data_20078 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of Antimicrobial Peptide Hedistin ; _BMRB_accession_number 20078 _BMRB_flat_file_name bmr20078.str _Entry_type original _Submission_date 2009-03-05 _Accession_date 2009-03-05 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'using NMR and Torsion Angle Molecular Dynamics' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Xu Guohua . . 2 Cui Yanfang . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 124 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-03-01 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Conformational and dynamics simulation study of antimicrobial peptide hedistin-heterogeneity of its helix-turn-helix motif.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19819221 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Xu Guohua . . 2 Wu Min . . 3 Wang Lin . . 4 Zhang Xu . . 5 Cao Shufen . . 6 Liu Maili . . 7 Cui Yanfang . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta, Biomembr.' _Journal_name_full 'Biochimica et Biophysica Acta, Biomembranes' _Journal_volume 1788 _Journal_issue 12 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2497 _Page_last 2508 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name HEDISTIN _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label HEDISTIN $HEDISTIN stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function 'antimicrobial action' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_HEDISTIN _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common HEDISTIN _Molecular_mass 2366 _Mol_thiol_state 'not present' loop_ _Biological_function 'antimicrobial action' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; LGAWLAGKVAGTVATYAWNR YV ; loop_ _Residue_seq_code _Residue_label 1 LEU 2 GLY 3 ALA 4 TRP 5 LEU 6 ALA 7 GLY 8 LYS 9 VAL 10 ALA 11 GLY 12 THR 13 VAL 14 ALA 15 THR 16 TYR 17 ALA 18 TRP 19 ASN 20 ARG 21 TYR 22 VAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-06-22 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 GB ABE01865 "preprohedistin [Hediste diversicolor]" 100.00 110 100.00 100.00 9.16e-06 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $HEDISTIN 'segmented worms' 6352 Eukaryota Metazoa Neanthes diversicolor 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 $HEDISTIN 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '2.0 mM hedistin peptide and 140 mM deuterated DPC(d-38) in 0.6 mL of H2O/D2O (90%/10%, v/v) at pH 5.2' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HEDISTIN 2 mM 'natural abundance' DPC 140 mM '[U-100% 2H]' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version v2.19 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_ProcheckNMR _Saveframe_category software _Name ProcheckNMR _Version . loop_ _Vendor _Address _Electronic_address 'Laskowski and MacArthur' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_Molmol _Saveframe_category software _Name Molmol _Version . loop_ _Vendor _Address _Electronic_address 'Koradi, Billeter and Wuthrich' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _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_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _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 310 . K pH 5.2 . pH stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_1H _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 external direct cylindrical 'insert at center of experimental sample tube' perpendicular 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_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-1H NOESY' '2D DQF-COSY' '2D 1H-1H TOCSY' '2D 1H-1H COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $1H _Mol_system_component_name HEDISTIN _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 LEU HA H 4.06 . . 