data_15359 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of arenicin-1 ; _BMRB_accession_number 15359 _BMRB_flat_file_name bmr15359.str _Entry_type new _Submission_date 2007-07-02 _Accession_date 2007-07-02 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Jakovkin Igor B. . 2 Hecht Oliver . . 3 Gelhaus Christoph . . 4 Krasnosdembskaya Anna D. . 5 Fedders Henning . . 6 Leippe Matthias . . 7 Groetzinger Joachim . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 121 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-25 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_title 'Structure and mode of action of the antimicrobial peptide arenicin' _Citation_status published _Citation_type journal _PubMed_ID 17935487 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Andra J. . . 2 Jakovkin Igor B. . 3 Groetzinger J. . . 4 Hecht Oliver . . 5 Krasnosdembskaya Anna D. . 6 Goldman T. . . 7 Gutsmann T. . . 8 Leippe Matthias . . stop_ _Journal_abbreviation 'Biochem. J.' _Journal_volume 410 _Journal_issue 1 _Page_first 113 _Page_last 122 _Year 2008 save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'arenicin monomer' loop_ _Mol_system_component_name _Mol_label entity $entity stop_ _System_physical_state native _System_oligomer_state ? _System_paramagnetic no save_ ######################## # Monomeric polymers # ######################## save_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 2766.365 _Mol_thiol_state 'all disulfide bound' ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; RWCVYAYVRVRGVLVRYRRC 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 VAL 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 2014-11-10 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 PDB 2JSB "Solution Structure Of Arenicin-1" 100.00 21 100.00 100.00 7.96e-04 GB AAV65142 "preproarenicin-1 [Arenicola marina]" 100.00 202 100.00 100.00 6.14e-05 SP Q5SC60 "RecName: Full=Arenicin-1; Flags: Precursor [Arenicola marina]" 100.00 202 100.00 100.00 6.14e-05 stop_ save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name single disulfide entity 3 3 SG entity 20 20 SG stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity 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 $entity 'chemical synthesis' . . . . ? stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 1.8 mg 'natural abundance' 'acetic acid' 2 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ save_ save_NMRView _Saveframe_category software _Name NMRView loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' stop_ save_ save_CYANA _Saveframe_category software _Name CYANA loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 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_1H-1H_NOESY_2 _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 loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 283 . K pH 3.5 . pH pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference 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 loop_ _Experiment_label '2D 1H-1H TOCSY' '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 entity 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 4.058 . 1 2 1 1 ARG HB2 H 1.694 . 2 3 1 1 ARG HD2 H 2.996 . 2 4 1 1 ARG HE H 7.149 . 1 5 1 1 ARG HG2 H 1.456 . 