data_15413 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; High resolution NMR structure of YW12D in the presence of Lipopolysaccharide (LPS) ; _BMRB_accession_number 15413 _BMRB_flat_file_name bmr15413.str _Entry_type original _Submission_date 2007-07-31 _Accession_date 2007-07-31 _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 Bhattacharjya S. . . 2 Bhunia A. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 72 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-10-30 update BMRB 'complete entry, etc.' 2008-08-18 original author 'original release' stop_ _Original_release_date 2007-08-02 save_ ############################# # Citation for this entry # ############################# save_citations_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Interactions of a designed peptide with lipopolysaccharide:Bound conformation and anti-endotoxic activity ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18328260 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bhunia Anirban . . 2 Chua 'Geok Lin' . . 3 Domadia Prerna N. . 4 Warshakoon Hemamali . . 5 Cromer Jens R. . 6 David Sunil A. . 7 Bhattacharjya Surajit . . stop_ _Journal_abbreviation 'Biochem. Biophys. Res. Commun.' _Journal_name_full 'Biochemical and Biophysical Research Communications' _Journal_volume 369 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 853 _Page_last 857 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name YW12D _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label YW12D $YW12D stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function 'antimicrobial activity' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_YW12D _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common YW12D _Molecular_mass 1657.134 _Mol_thiol_state 'not present' loop_ _Biological_function 'Antimicrobial peptide' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; YVKLWRMIKFIR ; loop_ _Residue_seq_code _Residue_label 1 TYR 2 VAL 3 LYS 4 LEU 5 TRP 6 ARG 7 MET 8 ILE 9 LYS 10 PHE 11 ILE 12 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 $YW12D . . . . . . 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 $YW12D 'chemical synthesis' . . . . . 'Standard F-moc solid phase peptide synthesised' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '90% H2O, 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $YW12D 0.6 mM 'natural abundance' H2O 90 % . D2O 10 % . 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 'Equipped with cryo-probe' save_ ############################# # NMR applied experiments # ############################# save_TOCSY,_transferred-NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'TOCSY, transferred-NOESY' _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 pH 4.8 . pH 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 . . . 1.0 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 $DYANA stop_ loop_ _Experiment_label 'TOCSY, transferred-NOESY' 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 YW12D _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 HB2 H 3.09 0.020 2 2 1 1 TYR HB3 H 3.09 0.020 2 3 1 1 TYR HD2 H 7.10 0.020 1 4 1 1 TYR HE2 H 6.83 0.020 1 5 2 2 VAL H H 8.29 0.020 1 6 2 2 VAL HA H 4.06 0.020 1 7 2 2 VAL HB H 1.93 0.020 1 8 2 2 VAL HG1 H 0.87 0.020 2 9 2 2 VAL HG2 H 0.87 0.020 2 10 3 3 LYS H H 8.37 0.020 1 11 3 3 LYS HA H 4.18 0.020 1 12 3 3 LYS HD3 H 1.64 0.020 2 13 3 3 LYS HE3 H 2.84 0.020 2 14 3 3 LYS HG2 H 1.33 0.020 2 15 3 3 LYS HG3 H 1.27 0.020 2 16 4 4 LEU H H 8.23 0.020 1 17 4 4 LEU HA H 4.35 0.020 1 18 4 4 LEU HB3 H 1.56 0.020 2 19 4 4 LEU HD1 H 0.88 0.020 2 20 4 4 LEU HD2 H 0.83 0.020 2 21 4 4 LEU HG H 1.45 0.020 1 22 5 5 TRP H H 8.21 0.020 1 23 5 5 TRP HA H 4.60 0.020 1 24 5 5 TRP HB2 H 3.24 0.020 2 25 5 5 TRP HD1 H 7.24 0.020 1 26 5 5 TRP HE1 H 10.18 0.020 1 27 5 5 TRP HE3 H 7.59 0.020 1 28 5 5 TRP HH2 H 7.22 0.020 1 29 5 5 TRP HZ2 H 7.49 0.020 1 30 5 5 TRP HZ3 H 7.13 0.020 1 31 6 6 ARG H H 7.93 0.020 1 32 6 6 ARG HA H 4.17 0.020 1 33 6 6 ARG HB2 H 1.67 0.020 2 34 6 6 ARG HB3 H 1.55 0.020 2 35 6 6 ARG HD2 H 3.07 0.020 2 36 6 6 ARG HE H 7.09 0.020 1 37 6 6 ARG HG2 H 1.40 0.020 2 38 7 7 MET H H 8.15 0.020 1 39 7 7 MET HA H 4.33 0.020 1 40 7 7 MET HB2 H 2.01 0.020 2 41 7 7 MET HB3 H 1.94 0.020 2 42 7 7 MET HE H 2.09 0.020 1 43 7 7 MET HG2 H 2.53 0.020 2 44 7 7 MET HG3 H 2.47 0.020 2 45 8 8 ILE H H 8.08 0.020 1 46 8 8 ILE HA H 4.08 0.020 1 47 8 8 ILE HD1 H 0.82 0.020 1 48 8 8 ILE HG12 H 1.12 0.020 2 49 9 9 LYS H H 8.24 0.020 1 50 9 9 LYS HA H 4.25 0.020 1 51 9 9 LYS HD3 H 1.65 0.020 2 52 9 9 LYS HE3 H 2.94 0.020 2 53 9 9 LYS HG2 H 1.35 0.020 2 54 9 9 LYS HG3 H 1.26 0.020 2 55 10 10 PHE H H 8.25 0.020 1 56 10 10 PHE HA H 4.62 0.020 1 57 10 10 PHE HB2 H 3.06 0.020 2 58 10 10 PHE HB3 H 3.01 0.020 2 59 10 10 PHE HD1 H 7.22 0.020 1 60 10 10 PHE HE1 H 7.32 0.020 1 61 11 11 ILE H H 8.09 0.020 1 62 11 11 ILE HA H 4.08 0.020 1 63 11 11 ILE HD1 H 0.83 0.020 1 64 11 11 ILE HG12 H 1.42 0.020 2 65 11 11 ILE HG13 H 1.12 0.020 2 66 12 12 ARG H H 8.28 0.020 1 67 12 12 ARG HA H 4.20 0.020 1 68 12 12 ARG HB2 H 1.80 0.020 2 69 12 12 ARG HB3 H 1.73 0.020 2 70 12 12 ARG HD2 H 3.22 0.020 2 71 12 12 ARG HE H 7.22 0.020 1 72 12 12 ARG HG2 H 1.64 0.020 2 stop_ save_