data_15460 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; High resolution structure of AK12 in the presence of Lipopolysaccharide (LPS) ; _BMRB_accession_number 15460 _BMRB_flat_file_name bmr15460.str _Entry_type new _Submission_date 2007-09-05 _Accession_date 2007-09-05 _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" 56 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-02-11 update BMRB 'complete entry citation' 2008-10-31 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Lipopolysaccharide bound structures of the active fragments of fowlicidin-1, a cathelicidin family of antimicrobial and antiendotoxic peptide from chicken, determined by transferred nuclear overhauser effect spectroscopy ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18844294 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bhunia Anirban . . 2 Mohanram Harini . . 3 Bhattacharjya Surajit . . stop_ _Journal_abbreviation Biopolymers _Journal_volume 92 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9 _Page_last 22 _Year 2009 _Details . loop_ _Keyword AK12 NMR LPS stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name AK12 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label AK12 $AK12 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function 'Antimicrobial peptide, hemolytic assay' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_AK12 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common AK12 _Molecular_mass 1428.736 _Mol_thiol_state 'not present' loop_ _Biological_function 'Antimicrobial peptide' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence AGYNLYRAIKKK loop_ _Residue_seq_code _Residue_label 1 ALA 2 GLY 3 TYR 4 ASN 5 LEU 6 TYR 7 ARG 8 ALA 9 ILE 10 LYS 11 LYS 12 LYS 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 $AK12 . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $AK12 'Standard F-moc solid phase peptide synthesised' . . . . 'Standard F-moc solid phase peptide synthesised' '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 . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $AK12 0.5 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_DYANA _Saveframe_category software _Name DYANA _Version . 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_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 . K pH 4.5 . 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_ _Software_label $DYANA stop_ loop_ _Experiment_label '2D 1H-1H trNOESY' '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 AK12 _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 ALA HA H 4.10 0.020 1 2 1 1 ALA HB H 1.51 0.020 1 3 2 2 GLY H H 8.64 0.020 1 4 2 2 GLY HA2 H 3.95 0.020 2 5 2 2 GLY HA3 H 3.95 0.020 2 6 3 3 TYR H H 8.30 0.020 1 7 3 3 TYR HA H 4.56 0.020 1 8 3 3 TYR HB2 H 3.00 0.020 2 9 3 3 TYR HB3 H 2.94 0.020 2 10 3 3 TYR HD2 H 7.10 0.020 1 11 3 3 TYR HE2 H 6.81 0.020 1 12 4 4 ASN H H 8.46 0.020 1 13 4 4 ASN HA H 4.61 0.020 1 14 4 4 ASN HB2 H 2.64 0.020 2 15 4 4 ASN HB3 H 2.72 0.020 2 16 4 4 ASN HD21 H 7.60 0.020 2 17 4 4 ASN HD22 H 6.94 0.020 2 18 5 5 LEU H H 8.14 0.020 1 19 5 5 LEU HA H 4.20 0.020 1 20 5 5 LEU HB3 H 1.46 0.020 2 21 5 5 LEU HD1 H 0.89 0.020 2 22 6 6 TYR H H 8.20 0.020 1 23 6 6 TYR HA H 4.49 0.020 1 24 6 6 TYR HB2 H 3.00 0.020 2 25 6 6 TYR HD2 H 7.10 0.020 1 26 6 6 TYR HE2 H 6.81 0.020 1 27 7 7 ARG H H 7.99 0.020 1 28 7 7 ARG HA H 4.21 0.020 1 29 7 7 ARG HB2 H 1.75 0.020 2 30 7 7 ARG HB3 H 1.65 0.020 2 31 7 7 ARG HD2 H 3.16 0.020 2 32 7 7 ARG HE H 7.18 0.020 1 33 7 7 ARG HG2 H 1.53 0.020 2 34 8 8 ALA H H 8.21 0.020 1 35 8 8 ALA HA H 4.23 0.020 1 36 8 8 ALA HB H 1.37 0.020 1 37 9 9 ILE H H 8.20 0.020 1 38 9 9 ILE HA H 4.11 0.020 1 39 9 9 ILE HB H 1.75 0.020 1 40 9 9 ILE HD1 H 0.84 0.020 1 41 9 9 ILE HG12 H 1.48 0.020 2 42 9 9 ILE HG13 H 1.19 0.020 2 43 10 10 LYS H H 8.21 0.020 1 44 10 10 LYS HA H 4.11 0.020 1 45 10 10 LYS HB2 H 1.75 0.020 2 46 10 10 LYS HD3 H 1.67 0.020 2 47 11 11 LYS H H 8.47 0.020 1 48 11 11 LYS HA H 4.31 0.020 1 49 11 11 LYS HB2 H 1.75 0.020 2 50 11 11 LYS HB3 H 1.80 0.020 2 51 11 11 LYS HE3 H 3.00 0.020 2 52 11 11 LYS HG2 H 1.45 0.020 2 53 12 12 LYS H H 8.49 0.020 1 54 12 12 LYS HA H 4.27 0.020 1 55 12 12 LYS HB2 H 1.78 0.020 2 56 12 12 LYS HE3 H 2.99 0.020 2 stop_ save_