data_18723 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; High resolution NMR solution structure of the theta-defensin RTD-1 ; _BMRB_accession_number 18723 _BMRB_flat_file_name bmr18723.str _Entry_type original _Submission_date 2012-09-18 _Accession_date 2012-09-18 _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" 87 "13C chemical shifts" 41 "15N chemical shifts" 12 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_ loop_ _Related_BMRB_accession_number _Relationship 18722 'symmetrical theta-defensin, BTD-2' 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 RTD-1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label RTD-1 $RTD-1 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_RTD-1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common RTD-1 _Molecular_mass 2110.656 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence GFCRCLCRRGVCRCICTR loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 GLY 2 2 PHE 3 3 CYS 4 4 ARG 5 5 CYS 6 6 LEU 7 7 CYS 8 8 ARG 9 9 ARG 10 10 GLY 11 11 VAL 12 12 CYS 13 13 ARG 14 14 CYS 15 15 ILE 16 16 CYS 17 17 THR 18 18 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-29 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 1HVZ "Rtd-1, A Cyclic Antimicrobial Defensin From Rhesus Macaque Leukocytes" 94.44 18 100.00 100.00 1.36e+00 PDB 2LYF "High Resolution Nmr Solution Structure Of The Theta-defensin Rtd-1" 100.00 18 100.00 100.00 2.34e-01 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 RTD-1 3 CYS SG RTD-1 16 CYS SG single disulfide RTD-1 5 CYS SG RTD-1 14 CYS SG single disulfide RTD-1 7 CYS SG RTD-1 12 CYS 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 $RTD-1 'Rhesus monkey' 9544 Eukaryota Metazoa Macacca mulatta 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 $RTD-1 '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 $RTD-1 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 3' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RTD-1 1.0 mM '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_ 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 4.0 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 RTD-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 GLY HA2 H 3.593 0.010 1 2 1 1 GLY HA3 H 4.127 0.010 1 3 1 1 GLY H H 8.599 0.010 1 4 1 1 GLY CA C 45.328 0.010 1 5 1 1 GLY N N 104.863 0.010 1 6 2 2 PHE H H 7.953 0.010 1 7 2 2 PHE HA H 4.898 0.010 1 8 2 2 PHE HB2 H 3.078 0.010 1 9 2 2 PHE HB3 H 3.184 0.010 1 10 2 2 PHE CA C 56.864 0.010 1 11 2 2 PHE CB C 40.850 0.010 1 12 2 2 PHE N N 121.029 0.010 1 13 3 3 CYS H H 8.741 0.010 1 14 3 3 CYS HA H 5.374 0.010 1 15 3 3 CYS HB2 H 2.590 0.010 1 16 3 3 CYS HB3 H 2.951 0.010 1 17 3 3 CYS CA C 55.415 0.010 1 18 3 3 CYS CB C 47.259 0.010 1 19 3 3 CYS N N 125.277 0.010 1 20 4 4 ARG H H 8.626 0.010 1 21 4 4 ARG HA H 4.606 0.010 1 22 4 4 ARG HB2 H 1.824 0.010 1 23 4 4 ARG HB3 H 1.877 0.010 1 24 4 4 ARG HD2 H 3.208 0.010 1 25 4 4 ARG HD3 H 3.273 0.010 1 26 4 4 ARG CA C 55.042 0.010 1 27 4 4 ARG CB C 32.493 0.010 1 28 4 4 ARG CD C 43.357 0.010 1 29 4 4 ARG N N 122.866 0.010 1 30 5 5 CYS H H 9.070 0.010 1 31 5 5 CYS HA H 5.489 0.010 1 32 5 5 CYS HB2 H 2.635 0.010 1 33 5 5 CYS HB3 H 3.065 0.010 1 34 5 5 CYS CA C 55.359 0.010 1 35 5 5 CYS CB C 48.035 0.010 1 36 6 6 LEU