data_18875 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; [Aba5,14]BTD-2 ; _BMRB_accession_number 18875 _BMRB_flat_file_name bmr18875.str _Entry_type original _Submission_date 2012-12-04 _Accession_date 2012-12-04 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Head-to-tail (Arg-Gly) cyclic peptide. Residues 5 and 14 are replaced by alpha-aminobuytyric acid.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Conibear Anne C. . 2 Rosengren 'K. Johan' . . 3 Daly Norelle L. . 4 'Troiera Henriques' Sonia . . 5 Craik David J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 106 "13C chemical shifts" 54 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-04-18 update BMRB 'update entry citation' 2013-02-27 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 18722 'High resolution NMR solution structure of a symmetrical theta-defensin, BTD-2' stop_ save_ ############################# # Citation for this entry # ############################# save_SSbonds_JBC _Saveframe_category entry_citation _Citation_full . _Citation_title 'The Cyclic Cystine Ladder in -Defensins Is Important for Structure and Stability, but Not Antibacterial Activity.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23430740 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Conibear Anne C. . 2 Rosengren 'K. Johan' . . 3 Daly Norelle L. . 4 Henriques 'Sonia Troeira' . . 5 Craik David J. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 288 _Journal_issue 15 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 10830 _Page_last 10840 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name '[Aba5,14]BTD-2, cyclic peptide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label [Aba5,14]BTD-2 $Aba5_14_BTD-2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Aba5_14_BTD-2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common [Aba5,14]BTD-2 _Molecular_mass 1884.371 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence GVCRXVCRRGVCRXVCRR loop_ _Residue_seq_code _Residue_label 1 GLY 2 VAL 3 CYS 4 ARG 5 ABU 6 VAL 7 CYS 8 ARG 9 ARG 10 GLY 11 VAL 12 CYS 13 ARG 14 ABU 15 VAL 16 CYS 17 ARG 18 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_ABU _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'GAMMA-AMINO-BUTANOIC ACID' _BMRB_code ABU _PDB_code ABU _Standard_residue_derivative . _Molecular_mass 103.120 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CA CA C . 0 . ? CB CB C . 0 . ? CD CD C . 0 . ? CG CG C . 0 . ? H H H . 0 . ? HA1 HA1 H . 0 . ? HA2 HA2 H . 0 . ? HB1 HB1 H . 0 . ? HB2 HB2 H . 0 . ? HE2 HE2 H . 0 . ? HG1 HG1 H . 0 . ? HG2 HG2 H . 0 . ? HN2 HN2 H . 0 . ? N N N . 0 . ? OE1 OE1 O . 0 . ? OE2 OE2 O . 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 H ? ? SING N HN2 ? ? SING CA CB ? ? SING CA HA1 ? ? SING CA HA2 ? ? SING CB CG ? ? SING CB HB1 ? ? SING CB HB2 ? ? SING CG CD ? ? SING CG HG1 ? ? SING CG HG2 ? ? DOUB CD OE1 ? ? SING CD OE2 ? ? SING OE2 HE2 ? ? 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 [Aba5,14]BTD-2 3 CYS SG [Aba5,14]BTD-2 16 CYS SG single disulfide [Aba5,14]BTD-2 7 CYS SG [Aba5,14]BTD-2 12 CYS SG single peptide [Aba5,14]BTD-2 1 GLY N [Aba5,14]BTD-2 18 ARG C stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $Aba5_14_BTD-2 'Olive Baboon' 9555 Eukaryota Metazoa Papio anubis '[Aba5,14]BTD-2 is an analogue of naturally-occurring BTD-2 from Papio anubis' 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 _Details $Aba5_14_BTD-2 'chemical synthesis' . . . . . 