data_18757 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; High resolution NMR structure of the theta-defensin HTD-2 (retrocyclin 2) ; _BMRB_accession_number 18757 _BMRB_flat_file_name bmr18757.str _Entry_type original _Submission_date 2012-10-02 _Accession_date 2012-10-02 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Head-to-tail (Arg-Gly) cyclic peptide' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Conibear Anne C. . 2 Rosengren 'K. Johan' . . 3 Harvey Peta J. . 4 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" 101 "13C chemical shifts" 49 "15N chemical shifts" 10 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-18 update BMRB 'update entry citation' 2012-11-27 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural Characterization of the Cyclic Cystine Ladder Motif of -Defensins.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23148585 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Conibear Anne C. . 2 Rosengren 'K. Johan' . . 3 Harvey Peta J. . 4 Craik David J. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 51 _Journal_issue 48 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9718 _Page_last 9726 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'theta-defensin HTD-2 (retrocyclin 2)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'theta-defensin HTD-2 (retrocyclin 2)' $HTD-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_HTD-2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common HTD-2 _Molecular_mass 2046.613 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence GICRCICGRRICRCICGR loop_ _Residue_seq_code _Residue_label 1 GLY 2 ILE 3 CYS 4 ARG 5 CYS 6 ILE 7 CYS 8 GLY 9 ARG 10 ARG 11 ILE 12 CYS 13 ARG 14 CYS 15 ILE 16 CYS 17 GLY 18 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-11-09 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 2LZI "High Resolution Nmr Structure Of The Theta-defensin Htd-2 (retrocyclin 2)" 100.00 18 100.00 100.00 1.14e+00 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $HTD-2 Human 9606 Eukaryota Metazoa Homo sapiens 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 $HTD-2 'chemical synthesis' . . . . . 'Solid phase peptide synthesis' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1.0 mM, pH 5' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HTD-2 1.0 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '1.0 mM, pH 5' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HTD-2 1.0 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . 