data_15115 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of antimicrobial peptide Arenicin-2 in water ; _BMRB_accession_number 15115 _BMRB_flat_file_name bmr15115.str _Entry_type original _Submission_date 2007-01-29 _Accession_date 2007-01-29 _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 Nadezhdin Kirill D. . 2 Shenkarev Zakhar O. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 120 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2007-10-17 original author . stop_ _Original_release_date 2007-10-17 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Recombinant expression, synthesis, purification, and solution structure of arenicin' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17585874 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ovchinnikovaa Tatiana V. . 2 Shenkareva Zakhar O. . 3 Nadezhdina Kirill D. . 4 Balandina Sergey V. . 5 Zhmaka Maxim N. . 6 Kudelinaa Irina A. . 7 Finkinaa Ekaterina I. . 8 Kokryakovb Vladimir N. . 9 Arseniev Alexander S. . stop_ _Journal_abbreviation 'Biochem. Biophys. Res. Commun.' _Journal_volume 360 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 156 _Page_last 162 _Year 2007 _Details . loop_ _Keyword antimicrobial beta-sheet peptide stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name arenicin-2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label arenicin-2 $antimicrobial_peptide stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function antimicrobial stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_antimicrobial_peptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common antimicrobial_peptide _Molecular_mass 2780.392 _Mol_thiol_state 'all disulfide bound' loop_ _Biological_function antimicrobial stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; RWCVYAYVRIRGVLVRYRRC W ; loop_ _Residue_seq_code _Residue_label 1 ARG 2 TRP 3 CYS 4 VAL 5 TYR 6 ALA 7 TYR 8 VAL 9 ARG 10 ILE 11 ARG 12 GLY 13 VAL 14 LEU 15 VAL 16 ARG 17 TYR 18 ARG 19 ARG 20 CYS 21 TRP stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-09-14 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 BMRB 17430 Arenicin-2 100.00 21 100.00 100.00 5.24e-04 PDB 2JNI "Spatial Structure Of Antimicrobial Peptide Arenicin-2 In Aqueous Solution" 100.00 21 100.00 100.00 5.24e-04 PDB 2L8X "Spatial Structure Of Antimicrobial Peptide Arenicin-2 Dimer In Dpc Micelles" 100.00 21 100.00 100.00 5.24e-04 GB AAV65143 "preproarenicin-2 [Arenicola marina]" 100.00 202 100.00 100.00 4.73e-05 SP Q5SC59 "RecName: Full=Arenicin-2; Flags: Precursor [Arenicola marina]" 100.00 202 100.00 100.00 4.73e-05 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $antimicrobial_peptide lugworm 6344 Eukaryota Metazoa Arenicola marina 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 $antimicrobial_peptide 'recombinant technology' . Escherichia coli 'BL-21 (DE3)' pET 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 $antimicrobial_peptide 0.6 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_XEASY _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection 'data analysis' processing stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unity _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H 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 'ionic strength' 0 . M pH 3.3 . pH pressure 1 . atm temperature 288 . 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 water H 1 protons ppm 4.9 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_ _Experiment_label '2D 1H-1H TOCSY' '2D DQF-COSY' '2D 1H-1H 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 arenicin-2 _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 ARG HA H 4.183 0.004 . 2 1 1 ARG HB2 H 1.546 0.004 . 3 1 1 ARG HG2 H 1.768 0.004 . 