data_15118 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; LPS-bound structure of a designed peptide ; _BMRB_accession_number 15118 _BMRB_flat_file_name bmr15118.str _Entry_type original _Submission_date 2007-01-30 _Accession_date 2007-01-30 _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 Bhattacharjya S. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 75 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-02 update BMRB 'complete entry citation' 2007-03-06 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'High-resolution solution structure of a designed peptide bound to lipopolysaccharide: transferred nuclear Overhauser effects, micelle selectivity, and anti-endotoxic activity' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17469802 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bhattacharjya S. . . 2 Domadia P. N. . 3 Bhunia A. . . 4 Malladi S. . . 5 David S. A. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 48 _Journal_issue 20 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5864 _Page_last 5874 _Year 2007 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'YW12 monomer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'YW12 monomer' $YW12 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_YW12 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common YW12 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence YVLWKRKRMIFI loop_ _Residue_seq_code _Residue_label 1 TYR 2 VAL 3 LEU 4 TRP 5 LYS 6 ARG 7 LYS 8 ARG 9 MET 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 $YW12 . . . . . . 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 $YW12 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution _Details '1mM peptide contain lipopolysaccharide to detect Tr-NOE; 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $YW12 1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Vendor _Address _Electronic_address 'Guentert, P.' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_Tr-NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name Tr-NOESY _Sample_label $sample save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample save_ save_Tr-NOESY _Saveframe_category NMR_applied_experiment _Experiment_name Tr-NOESY _BMRB_pulse_sequence_accession_number . _Details 'transferred NOESY experiment of YW12 in the presence of LPS' save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.7 . pH temperature 290 . 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 0.00 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 Tr-NOESY stop_ loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'YW12 monomer' _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 HA H 4.26 0.020 1 2 1 1 TYR HB2 H 3.09 0.020 1 3 1 1 TYR HB3 H 3.09 0.020 1 4 1 1 TYR HD2 H 7.03 0.020 1 5 1 1 TYR HE2 H 6.84 0.020 1 6 2 2 VAL H H 8.42 0.020 1 7 2 2 VAL HA H 4.06 0.020 1 8 2 2 VAL HB H 1.84 0.020 1 9 2 2 VAL HG1 H 0.82 0.020 2 10 2 2 VAL HG2 H 0.69 0.020 2 11 3 3 LEU H H 8.38 0.020 1 12 3 3 LEU HA H 4.34 0.020 1 13 3 3 LEU HB3 H 1.54 0.020 2 14 3 3 LEU HD1 H 0.95 0.020 2 15 3 3 LEU HD2 H 0.88 0.020 2 16 4 4 TRP H H 8.27 0.020 1 17 4 4 TRP HA H 4.64 0.020 1 18 4 4 TRP HB2 H 3.22 0.020 2 19 4 4 TRP HD1 H 7.27 0.020 1 20 4 4 TRP HE1 H 10.15 0.020 1 21 4 4 TRP HE3 H 7.65 0.020 1 22 4 4 TRP HZ2 H 7.48 0.020 1 23 4 4 TRP HZ3 H 7.15 0.020 1 24 4 4 TRP HH2 H 7.27 0.020 1 25 5 5 LYS H H 8.13 0.020 1 26 5 5 LYS HA H 4.19 0.020 1 27 5 5 LYS HB2 H 1.70 0.020 2 28 5 5 LYS HB3 H 1.58 0.020 2 29 5 5 LYS HG2 H 1.22 0.020 2 30 5 5 LYS HD3 H 1.58 0.020 2 31 5 5 LYS HE3 H 2.98 0.020 2 32 6 6 ARG H H 8.19 0.020 1 33 6 6 ARG HA H 4.12 0.020 1 34 6 6 ARG HB2 H 1.79 0.020 2 35 6 6 ARG HB3 H 1.72 0.020 2 36 6 6 ARG HG2 H 1.58 0.020 2 37 6 6 ARG HD2 H 3.15 0.020 2 38 6 6 ARG HE H 7.19 0.020 1 39 7 7 LYS H H 8.39 0.020 1 40 7 7 LYS HA H 4.22 0.020 1 41 7 7 LYS HB2 H 1.78 0.020 2 42 7 7 LYS HG2 H 1.44 0.020 2 43 7 7 LYS HD3 H 1.66 0.020 2 44 7 7 LYS HE3 H 2.96 0.020 2 45 8 8 ARG H H 8.37 0.020 1 46 8 8 ARG HA H 4.28 0.020 1 47 8 8 ARG HB2 H 1.74 0.020 2 48 8 8 ARG HB3 H 1.72 0.020 2 49 8 8 ARG HG2 H 1.59 0.020 2 50 8 8 ARG HD2 H 3.14 0.020 2 51 8 8 ARG HE H 7.16 0.020 1 52 9 9 MET H H 8.45 0.020 1 53 9 9 MET HA H 4.40 0.020 1 54 9 9 MET HB3 H 1.90 0.020 2 55 9 9 MET HG2 H 2.42 0.020 2 56 9 9 MET HG3 H 2.38 0.020 2 57 9 9 MET HE H 2.06 0.020 1 58 10 10 ILE H H 8.05 0.020 1 59 10 10 ILE HA H 4.13 0.020 1 60 10 10 ILE HB H 1.87 0.020 1 61 10 10 ILE HG12 H 1.36 0.020 2 62 10 10 ILE HG13 H 1.08 0.020 2 63 10 10 ILE HD1 H 0.80 0.020 1 64 11 11 PHE H H 8.44 0.020 1 65 11 11 PHE HA H 4.68 0.020 1 66 11 11 PHE HB2 H 3.14 0.020 2 67 11 11 PHE HB3 H 2.93 0.020 2 68 11 11 PHE HD1 H 7.22 0.020 1 69 11 11 PHE HE1 H 7.34 0.020 1 70 12 12 ILE H H 7.93 0.020 1 71 12 12 ILE HA H 4.14 0.020 1 72 12 12 ILE HB H 1.79 0.020 1 73 12 12 ILE HG12 H 1.39 0.020 2 74 12 12 ILE HG13 H 1.13 0.020 2 75 12 12 ILE HD1 H 0.86 0.020 1 stop_ save_