2 1 1 LEU HB2 H 1.80 . . 3 1 1 LEU HB3 H 1.80 . . 4 1 1 LEU HD1 H 0.99 . . 5 1 1 LEU HD2 H 0.97 . . 6 1 1 LEU HG H 1.80 . . 7 2 2 GLY H H 9.17 . . 8 2 2 GLY HA2 H 3.98 . . 9 2 2 GLY HA3 H 3.93 . . 10 3 3 ALA H H 8.61 . . 11 3 3 ALA HA H 4.10 . . 12 3 3 ALA HB H 1.51 . . 13 4 4 TRP H H 8.33 . . 14 4 4 TRP HA H 4.38 . . 15 4 4 TRP HB2 H 3.41 . . 16 4 4 TRP HB3 H 3.41 . . 17 4 4 TRP HD1 H 7.43 . . 18 4 4 TRP HE1 H 10.71 . . 19 4 4 TRP HE3 H 7.51 . . 20 4 4 TRP HH2 H 7.09 . . 21 4 4 TRP HZ2 H 7.54 . . 22 4 4 TRP HZ3 H 6.96 . . 23 5 5 LEU H H 7.95 . . 24 5 5 LEU HA H 3.79 . . 25 5 5 LEU HB2 H 1.55 . . 26 5 5 LEU HB3 H 1.55 . . 27 5 5 LEU HD1 H 0.87 . . 28 5 5 LEU HD2 H 0.82 . . 29 5 5 LEU HG H 1.47 . . 30 6 6 ALA H H 8.12 . . 31 6 6 ALA HA H 3.95 . . 32 6 6 ALA HB H 1.41 . . 33 7 7 GLY H H 8.13 . . 34 7 7 GLY HA2 H 3.96 . . 35 7 7 GLY HA3 H 3.81 . . 36 8 8 LYS H H 7.88 . . 37 8 8 LYS HA H 4.19 . . 38 8 8 LYS HB2 H 1.77 . . 39 8 8 LYS HB3 H 1.71 . . 40 8 8 LYS HD2 H 1.57 . . 41 8 8 LYS HD3 H 1.57 . . 42 8 8 LYS HE2 H 2.88 . . 43 8 8 LYS HE3 H 2.77 . . 44 8 8 LYS HG2 H 1.23 . . 45 8 8 LYS HG3 H 1.08 . . 46 9 9 VAL H H 8.22 . . 47 9 9 VAL HA H 3.77 . . 48 9 9 VAL HB H 2.20 . . 49 9 9 VAL HG1 H 0.84 . . 50 9 9 VAL HG2 H 0.84 . . 51 10 10 ALA H H 8.41 . . 52 10 10 ALA HA H 3.96 . . 53 10 10 ALA HB H 1.47 . . 54 11 11 GLY H H 8.44 . . 55 11 11 GLY HA2 H 4.05 . . 56 11 11 GLY HA3 H 3.82 . . 57 12 12 THR H H 7.91 . . 58 12 12 THR HA H 4.32 . . 59 12 12 THR HB H 4.11 . . 60 12 12 THR HG2 H 1.27 . . 61 13 13 VAL H H 8.32 . . 62 13 13 VAL HA H 3.72 . . 63 13 13 VAL HB H 2.24 . . 64 13 13 VAL HG1 H 1.07 . . 65 13 13 VAL HG2 H 1.00 . . 66 14 14 ALA H H 8.48 . . 67 14 14 ALA HA H 4.10 . . 68 15 15 THR H H 7.99 . . 69 15 15 THR HA H 4.32 . . 70 15 15 THR HB H 3.99 . . 71 15 15 THR HG2 H 1.29 . . 72 16 16 TYR H H 8.01 . . 73 16 16 TYR HA H 4.32 . . 74 16 16 TYR HB2 H 3.19 . . 75 16 16 TYR HB3 H 3.19 . . 76 16 16 TYR HD1 H 7.12 . . 77 16 16 TYR HD2 H 7.12 . . 78 16 16 TYR HE1 H 6.80 . . 79 16 16 TYR HE2 H 6.80 . . 80 17 17 ALA H H 8.70 . . 81 17 17 ALA HA H 3.99 . . 82 17 17 ALA HB H 1.62 . . 83 18 18 TRP H H 8.68 . . 84 18 18 TRP HA H 4.21 . . 85 18 18 TRP HB2 H 3.42 . . 86 18 18 TRP HB3 H 3.42 . . 87 18 18 TRP HD1 H 7.20 . . 88 18 18 TRP HE1 H 10.49 . . 89 18 18 TRP HE3 H 7.47 . . 90 18 18 TRP HH2 H 7.15 . . 91 18 18 TRP HZ2 H 7.51 . . 92 18 18 TRP HZ3 H 6.98 . . 93 19 19 ASN H H 8.35 . . 94 19 19 ASN HA H 4.34 . . 95 19 19 ASN HB2 H 2.92 . . 96 19 19 ASN HB3 H 2.71 . . 97 19 19 ASN HD21 H 7.58 . . 98 19 19 ASN HD22 H 6.99 . . 99 20 20 ARG H H 7.91 . . 100 20 20 ARG HA H 3.99 . . 101 20 20 ARG HB2 H 1.49 . . 102 20 20 ARG HB3 H 1.49 . . 103 20 20 ARG HD2 H 3.04 . . 104 20 20 ARG HD3 H 2.86 . . 105 20 20 ARG HE H 7.35 . . 106 20 20 ARG HG2 H 1.15 . . 107 20 20 ARG HG3 H 1.09 . . 108 20 20 ARG HH11 H 6.96 . . 109 20 20 ARG HH12 H 6.96 . . 110 20 20 ARG HH21 H 6.87 . . 111 20 20 ARG HH22 H 6.87 . . 112 21 21 TYR H H 7.95 . . 113 21 21 TYR HA H 4.34 . . 114 21 21 TYR HB2 H 3.01 . . 115 21 21 TYR HB3 H 2.80 . . 116 21 21 TYR HD1 H 6.98 . . 117 21 21 TYR HD2 H 6.98 . . 118 21 21 TYR HE1 H 6.74 . . 119 21 21 TYR HE2 H 6.74 . . 120 22 22 VAL H H 7.83 . . 121 22 22 VAL HA H 3.65 . . 122 22 22 VAL HB H 1.29 . . 123 22 22 VAL HG1 H 0.43 . . 124 22 22 VAL HG2 H 0.43 . . stop_ save_