data_30291 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of a Turripeptide from Unedogemmula bisaya venom ; _BMRB_accession_number 30291 _BMRB_flat_file_name bmr30291.str _Entry_type original _Submission_date 2017-05-09 _Accession_date 2017-05-09 _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 Daly N. L. . 2 Imperial J. S. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 70 "13C chemical shifts" 25 "15N chemical shifts" 16 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-11-20 update BMRB 'update entry citation' 2017-11-08 original author 'original release' stop_ _Original_release_date 2017-05-24 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure and Biological Activity of a Turripeptide from Unedogemmula bisaya Venom. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 29090914 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Omaga Carla A. . 2 Carpio Louie D. . 3 Imperial Julita S. . 4 Daly Norelle L. . 5 Gajewiak Joanna . . 6 Flores Malem S. . 7 Espino Samuel S. . 8 Christensen Sean . . 9 Filchakova Olena M. . 10 Lopez-Vera Estuardo . . 11 Raghuraman Shrinivasan . . 12 Olivera Baldomero M. . 13 Concepcion Gisela P. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 56 _Journal_issue 45 _Journal_ISSN 1520-4995 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6051 _Page_last 6060 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Turripeptide _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass 1807.174 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence ; DCCXCXAGAVRCRFACCX ; loop_ _Residue_seq_code _Residue_label 1 ASP 2 CYS 3 CYS 4 HYP 5 CYS 6 HYP 7 ALA 8 GLY 9 ALA 10 VAL 11 ARG 12 CYS 13 ARG 14 PHE 15 ALA 16 CYS 17 CYS 18 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_HYP _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 4-HYDROXYPROLINE _BMRB_code HYP _PDB_code HYP _Standard_residue_derivative . _Molecular_mass 131.130 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? OD1 OD1 O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG HG H . 0 . ? HD22 HD22 H . 0 . ? HD23 HD23 H . 0 . ? HD1 HD1 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N CD ? ? SING N H ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG OD1 ? ? SING CG HG ? ? SING CD HD22 ? ? SING CD HD23 ? ? SING OD1 HD1 ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N HN1 ? ? SING N HN2 ? ? 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_1 'Unedogemmula bisaya' 746885 Eukaryota Metazoa Unedogemmula bisaya 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_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1.5 mM ubi3a, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.5 mM '[U-13C; U-15N]' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name CcpNMR _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _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 . mM pH 5 . pH pressure 1 . atm temperature 290 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D DQF-COSY' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_1 _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 ASP HA H 4.248 0.001 . 2 1 1 ASP HB2 H 2.936 0.000 . 3 1 1 ASP HB3 H 2.828 0.000 . 4 1 1 ASP CA C 52.376 0.000 . 5 2 2 CYS H H 8.559 0.001 . 6 2 2 CYS HA H 4.131 0.001 . 7 2 2 CYS HB2 H 3.011 0.003 . 8 2 2 CYS HB3 H 2.621 0.002 . 