2 6 2 2 TRP H H 8.553 . 1 7 2 2 TRP HA H 4.655 . 1 8 2 2 TRP HB2 H 2.643 . 2 9 2 2 TRP HB3 H 2.316 . 2 10 2 2 TRP HD1 H 6.844 . 1 11 2 2 TRP HE1 H 9.986 . 2 12 2 2 TRP HE3 H 7.369 . 2 13 2 2 TRP HH2 H 7.055 . 1 14 2 2 TRP HZ2 H 7.314 . 2 15 3 3 CYS H H 7.998 . 1 16 3 3 CYS HA H 5.521 . 1 17 3 3 CYS HB2 H 2.656 . 2 18 3 3 CYS HB3 H 2.311 . 2 19 4 4 VAL H H 8.978 . 1 20 4 4 VAL HA H 4.398 . 1 21 4 4 VAL HB H 2.211 . 1 22 4 4 VAL HG1 H 1.008 . 4 23 4 4 VAL HG2 H 0.952 . 4 24 5 5 TYR H H 8.458 . 1 25 5 5 TYR HA H 5.087 . 1 26 5 5 TYR HB2 H 2.684 . 2 27 5 5 TYR HB3 H 2.443 . 2 28 5 5 TYR HD1 H 6.880 . 2 29 5 5 TYR HE1 H 6.657 . 2 30 6 6 ALA H H 8.823 . 1 31 6 6 ALA HA H 4.498 . 1 32 6 6 ALA HB H 1.032 . 1 33 7 7 TYR H H 8.512 . 1 34 7 7 TYR HA H 5.585 . 1 35 7 7 TYR HB2 H 2.735 . 2 36 7 7 TYR HB3 H 2.688 . 2 37 7 7 TYR HD1 H 6.918 . 2 38 7 7 TYR HE1 H 6.516 . 2 39 8 8 VAL H H 9.229 . 1 40 8 8 VAL HA H 4.500 . 1 41 8 8 VAL HB H 2.010 . 1 42 8 8 VAL HG1 H 0.833 . 4 43 8 8 VAL HG2 H 0.794 . 4 44 9 9 ARG H H 8.692 . 1 45 9 9 ARG HA H 4.490 . 1 46 9 9 ARG HB2 H 1.606 . 2 47 9 9 ARG HD2 H 3.000 . 2 48 9 9 ARG HE H 7.338 . 1 49 9 9 ARG HG2 H 1.302 . 2 50 10 10 VAL H H 9.249 . 1 51 10 10 VAL HA H 4.120 . 1 52 10 10 VAL HB H 1.917 . 1 53 10 10 VAL HG1 H 0.862 . 4 54 11 11 ARG H H 9.613 . 1 55 11 11 ARG HA H 3.808 . 1 56 11 11 ARG HB2 H 1.959 . 2 57 11 11 ARG HB3 H 1.831 . 2 58 11 11 ARG HD2 H 3.225 . 2 59 11 11 ARG HE H 7.238 . 1 60 11 11 ARG HG2 H 1.570 . 2 61 12 12 GLY H H 8.505 . 1 62 12 12 GLY HA2 H 4.188 . 2 63 12 12 GLY HA3 H 3.501 . 2 64 13 13 VAL H H 7.804 . 1 65 13 13 VAL HA H 4.205 . 1 66 13 13 VAL HB H 2.046 . 1 67 13 13 VAL HG1 H 0.870 . 4 68 14 14 LEU H H 8.690 . 1 69 14 14 LEU HA H 4.497 . 1 70 14 14 LEU HB2 H 1.477 . 2 71 14 14 LEU HD1 H 0.712 . 4 72 14 14 LEU HD2 H 0.654 . 4 73 15 15 VAL H H 9.423 . 1 74 15 15 VAL HA H 4.244 . 1 75 15 15 VAL HB H 2.080 . 1 76 15 15 VAL HG1 H 0.911 . 4 77 15 15 VAL HG2 H 0.808 . 4 78 16 16 ARG H H 8.491 . 1 79 16 16 ARG HA H 4.588 . 1 80 16 16 ARG HB2 H 1.640 . 2 81 16 16 ARG HB3 H 1.399 . 2 82 16 16 ARG HD2 H 2.716 . 2 83 16 16 ARG HD3 H 2.443 . 2 84 16 16 ARG HE H 6.670 . 1 85 16 16 ARG HG2 H 1.136 . 2 86 16 16 ARG HG3 H 0.861 . 2 87 17 17 TYR H H 9.263 . 1 88 17 17 TYR HA H 4.585 . 1 89 17 17 TYR HB2 H 2.856 . 2 90 17 17 TYR HD1 H 6.905 . 2 91 17 17 TYR HE1 H 6.704 . 2 92 18 18 ARG H H 8.666 . 1 93 18 18 ARG HA H 4.490 . 1 94 18 18 ARG HB2 H 1.638 . 2 95 18 18 ARG HB3 H 1.390 . 2 96 18 18 ARG HD2 H 2.852 . 2 97 18 18 ARG HE H 6.913 . 1 98 18 18 ARG HG2 H 1.211 . 2 99 18 18 ARG HG3 H 0.946 . 2 100 19 19 ARG H H 8.824 . 1 101 19 19 ARG HA H 4.501 . 1 102 19 19 ARG HB2 H 1.628 . 2 103 19 19 ARG HB3 H 1.458 . 2 104 19 19 ARG HD2 H 3.042 . 2 105 19 19 ARG HD3 H 2.970 . 2 106 19 19 ARG HE H 6.946 . 1 107 19 19 ARG HG2 H 1.310 . 2 108 20 20 CYS H H 8.529 . 1 109 20 20 CYS HA H 5.738 . 1 110 20 20 CYS HB2 H 2.843 . 2 111 20 20 CYS HB3 H 2.696 . 2 112 21 21 TRP H H 9.028 . 1 113 21 21 TRP HA H 4.629 . 1 114 21 21 TRP HB2 H 3.258 . 2 115 21 21 TRP HB3 H 3.068 . 2 116 21 21 TRP HD1 H 7.118 . 1 117 21 21 TRP HE1 H 9.872 . 2 118 21 21 TRP HE3 H 7.199 . 2 119 21 21 TRP HH2 H 6.868 . 1 120 21 21 TRP HZ2 H 7.203 . 2 121 21 21 TRP HZ3 H 7.012 . 2 stop_ save_