data_25408 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR resolved structure of VG16KRKP, an antimicrobial peptide in D8PG micelles ; _BMRB_accession_number 25408 _BMRB_flat_file_name bmr25408.str _Entry_type original _Submission_date 2015-01-01 _Accession_date 2015-01-01 _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 Bhunia Anirban . . 2 Datta Aritreyee . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 83 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-02-02 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 25409 'VG16KRKP, an antimicrobial peptide in SDS' stop_ _Original_release_date 2015-02-02 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'De-novo design of antimicrobial peptides:insights into membrane permeabilisation, lipopolysachharide fragmentation and application in plant disease control' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bhunia Anirban . . 2 Datta Aritreyee . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'VG16KRKP, an antimicrobial peptide in D8PG micelles' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label antimicrobial_peptide $antimicrobial_peptide 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_antimicrobial_peptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common antimicrobial_peptide _Molecular_mass 1765.171 _Mol_thiol_state 'all free' _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 2015-03-04 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 25335 entity 100.00 17 100.00 100.00 2.42e-01 BMRB 25409 antimicrobial_peptide 100.00 16 100.00 100.00 2.18e-01 PDB 2MXG "Nmr Resolved Structure Of Vg16krkp, An Antimicrobial Peptide In D8pg Micelles" 100.00 16 100.00 100.00 2.18e-01 PDB 2MXH "Nmr Resolved Structure Of Vg16krkp, An Antimicrobial Peptide In Sds" 100.00 16 100.00 100.00 2.18e-01 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $antimicrobial_peptide . . . . . . 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 $antimicrobial_peptide '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 $antimicrobial_peptide 0.5 mM 'natural abundance' H2O 90 % 'natural abundance' 'Dioctanoyl phosphatidyl glycerol' 10 mM 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . 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 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 $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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 4.5 . pH pressure 1 . atm 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 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 _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 1.975 0.008 1 2 1 1 VAL HG1 H 1.032 -0.035 1 3 1 1 VAL HG2 H 1.032 -0.035 1 4 2 2 ALA H H 8.658 -0.035 1 5 2 2 ALA HA H 4.387 0.002 1 6 2 2 ALA HB H 1.406 0.008 1 7 3 3 ARG H H 8.368 0.003 1 8 3 3 ARG HA H 4.292 0.011 1 9 3 3 ARG HB2 H 1.737 -0.005 2 10 3 3 ARG HB3 H 1.737 -0.005 2 11 3 3 ARG HG2 H 1.643 -0.002 2 12 3 3 ARG HG3 H 1.643 -0.002 2 13 3 3 ARG HD2 H 3.165 +0.007 2 14 3 3 ARG HD3 H 3.165 +0.007 2 15 4 4 GLY H H 8.413 0.007 1 16 4 4 GLY HA2 H 3.945 -0.919 2 17 4 4 GLY HA3 H 3.945 -0.919 2 18 5 5 TRP H H 7.909 -0.006 1 19 5 5 TRP HA H 3.283 0.003 1 20 5 5 TRP HB2 H 3.275 0.002 2 21 5 5 TRP HB3 H 3.275 0.002 2 22 5 5 TRP HD1 H 7.321 0.010 1 23 5 5 TRP HE3 H 7.530 0.002 1 24 6 6 LYS H H 7.972 0.002 1 25 6 6 LYS HA H 4.103 0.004 1 26 6 6 LYS HB2 H 1.691 0.001 2 27 6 6 LYS HB3 H 1.691 0.001 2 28 6 6 LYS HG2 H 1.138 -0.003 2 29 6 6 LYS HG3 H 1.138 -0.003 2 30 6 6 LYS HD2 H 1.564 -0.004 2 31 6 6 LYS HD3 H 1.564 -0.004 2 32 7 7 ARG H H 7.759 0.004 1 33 7 7 ARG HA H 4.229 0.005 1 34 7 7 ARG HB2 H 1.769 0.003 2 35 7 7 ARG HB3 H 1.769 0.003 2 36 7 7 ARG HG2 H 1.580 0.001 2 37 7 7 ARG HG3 H 1.580 0.001 2 38 8 8 LYS H H 8.145 0.004 1 39 8 8 LYS HA H 4.332 0.003 1 40 8 8 LYS HB2 H 1.816 0.002 2 41 8 8 LYS HB3 H 1.816 0.002 2 42 8 8 LYS HG2 H 1.453 0.005 2 43 8 8 LYS HG3 H 1.453 0.005 2 44 8 8 LYS HD2 H 1.556 0.002 2 45 8 8 LYS HD3 H 1.556 0.002 2 46 9 9 CYS H H 8.208 0.003 1 47 9 9 CYS HA H 4.821 0.004 1 48 9 9 CYS HB2 H 2.928 0.003 1 49 9 9 CYS HB3 H 2.928 0.003 1 50 10 10 PRO HB2 H 2.281 0.001 1 51 10 10 PRO HB3 H 1.982 0.003 1 52 10 10 PRO HG2 H 1.887 -0.002 2 53 10 10 PRO HG3 H 1.887 -0.002 2 54 11 11 LEU H H 7.840 0.002 1 55 11 11 LEU HA H 4.190 -0.003 1 56 11 11 LEU HB2 H 1.446 +0.002 2 57 11 11 LEU HB3 H 1.446 +0.002 2 58 11 11 LEU HG H 1.343 0.003 1 59 11 11 LEU HD1 H 0.848 0.001 1 60 11 11 LEU HD2 H 0.848 0.001 1 61 12 12 PHE H H 7.871 0.002 1 62 12 12 PHE HA H 4.671 0.002 1 63 12 12 PHE HB2 H 3.267 0.002 1 64 12 12 PHE HB3 H 3.031 0.002 1 65 12 12 PHE HD1 H 7.295 0.002 1 66 12 12 PHE HD2 H 7.295 0.002 1 67 13 13 GLY H H 8.188 0.004 1 68 13 13 GLY HA2 H 3.977 0.002 1 69 13 13 GLY HA3 H 3.977 0.002 1 70 14 14 LYS H H 8.190 0.003 1 71 14 14 LYS HA H 4.395 0.002 1 72 14 14 LYS HB2 H 1.903 0.001 2 73 14 14 LYS HB3 H 1.903 0.001 2 74 14 14 LYS HG2 H 1.453 0.002 2 75 14 14 LYS HG3 H 1.453 0.002 2 76 14 14 LYS HD2 H 1.793 0.002 2 77 14 14 LYS HD3 H 1.793 0.002 2 78 15 15 GLY H H 8.472 0.003 1 79 15 15 GLY HA2 H 3.958 0.002 2 80 15 15 GLY HA3 H 3.958 0.002 2 81 16 16 GLY H H 7.904 0.003 1 82 16 16 GLY HA2 H 3.757 0.002 2 83 16 16 GLY HA3 H 3.757 0.002 2 stop_ save_