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_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _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_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_ECOSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ECOSY' _Sample_label $sample_2 save_ save_2D_1H-15N_HSQC_6 _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 temperature 298 . K pH 5.0 1.0 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 water N 15 protons ppm 0.00 na indirect . . . -0.101363 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' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'theta-defensin HTD-2 (retrocyclin 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 HA2 H 3.782 0.002 . 2 1 1 GLY HA3 H 4.129 0.004 . 3 1 1 GLY H H 8.487 0.002 . 4 1 1 GLY CA C 45.078 0.020 . 5 2 2 ILE H H 7.927 0.006 . 6 2 2 ILE HA H 4.494 0.005 . 7 2 2 ILE HB H 1.861 0.007 . 8 2 2 ILE HG12 H 1.164 0.006 . 9 2 2 ILE HG13 H 1.442 0.106 . 10 2 2 ILE HG2 H 0.881 0.002 . 11 2 2 ILE HD1 H 0.855 0.002 . 12 2 2 ILE CA C 59.956 0.000 . 13 2 2 ILE CB C 40.197 0.000 . 14 2 2 ILE CG1 C 27.176 0.012 . 15 2 2 ILE CG2 C 17.536 0.000 . 16 2 2 ILE CD1 C 12.701 0.000 . 17 2 2 ILE N N 120.907 0.000 . 18 3 3 CYS H H 8.899 0.007 . 19 3 3 CYS HA H 5.308 0.005 . 20 3 3 CYS HB2 H 2.745 0.002 . 21 3 3 CYS HB3 H 3.014 0.002 . 22 3 3 CYS CA C 56.013 0.000 . 23 3 3 CYS N N 124.107 0.000 . 24 4 4 ARG H H 8.714 0.005 . 25 4 4 ARG HA H 4.663 0.002 . 26 4 4 ARG HB2 H 1.804 0.002 . 27 4 4 ARG HB3 H 1.804 0.002 . 28 4 4 ARG HG2 H 1.574 0.004 . 29 4 4 ARG HG3 H 1.649 0.003 . 30 4 4 ARG HD2 H 3.207 0.004 . 31 4 4 ARG HD3 H 3.207 0.004 . 32 4 4 ARG CA C 55.267 0.000 . 33 4 4 ARG CB C 31.817 0.000 . 34 4 4 ARG CG C 27.346 0.013 . 35 4 4 ARG CD C 43.284 0.000 . 36 4 4 ARG N N 123.254 0.000 . 37 5 5 CYS H H 9.020 0.009 . 38 5 5 CYS HA H 5.404 0.004 . 39 5 5 CYS HB2 H 2.742 0.002 . 40 5 5 CYS HB3 H 3.099 0.006 . 41 5 5 CYS CA C 55.641 0.000 . 42 5 5 CYS CB C 46.464 0.026 . 43 5 5 CYS N N 123.464 0.000 . 44 6 6 ILE H H 8.780 0.005 . 45 6 6 ILE HA H 4.364 0.002 . 46 6 6 ILE HB H 1.845 0.005 . 47 6 6 ILE HG12 H 1.184 0.002 . 48 6 6 ILE HG13 H 1.482 0.122 . 49 6 6 ILE HG2 H 0.911 0.005 . 50 6 6 ILE HD1 H 0.865 0.006 . 51 6 6 ILE CA C 60.712 0.000 . 52 6 6 ILE CB C 39.591 0.000 . 53 6 6 ILE CG1 C 27.348 0.014 . 54 6 6 ILE CG2 C 17.456 0.000 . 55 6 6 ILE CD1 C 12.701 0.000 . 56 6 6 ILE N N 124.141 0.000 . 57 7 7 CYS H H 9.135 0.005 . 58 7 7 CYS HA H 5.331 0.005 . 59 7 7 CYS HB2 H 2.964 0.003 . 60 7 7 CYS HB3 H 3.112 0.004 . 61 7 7 CYS CA C 55.862 0.000 . 62 8 8 GLY H H 8.588 0.004 . 63 8 8 GLY HA2 H 3.877 0.002 . 64 8 8 GLY HA3 H 4.228 0.001 . 65 8 8 GLY CA C 45.142 0.000 . 66 9 9 ARG H H 8.873 0.004 . 67 9 9 ARG HA H 4.130 0.003 . 68 9 9 ARG HB2 H 1.836 0.003 . 69 9 9 ARG HB3 H 1.942 0.003 . 70 9 9 ARG HG2 H 1.674 0.014 . 71 9 9 ARG HG3 H 1.674 0.014 . 72 9 9 ARG HD2 H 3.230 0.006 . 73 9 9 ARG HD3 H 3.230 0.006 . 74 9 9 ARG CA C 57.376 0.000 . 75 9 9 ARG CB C 29.621 0.003 . 76 9 9 ARG CG C 27.359 0.000 . 77 9 9 ARG CD C 43.222 0.000 . 