data_20057 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of designed peptide, YI12WF in the presence of Lipopolysaccharide ; _BMRB_accession_number 20057 _BMRB_flat_file_name bmr20057.str _Entry_type new _Submission_date 2008-11-30 _Accession_date 2008-11-30 _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 Bhattacharjya Surajit . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 69 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-08-27 update BMRB 'complete entry citation' 2009-06-29 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 20058 YI12WW 20059 YI12WY 20060 YI12FF stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Designed beta-boomerang antiendotoxic and antimicrobial peptides: structures and activities in lipopolysaccharide' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19520860 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bhunia Anirban . . 2 Mohanram Harini . . 3 Domadia Prerna N. . 4 Torres Jaume . . 5 Bhattacharjya Surajit . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 284 _Journal_issue 33 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 21991 _Page_last 22004 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name YI12WF _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label YI12WF $YI12WF stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function 'Antimicrobial peptide' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_YI12WF _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common YI12WF _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function 'Antimicrobial peptide' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence YVLWKRKRFIFI loop_ _Residue_seq_code _Residue_label 1 TYR 2 VAL 3 LEU 4 TRP 5 LYS 6 ARG 7 LYS 8 ARG 9 PHE 10 ILE 11 PHE 12 ILE 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 $YI12WF . . . . . . 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 $YI12WF 'recombinant technology' . . . . . 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 $YI12WF 0.5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_trNOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H trNOESY' _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 288 0.2 K pH 4.5 0.2 pH 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 0.00 internal direct . . . 1.000000000 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 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 YI12WF _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 TYR HD2 H 7.07 0.020 1 2 1 1 TYR HE2 H 6.84 0.020 1 3 2 2 VAL H H 8.44 0.020 1 4 2 2 VAL HA H 4.09 0.020 1 5 2 2 VAL HB H 1.83 0.020 1 6 2 2 VAL HG1 H 0.78 0.020 2 7 2 2 VAL HG2 H 0.78 0.020 2 8 3 3 LEU H H 8.41 0.020 1 9 3 3 LEU HA H 4.34 0.020 1 10 3 3 LEU HB3 H 1.56 0.020 2 11 3 3 LEU HD1 H 0.72 0.020 2 12 3 3 LEU HD2 H 0.88 0.020 2 13 4 4 TRP H H 8.23 0.020 1 14 4 4 TRP HA H 4.64 0.020 1 15 4 4 TRP HB2 H 3.24 0.020 2 16 4 4 TRP HD1 H 7.24 0.020 1 17 4 4 TRP HE1 H 10.18 0.020 1 18 4 4 TRP HE3 H 7.55 0.020 1 19 4 4 TRP HZ2 H 7.47 0.020 1 20 4 4 TRP HZ3 H 7.11 0.020 1 21 5 5 LYS H H 8.11 0.020 1 22 5 5 LYS HA H 4.18 0.020 1 23 5 5 LYS HB2 H 1.70 0.020 2 24 5 5 LYS HB3 H 1.58 0.020 2 25 5 5 LYS HD3 H 1.58 0.020 2 26 5 5 LYS HE3 H 2.98 0.020 2 27 5 5 LYS HG2 H 1.23 0.020 2 28 6 6 ARG H H 8.17 0.020 1 29 6 6 ARG HA H 4.13 0.020 1 30 6 6 ARG HB2 H 1.70 0.020 2 31 6 6 ARG HB3 H 1.70 0.020 2 32 6 6 ARG HD2 H 3.16 0.020 2 33 6 6 ARG HE H 7.19 0.020 1 34 6 6 ARG HG2 H 1.57 0.020 2 35 7 7 LYS H H 8.39 0.020 1 36 7 7 LYS HA H 4.19 0.020 1 37 7 7 LYS HB2 H 1.72 0.020 2 38 7 7 LYS HD3 H 1.66 0.020 2 39 7 7 LYS HE3 H 2.96 0.020 2 40 7 7 LYS HG2 H 1.40 0.020 2 41 8 8 ARG H H 8.32 0.020 1 42 8 8 ARG HA H 4.25 0.020 1 43 8 8 ARG HB2 H 1.70 0.020 2 44 8 8 ARG HB3 H 1.70 0.020 2 45 8 8 ARG HD2 H 3.12 0.020 2 46 8 8 ARG HE H 7.16 0.020 1 47 8 8 ARG HG2 H 1.50 0.020 2 48 9 9 PHE H H 8.43 0.020 1 49 9 9 PHE HA H 4.60 0.020 1 50 9 9 PHE HB3 H 2.96 0.020 2 51 9 9 PHE HD1 H 7.18 0.020 1 52 9 9 PHE HE1 H 7.31 0.020 1 53 10 10 ILE H H 7.99 0.020 1 54 10 10 ILE HA H 4.08 0.020 1 55 10 10 ILE HB H 1.70 0.020 1 56 10 10 ILE HD1 H 0.80 0.020 1 57 10 10 ILE HG12 H 1.36 0.020 2 58 10 10 ILE HG13 H 1.07 0.020 2 59 11 11 PHE H H 8.44 0.020 1 60 11 11 PHE HA H 4.57 0.020 1 61 11 11 PHE HB2 H 3.03 0.020 2 62 11 11 PHE HD1 H 7.27 0.020 1 63 11 11 PHE HE1 H 7.36 0.020 1 64 12 12 ILE H H 8.07 0.020 1 65 12 12 ILE HA H 4.06 0.020 1 66 12 12 ILE HB H 1.74 0.020 1 67 12 12 ILE HD1 H 0.82 0.020 1 68 12 12 ILE HG12 H 1.39 0.020 2 69 12 12 ILE HG13 H 1.10 0.020 2 stop_ save_