4 1 1 ARG HD2 H 3.074 0.005 . 5 1 1 ARG HE H 7.173 0.004 . 6 2 2 TRP H H 8.877 0.003 . 7 2 2 TRP HA H 4.747 0.005 . 8 2 2 TRP HB2 H 2.729 0.000 . 9 2 2 TRP HB3 H 2.502 0.005 . 10 2 2 TRP HD1 H 6.885 0.003 . 11 2 2 TRP HE1 H 10.015 0.004 . 12 2 2 TRP HE3 H 7.525 0.002 . 13 2 2 TRP HZ2 H 7.384 0.004 . 14 2 2 TRP HZ3 H 7.116 0.002 . 15 2 2 TRP HH2 H 7.145 0.004 . 16 3 3 CYS H H 7.992 0.000 . 17 3 3 CYS HA H 5.571 0.002 . 18 3 3 CYS HB2 H 2.725 0.000 . 19 3 3 CYS HB3 H 2.351 0.001 . 20 4 4 VAL H H 9.000 0.004 . 21 4 4 VAL HA H 4.423 0.004 . 22 4 4 VAL HB H 2.248 0.003 . 23 4 4 VAL HG2 H 0.994 0.006 . 24 5 5 TYR H H 8.501 0.005 . 25 5 5 TYR HA H 5.103 0.002 . 26 5 5 TYR HB2 H 2.741 0.005 . 27 5 5 TYR HB3 H 2.508 0.004 . 28 5 5 TYR HD1 H 6.931 0.002 . 29 5 5 TYR HE1 H 6.734 0.015 . 30 6 6 ALA H H 8.851 0.005 . 31 6 6 ALA HA H 4.542 0.004 . 32 6 6 ALA HB H 1.089 0.004 . 33 7 7 TYR H H 8.550 0.004 . 34 7 7 TYR HA H 5.648 0.004 . 35 7 7 TYR HB2 H 2.774 0.007 . 36 7 7 TYR HD1 H 6.966 0.001 . 37 7 7 TYR HE1 H 6.777 0.002 . 38 8 8 VAL H H 9.307 0.004 . 39 8 8 VAL HA H 4.581 0.001 . 40 8 8 VAL HB H 2.077 0.002 . 41 8 8 VAL HG1 H 0.874 0.000 . 42 8 8 VAL HG2 H 0.874 0.000 . 43 9 9 ARG H H 8.712 0.002 . 44 9 9 ARG HA H 5.014 0.005 . 45 9 9 ARG HB2 H 1.657 0.004 . 46 9 9 ARG HG2 H 1.324 0.004 . 47 9 9 ARG HD2 H 3.066 0.000 . 48 9 9 ARG HE H 7.398 0.004 . 49 10 10 ILE H H 9.156 0.002 . 50 10 10 ILE HA H 4.283 0.004 . 51 10 10 ILE HB H 1.778 0.002 . 52 10 10 ILE HG13 H 1.038 0.000 . 53 10 10 ILE HG2 H 0.894 0.002 . 54 10 10 ILE HD1 H 0.799 0.002 . 55 11 11 ARG H H 9.660 0.002 . 56 11 11 ARG HA H 3.872 0.004 . 57 11 11 ARG HB2 H 1.889 0.006 . 58 11 11 ARG HB3 H 2.048 0.002 . 59 11 11 ARG HG2 H 1.664 0.003 . 60 11 11 ARG HD2 H 3.242 0.004 . 61 11 11 ARG HE H 7.302 0.001 . 62 12 12 GLY H H 8.574 0.004 . 63 12 12 GLY HA2 H 4.252 0.003 . 64 12 12 GLY HA3 H 3.549 0.004 . 65 13 13 VAL H H 7.850 0.003 . 66 13 13 VAL HA H 4.257 0.001 . 67 13 13 VAL HB H 2.097 0.003 . 68 13 13 VAL HG1 H 0.943 0.007 . 69 13 13 VAL HG2 H 0.943 0.007 . 70 14 14 LEU H H 8.721 0.004 . 71 14 14 LEU HA H 4.566 0.002 . 72 14 14 LEU HB2 H 1.529 0.004 . 73 14 14 LEU HG H 1.536 0.004 . 74 14 14 LEU HD1 H 0.776 0.004 . 75 15 15 VAL H H 9.502 0.002 . 76 15 15 VAL HA H 4.307 0.003 . 77 15 15 VAL HB H 2.130 0.002 . 78 15 15 VAL HG2 H 0.902 0.002 . 79 16 16 ARG H H 8.572 0.002 . 80 16 16 ARG HA H 4.639 0.000 . 81 16 16 ARG HB2 H 1.208 0.003 . 82 16 16 ARG HB3 H 0.908 0.004 . 83 16 16 ARG HG2 H 1.473 0.005 . 84 16 16 ARG HG3 H 1.695 0.004 . 85 16 16 ARG HD2 H 2.527 0.002 . 86 16 16 ARG HD3 H 2.825 0.004 . 87 16 16 ARG HE H 6.727 0.004 . 88 17 17 TYR H H 9.323 0.005 . 89 17 17 TYR HA H 4.930 0.008 . 90 17 17 TYR HB2 H 2.925 0.007 . 91 17 17 TYR HD1 H 6.971 0.003 . 92 17 17 TYR HE1 H 6.584 0.004 . 93 18 18 ARG H H 8.675 0.002 . 94 18 18 ARG HA H 4.513 0.001 . 95 18 18 ARG HB2 H 1.210 0.002 . 96 18 18 ARG HB3 H 1.677 0.005 . 97 18 18 ARG HG2 H 1.418 0.004 . 98 18 18 ARG HG3 H 0.915 0.004 . 99 18 18 ARG HD2 H 2.893 0.002 . 100 18 18 ARG HE H 6.927 0.003 . 101 19 19 ARG H H 8.847 0.003 . 102 19 19 ARG HA H 4.553 0.006 . 103 19 19 ARG HB2 H 1.487 0.005 . 104 19 19 ARG HB3 H 1.332 0.004 . 105 19 19 ARG HG2 H 1.673 0.009 . 106 19 19 ARG HE H 6.966 0.002 . 107 20 20 CYS H H 8.538 0.007 . 108 20 20 CYS HA H 5.785 0.005 . 109 20 20 CYS HB2 H 2.912 0.004 . 110 20 20 CYS HB3 H 2.761 0.005 . 111 21 21 TRP H H 9.083 0.002 . 112 21 21 TRP HA H 4.568 0.000 . 113 21 21 TRP HB2 H 3.321 0.005 . 114 21 21 TRP HB3 H 3.091 0.005 . 115 21 21 TRP HD1 H 7.164 0.004 . 116 21 21 TRP HE1 H 9.903 0.004 . 117 21 21 TRP HE3 H 7.313 0.005 . 118 21 21 TRP HZ2 H 7.286 0.005 . 119 21 21 TRP HZ3 H 6.926 0.004 . 120 21 21 TRP HH2 H 7.087 0.004 . stop_ save_