'Solid phase peptide synthesis' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_H2O_D2Osample _Saveframe_category sample _Sample_type solution _Details '0.6 mM, pH 4' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Aba5_14_BTD-2 0.6 mM 'natural abundance' DSS 10 ug 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_D2Osample _Saveframe_category sample _Sample_type solution _Details '0.6 mM, pH 4' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Aba5_14_BTD-2 0.6 mM 'natural abundance' DSS 10 ug 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CcpNmr _Saveframe_category software _Name CcpNmr _Version 2.1 loop_ _Vendor _Address _Electronic_address CCPN . http://www.ccpn.ac.uk/software/analysis stop_ loop_ _Task 'data analysis' 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 3.0 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _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 $H2O_D2Osample save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $H2O_D2Osample save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $D2Osample save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $H2O_D2Osample save_ save_2D_1H-1H_ECOSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ECOSY' _Sample_label $D2Osample save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 4 . pH pressure 1 . atm 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 DSS C 13 'methyl protons' ppm 0.00 internal indirect . . . 0.251449530 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 1H-13C HSQC' stop_ loop_ _Sample_label $H2O_D2Osample $D2Osample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name [Aba5,14]BTD-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 GLY H H 8.688 0.002 1 2 1 1 GLY HA2 H 3.602 0.003 2 3 1 1 GLY HA3 H 4.176 0.004 2 4 1 1 GLY CA C 45.255 0.01 1 5 2 2 VAL H H 7.800 0.002 1 6 2 2 VAL HA H 4.275 0.002 1 7 2 2 VAL HB H 2.132 0.009 1 8 2 2 VAL HG1 H 0.938 0.003 2 9 2 2 VAL HG2 H 0.938 0.003 2 10 2 2 VAL CA C 61.930 0.01 1 11 2 2 VAL CB C 33.240 0.01 1 12 2 2 VAL CG1 C 20.894 0.01 2 13 2 2 VAL CG2 C 20.894 0.01 2 14 3 3 CYS H H 9.072 0.01 1 15 3 3 CYS HA H 5.481 0.002 1 16 3 3 CYS HB2 H 2.974 0.003 2 17 3 3 CYS HB3 H 2.584 0.002 2 18 3 3 CYS CA C 55.307 0.01 1 19 3 3 CYS CB C 46.464 0.034 1 20 4 4 ARG H H 8.701 0.001 1 21 4 4 ARG HA H 4.650 0.003 1 22 4 4 ARG HB2 H 1.834 0.001 2 23 4 4 ARG HB3 H 1.766 0.002 2 24 4 4 ARG HG2 H 1.600 0.012 2 25 4 4 ARG HG3 H 1.535 0.009 2 26 4 4 ARG HD2 H 3.188 0.002 2 27 4 4 ARG HD3 H 3.188 0.002 2 28 4 4 ARG HE H 7.137 0.01 1 29 4 4 ARG CA C 54.333 0.01 1 30 4 4 ARG CB C 33.653 0.016 1 31 4 4 ARG CG C 27.079 0.01 1 32 4 4 ARG CD C 43.370 0.01 1 33 5 5 ABU CA C 57.902 0.01 1 34 5 5 ABU CB C 27.157 0.01 1 35 5 5 ABU H H 8.693 0.002 1 36 5 5 ABU HA H 4.559 0.004 1 37 5 5 ABU HG H 0.814 0.002 1 38 5 5 ABU HB1 H 1.663 0.01 1 39 5 5 ABU HB2 H 1.663 0.01 1 40 6 6 VAL H H 8.989 0.001 1 41 6 6 VAL HA H 4.302 0.003 1 42 6 6 VAL HB H 2.007 0.001 1 43 6 6 VAL HG1 H 0.929 0.006 2 44 6 6 VAL HG2 H 0.929 0.006 2 45 6 6 VAL CA C 61.833 0.01 1 46 6 6 VAL CB C 34.385 0.01 1 47 6 6 VAL CG1 C 20.894 0.01 2 48 6 6 VAL CG2 C 20.894 0.01 2 49 7 7 CYS H H 9.093 0.001 1 50 7 7 CYS HA H 5.583 0.002 1 51 7 7 CYS HB2 H 3.087 0.002 2 52 7 7 CYS HB3 H 2.650 0.002 2 53 7 7 CYS CA C 55.198 0.01 1 54 7 7 CYS CB C 47.739 0.01 1 55 8 8 ARG H H 8.684 0.003 1 56 