78 10 10 ARG H H 8.382 0.003 . 79 10 10 ARG HA H 4.339 0.004 . 80 10 10 ARG HB2 H 1.944 0.008 . 81 10 10 ARG HB3 H 1.944 0.008 . 82 10 10 ARG HG2 H 1.608 0.007 . 83 10 10 ARG HG3 H 1.608 0.007 . 84 10 10 ARG HD2 H 3.224 0.003 . 85 10 10 ARG HD3 H 3.224 0.003 . 86 10 10 ARG CA C 56.589 0.000 . 87 10 10 ARG CB C 31.418 0.000 . 88 10 10 ARG CG C 27.482 0.000 . 89 10 10 ARG CD C 43.222 0.000 . 90 11 11 ILE H H 8.002 0.006 . 91 11 11 ILE HA H 4.483 0.003 . 92 11 11 ILE HB H 1.864 0.004 . 93 11 11 ILE HG12 H 1.201 0.006 . 94 11 11 ILE HG13 H 1.488 0.002 . 95 11 11 ILE HG2 H 0.878 0.004 . 96 11 11 ILE HD1 H 0.853 0.004 . 97 11 11 ILE CA C 60.141 0.000 . 98 11 11 ILE CB C 40.197 0.000 . 99 11 11 ILE CG2 C 17.536 0.000 . 100 11 11 ILE CD1 C 12.701 0.000 . 101 11 11 ILE N N 119.146 0.000 . 102 12 12 CYS H H 8.821 0.003 . 103 12 12 CYS HA H 5.302 0.004 . 104 12 12 CYS HB2 H 2.746 0.002 . 105 12 12 CYS HB3 H 3.101 0.005 . 106 12 12 CYS CA C 56.013 0.000 . 107 13 13 ARG H H 8.680 0.007 . 108 13 13 ARG HA H 4.664 0.002 . 109 13 13 ARG HB2 H 1.801 0.004 . 110 13 13 ARG HB3 H 1.801 0.004 . 111 13 13 ARG HG2 H 1.567 0.002 . 112 13 13 ARG HG3 H 1.643 0.001 . 113 13 13 ARG HD2 H 3.209 0.009 . 114 13 13 ARG HD3 H 3.209 0.009 . 115 13 13 ARG CA C 55.267 0.000 . 116 13 13 ARG CB C 31.817 0.000 . 117 13 13 ARG CG C 27.345 0.011 . 118 13 13 ARG CD C 43.222 0.000 . 119 13 13 ARG N N 122.886 0.000 . 120 14 14 CYS H H 9.020 0.009 . 121 14 14 CYS HA H 5.404 0.003 . 122 14 14 CYS HB2 H 2.743 0.002 . 123 14 14 CYS HB3 H 3.099 0.006 . 124 14 14 CYS CA C 55.641 0.000 . 125 14 14 CYS CB C 46.464 0.026 . 126 14 14 CYS N N 123.464 0.000 . 127 15 15 ILE H H 8.780 0.005 . 128 15 15 ILE HA H 4.362 0.003 . 129 15 15 ILE HB H 1.844 0.005 . 130 15 15 ILE HG12 H 1.184 0.003 . 131 15 15 ILE HG13 H 1.534 0.003 . 132 15 15 ILE HG2 H 0.913 0.003 . 133 15 15 ILE HD1 H 0.865 0.006 . 134 15 15 ILE CA C 60.712 0.000 . 135 15 15 ILE CB C 39.591 0.000 . 136 15 15 ILE CG2 C 17.456 0.000 . 137 15 15 ILE CD1 C 12.701 0.000 . 138 15 15 ILE N N 124.141 0.000 . 139 16 16 CYS H H 8.973 0.005 . 140 16 16 CYS HA H 5.547 0.004 . 141 16 16 CYS HB2 H 2.911 0.003 . 142 16 16 CYS HB3 H 3.133 0.005 . 143 16 16 CYS CA C 55.098 0.000 . 144 17 17 GLY H H 8.760 0.007 . 145 17 17 GLY HA2 H 3.915 0.001 . 146 17 17 GLY HA3 H 4.087 0.010 . 147 17 17 GLY CA C 46.061 0.024 . 148 17 17 GLY N N 111.815 0.000 . 149 18 18 ARG H H 9.110 0.004 . 150 18 18 ARG HA H 4.096 0.005 . 151 18 18 ARG HB2 H 1.865 0.007 . 152 18 18 ARG HB3 H 2.038 0.003 . 153 18 18 ARG HG2 H 1.640 0.006 . 154 18 18 ARG HG3 H 1.640 0.006 . 155 18 18 ARG HD2 H 3.219 0.001 . 156 18 18 ARG HD3 H 3.219 0.001 . 157 18 18 ARG CA C 56.658 0.000 . 158 18 18 ARG CB C 28.535 0.015 . 159 18 18 ARG CG C 27.355 0.000 . 160 18 18 ARG CD C 43.222 0.000 . stop_ save_