9 2 2 CYS CA C 55.409 0.000 . 10 2 2 CYS CB C 44.746 0.000 . 11 2 2 CYS N N 116.695 0.000 . 12 3 3 CYS H H 7.178 0.005 . 13 3 3 CYS HA H 4.913 0.005 . 14 3 3 CYS HB2 H 1.901 0.003 . 15 3 3 CYS HB3 H 3.390 0.001 . 16 3 3 CYS CA C 55.335 0.000 . 17 3 3 CYS CB C 45.088 0.024 . 18 3 3 CYS N N 120.084 0.000 . 19 5 5 CYS H H 8.548 0.002 . 20 5 5 CYS HA H 4.942 0.002 . 21 5 5 CYS HB2 H 3.243 0.004 . 22 5 5 CYS HB3 H 2.754 0.001 . 23 5 5 CYS CA C 52.371 0.000 . 24 5 5 CYS CB C 43.509 0.034 . 25 5 5 CYS N N 121.921 0.000 . 26 7 7 ALA H H 7.841 0.002 . 27 7 7 ALA HA H 4.312 0.004 . 28 7 7 ALA HB H 1.174 0.001 . 29 7 7 ALA CB C 20.656 0.000 . 30 7 7 ALA N N 118.266 0.000 . 31 8 8 GLY H H 8.177 0.002 . 32 8 8 GLY HA2 H 4.057 0.001 . 33 8 8 GLY HA3 H 3.597 0.000 . 34 8 8 GLY CA C 44.468 0.033 . 35 8 8 GLY N N 107.501 0.000 . 36 9 9 ALA H H 8.162 0.002 . 37 9 9 ALA HA H 3.994 0.000 . 38 9 9 ALA HB H 1.230 0.003 . 39 9 9 ALA CA C 53.579 0.000 . 40 9 9 ALA CB C 19.278 0.000 . 41 9 9 ALA N N 121.959 0.000 . 42 10 10 VAL H H 7.703 0.002 . 43 10 10 VAL HA H 3.920 0.001 . 44 10 10 VAL HB H 1.741 0.000 . 45 10 10 VAL HG1 H 0.770 0.000 . 46 10 10 VAL HG2 H 0.770 0.000 . 47 10 10 VAL CA C 61.899 0.000 . 48 10 10 VAL CB C 32.027 0.000 . 49 10 10 VAL N N 118.039 0.000 . 50 11 11 ARG H H 8.274 0.002 . 51 11 11 ARG HA H 3.876 0.000 . 52 11 11 ARG HB2 H 1.587 0.006 . 53 11 11 ARG HB3 H 1.694 0.002 . 54 11 11 ARG HG2 H 1.494 0.002 . 55 11 11 ARG HG3 H 1.494 0.002 . 56 11 11 ARG HD2 H 3.026 0.000 . 57 11 11 ARG HD3 H 3.026 0.000 . 58 11 11 ARG HE H 7.034 0.002 . 59 11 11 ARG CA C 57.653 0.000 . 60 11 11 ARG CB C 30.142 0.005 . 61 11 11 ARG CG C 26.391 0.000 . 62 11 11 ARG N N 124.459 0.000 . 63 11 11 ARG NE N 124.819 0.000 . 64 12 12 CYS H H 7.753 0.002 . 65 12 12 CYS HA H 4.887 0.000 . 66 12 12 CYS HB2 H 2.946 0.003 . 67 12 12 CYS HB3 H 2.734 0.002 . 68 12 12 CYS CB C 46.501 0.011 . 69 12 12 CYS N N 119.838 0.000 . 70 13 13 ARG H H 8.426 0.002 . 71 13 13 ARG HA H 4.800 0.000 . 72 13 13 ARG HB2 H 1.769 0.005 . 73 13 13 ARG HB3 H 2.072 0.005 . 74 13 13 ARG HG2 H 1.570 0.006 . 75 13 13 ARG HG3 H 1.570 0.006 . 76 13 13 ARG HD2 H 3.213 0.000 . 77 13 13 ARG HD3 H 3.128 0.000 . 78 13 13 ARG HE H 6.887 0.002 . 79 13 13 ARG CB C 35.263 0.013 . 80 13 13 ARG N N 123.550 0.000 . 81 13 13 ARG NE N 124.610 0.000 . 82 14 14 PHE H H 9.746 0.003 . 83 14 14 PHE HA H 4.439 0.001 . 84 14 14 PHE HB2 H 3.327 0.002 . 85 14 14 PHE HB3 H 2.894 0.003 . 86 14 14 PHE HD1 H 7.093 0.001 . 87 14 14 PHE HD2 H 7.093 0.001 . 88 14 14 PHE HE1 H 7.151 0.000 . 89 14 14 PHE HE2 H 7.151 0.000 . 90 14 14 PHE CA C 61.807 0.000 . 91 14 14 PHE CB C 37.757 0.019 . 92 14 14 PHE N N 130.168 0.000 . 93 15 15 ALA H H 8.709 0.001 . 94 15 15 ALA HA H 3.886 0.002 . 95 15 15 ALA HB H 1.277 0.000 . 96 15 15 ALA CA C 54.097 0.000 . 97 15 15 ALA CB C 18.346 0.000 . 98 15 15 ALA N N 119.800 0.000 . 99 16 16 CYS H H 7.019 0.003 . 100 16 16 CYS HA H 4.145 0.002 . 101 16 16 CYS HB2 H 3.672 0.003 . 102 16 16 CYS HB3 H 3.085 0.002 . 103 16 16 CYS CA C 55.042 0.000 . 104 16 16 CYS CB C 43.254 0.005 . 105 16 16 CYS N N 112.417 0.000 . 106 17 17 CYS H H 7.666 0.004 . 107 17 17 CYS HA H 4.306 0.002 . 108 17 17 CYS HB2 H 2.969 0.002 . 109 17 17 CYS HB3 H 2.507 0.002 . 110 17 17 CYS CB C 40.588 0.025 . 111 17 17 CYS N N 119.043 0.000 . stop_ save_