8 8 ARG HA H 4.507 0.001 1 57 8 8 ARG HB2 H 1.777 0.001 2 58 8 8 ARG HB3 H 1.777 0.001 2 59 8 8 ARG HG2 H 1.519 0.001 2 60 8 8 ARG HG3 H 1.625 0.002 2 61 8 8 ARG HD2 H 3.207 0.003 2 62 8 8 ARG HD3 H 3.207 0.003 2 63 8 8 ARG HE H 7.225 0.01 1 64 8 8 ARG CA C 55.577 0.01 1 65 8 8 ARG CB C 32.596 0.01 1 66 8 8 ARG CG C 27.139 0.001 1 67 8 8 ARG CD C 43.265 0.01 1 68 9 9 ARG H H 9.602 0.001 1 69 9 9 ARG HA H 3.911 0.003 1 70 9 9 ARG HB2 H 2.085 0.008 2 71 9 9 ARG HB3 H 1.830 0.002 2 72 9 9 ARG HG2 H 1.633 0.001 2 73 9 9 ARG HG3 H 1.633 0.001 2 74 9 9 ARG HD2 H 3.226 0.002 2 75 9 9 ARG HD3 H 3.226 0.002 2 76 9 9 ARG HE H 7.230 0.01 1 77 9 9 ARG CA C 57.091 0.01 1 78 9 9 ARG CB C 28.163 0.01 1 79 9 9 ARG CG C 27.774 0.01 1 80 9 9 ARG CD C 43.300 0.01 1 81 10 10 GLY H H 8.688 0.002 1 82 10 10 GLY HA2 H 3.602 0.003 2 83 10 10 GLY HA3 H 4.176 0.004 2 84 10 10 GLY CA C 45.255 0.01 1 85 11 11 VAL H H 7.800 0.002 1 86 11 11 VAL HA H 4.275 0.002 1 87 11 11 VAL HB H 2.132 0.009 1 88 11 11 VAL HG1 H 0.938 0.003 2 89 11 11 VAL HG2 H 0.938 0.003 2 90 11 11 VAL CA C 61.930 0.01 1 91 11 11 VAL CB C 33.240 0.01 1 92 11 11 VAL CG1 C 20.894 0.01 2 93 11 11 VAL CG2 C 20.894 0.01 2 94 12 12 CYS H H 9.072 0.01 1 95 12 12 CYS HA H 5.481 0.002 1 96 12 12 CYS HB2 H 2.974 0.003 2 97 12 12 CYS HB3 H 2.584 0.002 2 98 12 12 CYS CA C 55.307 0.01 1 99 12 12 CYS CB C 46.464 0.034 1 100 13 13 ARG H H 8.701 0.001 1 101 13 13 ARG HA H 4.650 0.003 1 102 13 13 ARG HB2 H 1.834 0.001 2 103 13 13 ARG HB3 H 1.766 0.002 2 104 13 13 ARG HG2 H 1.600 0.012 2 105 13 13 ARG HG3 H 1.535 0.009 2 106 13 13 ARG HD2 H 3.188 0.002 2 107 13 13 ARG HD3 H 3.188 0.002 2 108 13 13 ARG HE H 7.137 0.01 1 109 13 13 ARG CA C 54.333 0.01 1 110 13 13 ARG CB C 33.653 0.016 1 111 13 13 ARG CG C 27.079 0.01 1 112 13 13 ARG CD C 43.370 0.01 1 113 14 14 ABU CA C 57.902 0.01 1 114 14 14 ABU CB C 27.157 0.01 1 115 14 14 ABU H H 8.693 0.002 1 116 14 14 ABU HA H 4.559 0.004 1 117 14 14 ABU HG H 0.814 0.002 1 118 14 14 ABU HB1 H 1.663 0.01 1 119 14 14 ABU HB2 H 1.663 0.01 1 120 15 15 VAL H H 8.989 0.001 1 121 15 15 VAL HA H 4.302 0.003 1 122 15 15 VAL HB H 2.007 0.001 1 123 15 15 VAL HG1 H 0.929 0.006 2 124 15 15 VAL HG2 H 0.929 0.006 2 125 15 15 VAL CA C 61.833 0.01 1 126 15 15 VAL CB C 34.385 0.01 1 127 15 15 VAL CG1 C 20.894 0.01 2 128 15 15 VAL CG2 C 20.894 0.01 2 129 16 16 CYS H H 9.093 0.001 1 130 16 16 CYS HA H 5.583 0.002 1 131 16 16 CYS HB2 H 3.087 0.002 2 132 16 16 CYS HB3 H 2.650 0.002 2 133 16 16 CYS CA C 55.198 0.01 1 134 16 16 CYS CB C 47.739 0.01 1 135 17 17 ARG H H 8.684 0.003 1 136 17 17 ARG HA H 4.507 0.001 1 137 17 17 ARG HB2 H 1.777 0.001 2 138 17 17 ARG HB3 H 1.777 0.001 2 139 17 17 ARG HG2 H 1.519 0.001 2 140 17 17 ARG HG3 H 1.625 0.002 2 141 17 17 ARG HD2 H 3.207 0.003 2 142 17 17 ARG HD3 H 3.207 0.003 2 143 17 17 ARG HE H 7.225 0.01 1 144 17 17 ARG CA C 55.577 0.01 1 145 17 17 ARG CB C 32.596 0.01 1 146 17 17 ARG CG C 27.139 0.001 1 147 17 17 ARG CD C 43.265 0.01 1 148 18 18 ARG H H 9.602 0.001 1 149 18 18 ARG HA H 3.911 0.003 1 150 18 18 ARG HB2 H 2.085 0.008 2 151 18 18 ARG HB3 H 1.830 0.002 2 152 18 18 ARG HG2 H 1.633 0.001 2 153 18 18 ARG HG3 H 1.633 0.001 2 154 18 18 ARG HD2 H 3.226 0.002 2 155 18 18 ARG HD3 H 3.226 0.002 2 156 18 18 ARG HE H 7.230 0.01 1 157 18 18 ARG CA C 57.091 0.01 1 158 18 18 ARG CB C 28.163 0.01 1 159 18 18 ARG CG C 27.774 0.01 1 160 18 18 ARG CD C 43.300 0.01 1 stop_ save_