRKCPLFGKGG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 VAL 2 2 ALA 3 3 ARG 4 4 GLY 5 5 TRP 6 6 LYS 7 7 ARG 8 8 LYS 9 9 CYS 10 10 PRO 11 11 LEU 12 12 PHE 13 13 GLY 14 14 LYS 15 15 GLY 16 16 GLY 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 $entity . . . . . . 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 $entity '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 $entity 1 mM 'natural abundance' D2O 10 % [U-2H] H2O 90 % 'natural abundance' DSS 1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement 'structure solution' 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_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_trNOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H trNOESY' _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 'ionic strength' 0 . M pH 4.5 . pH pressure 1 . atm temperature 298 . 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 DSS H 1 'methyl protons' ppm 0 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 trNOESY' 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 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 VAL HB H 2.155 0.008 1 2 1 1 VAL HG1 H 0.976 0.035 2 3 1 1 VAL HG2 H 0.976 0.035 2 4 2 2 ALA H H 8.643 0.035 1 5 2 2 ALA HA H 4.387 0.002 1 6 2 2 ALA HB H 1.390 0.008 1 7 3 3 ARG H H 8.503 0.003 1 8 3 3 ARG HA H 4.276 0.011 1 9 3 3 ARG HB2 H 1.760 0.005 2 10 3 3 ARG HB3 H 1.760 0.005 2 11 3 3 ARG HG2 H 1.618 0.002 2 12 3 3 ARG HG3 H 1.618 0.002 2 13 3 3 ARG HD2 H 3.167 0.007 2 14 3 3 ARG HD3 H 3.167 0.007 2 15 4 4 GLY H H 8.475 0.007 1 16 4 4 GLY HA2 H 3.925 0.019 2 17 4 4 GLY HA3 H 3.925 0.019 2 18 5 5 TRP H H 7.981 0.006 1 19 5 5 TRP HA H 4.606 0.003 1 20 5 5 TRP HB2 H 3.255 0.002 2 21 5 5 TRP HB3 H 3.255 0.002 2 22 5 5 TRP HD1 H 7.251 0.010 1 23 5 5 TRP HE1 H 10.14 0.018 1 24 5 5 TRP HE3 H 7.559 0.004 1 25 5 5 TRP HZ2 H 7.484 0.008 1 26 5 5 TRP HZ3 H 7.139 0.002 1 27 5 5 TRP HH2 H 7.218 0.012 1 28 6 6 LYS H H 8.014 0.002 1 29 6 6 LYS HA H 4.154 0.004 1 30 6 6 LYS HB2 H 1.673 0.001 2 31 6 6 LYS HB3 H 1.673 0.001 2 32 6 6 LYS HG2 H 1.233 0.003 2 33 6 6 LYS HG3 H 1.233 0.003 2 34 6 6 LYS HD2 H 1.560 0.004 2 35 6 6 LYS HD3 H 1.560 0.004 2 36 7 7 ARG H H 8.080 0.004 1 37 7 7 ARG HA H 4.106 0.005 1 38 7 7 ARG HB2 H 1.763 0.003 2 39 7 7 ARG HB3 H 1.763 0.003 2 40 7 7 ARG HG2 H 1.583 0.001 2 41 7 7 ARG HG3 H 1.583 0.001 2 42 8 8 LYS H H 8.428 0.004 1 43 8 8 LYS HA H 4.267 0.003 1 44 8 8 LYS HB2 H 1.763 0.002 2 45 8 8 LYS HB3 H 1.763 0.002 2 46 8 8 LYS HG2 H 1.406 0.005 2 47 8 8 LYS HG3 H 1.406 0.005 2 48 8 8 LYS HD2 H 1.556 0.002 2 49 8 8 LYS HD3 H 1.556 0.002 2 50 9 9 CYS H H 8.361 0.003 1 51 9 9 CYS HA H 4.765 0.004 1 52 9 9 CYS HB2 H 2.886 0.003 1 53 9 9 CYS HB3 H 2.886 0.003 1 54 10 10 PRO HB2 H 1.982 0.003 1 55 10 10 PRO HB3 H 2.213 0.001 1 56 10 10 PRO HD2 H 3.747 0.002 2 57 10 10 PRO HD3 H 3.747 0.002 2 58 11 11 LEU H H 8.166 0.002 1 59 11 11 LEU HA H 4.255 0.003 1 60 11 11 LEU HB2 H 1.509 0.002 2 61 11 11 LEU HB3 H 1.509 0.002 2 62 11 11 LEU HG H 1.442 0.003 1 63 11 11 LEU HD1 H 0.856 0.001 2 64 11 11 LEU HD2 H 0.856 0.001 2 65 12 12 PHE H H 8.178 0.002 1 66 12 12 PHE HA H 4.603 0.002 1 67 12 12 PHE HB2 H 3.160 0.002 1 68 12 12 PHE HB3 H 3.054 0.002 1 69 12 12 PHE HD1 H 7.250 0.002 3 70 12 12 PHE HD2 H 7.250 0.002 3 71 12 12 PHE HE1 H 7.343 0.002 3 72 12 12 PHE HE2 H 7.343 0.002 3 73 12 12 PHE HZ H 7.327 0.002 1 74 13 13 GLY H H 8.300 0.004 1 75 13 13 GLY HA2 H 3.956 0.002 2 76 13 13 GLY HA3 H 3.956 0.002 2 77 14 14 LYS H H 7.928 0.003 1 78 14 14 LYS HA H 4.372 0.002 1 79 14 14 LYS HB2 H 1.891 0.001 2 80 14 14 LYS HB3 H 1.891 0.001 2 81 14 14 LYS HG2 H 1.438 0.002 2 82 14 14 LYS HG3 H 1.438 0.002 2 83 14 14 LYS HD2 H 1.772 0.002 2 84 14 14 LYS HD3 H 1.772 0.002 2 85 14 14 LYS HE2 H 2.987 0.002 2 86 14 14 LYS HE3 H 2.987 0.002 2 87 15 15 GLY H H 8.444 0.003 1 88 15 15 GLY HA2 H 3.938 0.002 2 89 15 15 GLY HA3 H 3.938 0.002 2 90 16 16 GLY H H 7.903 0.003 1 91 16 16 GLY HA2 H 3.752 0.002 2 92 16 16 GLY HA3 H 3.752 0.002 2 stop_ save_