H H 8.696 0.010 1 37 6 6 LEU HA H 4.718 0.010 1 38 6 6 LEU HB2 H 1.814 0.010 1 39 6 6 LEU HB3 H 1.735 0.010 1 40 6 6 LEU HG H 1.553 0.010 1 41 6 6 LEU HD1 H 0.930 0.010 1 42 6 6 LEU HD2 H 0.930 0.010 1 43 6 6 LEU CA C 54.396 0.010 1 44 6 6 LEU CB C 44.460 0.010 1 45 6 6 LEU N N 123.254 0.010 1 46 7 7 CYS H H 9.111 0.010 1 47 7 7 CYS HA H 5.571 0.010 1 48 7 7 CYS HB2 H 2.895 0.010 1 49 7 7 CYS HB3 H 2.870 0.010 1 50 7 7 CYS CA C 55.437 0.010 1 51 7 7 CYS CB C 48.035 0.010 1 52 8 8 ARG H H 8.686 0.010 1 53 8 8 ARG HA H 4.522 0.010 1 54 8 8 ARG HB2 H 1.814 0.010 1 55 8 8 ARG HB3 H 1.865 0.010 1 56 8 8 ARG HD2 H 3.232 0.010 1 57 8 8 ARG HD3 H 3.228 0.010 1 58 8 8 ARG CA C 55.655 0.010 1 59 8 8 ARG CB C 32.469 0.010 1 60 8 8 ARG CD C 43.321 0.010 1 61 8 8 ARG N N 123.295 0.010 1 62 9 9 ARG H H 9.570 0.010 1 63 9 9 ARG HA H 3.925 0.010 1 64 9 9 ARG HB2 H 1.848 0.010 1 65 9 9 ARG HB3 H 2.098 0.010 1 66 9 9 ARG HD2 H 3.239 0.010 1 67 9 9 ARG HD3 H 3.237 0.010 1 68 9 9 ARG CA C 57.049 0.010 1 69 9 9 ARG CB C 28.131 0.010 1 70 9 9 ARG CD C 43.163 0.010 1 71 9 9 ARG N N 125.074 0.010 1 72 10 10 GLY H H 8.682 0.010 1 73 10 10 GLY HA2 H 3.609 0.010 1 74 10 10 GLY HA3 H 4.180 0.010 1 75 10 10 GLY CA C 45.318 0.010 1 76 10 10 GLY N N 104.449 0.010 1 77 11 11 VAL H H 7.807 0.010 1 78 11 11 VAL HA H 4.301 0.010 1 79 11 11 VAL HB H 2.139 0.010 1 80 11 11 VAL HG1 H 0.945 0.010 1 81 11 11 VAL HG2 H 0.945 0.010 1 82 11 11 VAL CA C 61.766 0.010 1 83 11 11 VAL CB C 33.509 0.010 1 84 11 11 VAL N N 121.730 0.010 1 85 12 12 CYS H H 9.082 0.010 1 86 12 12 CYS HA H 5.467 0.010 1 87 12 12 CYS HB2 H 3.040 0.010 1 88 12 12 CYS HB3 H 2.765 0.010 1 89 12 12 CYS CA C 55.302 0.010 1 90 12 12 CYS CB C 48.215 0.010 1 91 13 13 ARG H H 8.676 0.010 1 92 13 13 ARG HA H 4.691 0.010 1 93 13 13 ARG HB2 H 1.648 0.010 1 94 13 13 ARG HB3 H 1.731 0.010 1 95 13 13 ARG HD2 H 3.235 0.010 1 96 13 13 ARG HD3 H 3.234 0.010 1 97 13 13 ARG CA C 55.059 0.010 1 98 13 13 ARG CB C 32.909 0.010 1 99 13 13 ARG CD C 43.177 0.010 1 100 13 13 ARG N N 123.309 0.010 1 101 14 14 CYS H H 9.111 0.010 1 102 14 14 CYS HA H 5.528 0.010 1 103 14 14 CYS HB2 H 2.600 0.010 1 104 14 14 CYS HB3 H 3.067 0.010 1 105 14 14 CYS CA C 55.606 0.010 1 106 14 14 CYS CB C 48.219 0.010 1 107 15 15 ILE H H 8.782 0.010 1 108 15 15 ILE HA H 4.409 0.010 1 109 15 15 ILE HB H 1.831 0.010 1 110 15 15 ILE HG12 H 1.169 0.010 1 111 15 15 ILE HG13 H 1.169 0.010 1 112 15 15 ILE HG2 H 0.920 0.010 1 113 15 15 ILE HD1 H 0.920 0.010 1 114 15 15 ILE CA C 60.358 0.010 1 115 15 15 ILE CB C 40.460 0.010 1 116 15 15 ILE CG1 C 27.431 0.010 1 117 15 15 ILE N N 123.850 0.010 1 118 16 16 CYS H H 9.138 0.010 1 119 16 16 CYS HA H 5.598 0.010 1 120 16 16 CYS HB2 H 2.716 0.010 1 121 16 16 CYS HB3 H 3.109 0.010 1 122 16 16 CYS CA C 55.471 0.010 1 123 16 16 CYS CB C 47.821 0.010 1 124 17 17 THR H H 8.804 0.010 1 125 17 17 THR HA H 4.486 0.010 1 126 17 17 THR HB H 4.155 0.010 1 127 17 17 THR HG2 H 1.231 0.010 1 128 17 17 THR CA C 61.120 0.010 1 129 17 17 THR CB C 70.385 0.010 1 130 17 17 THR CG2 C 21.086 0.010 1 131 17 17 THR N N 118.568 0.010 1 132 18 18 ARG H H 9.404 0.010 1 133 18 18 ARG HA H 3.937 0.010 1 134 18 18 ARG HB2 H 1.944 0.010 1 135 18 18 ARG HB3 H 2.106 0.010 1 136 18 18 ARG HD2 H 3.286 0.010 1 137 18 18 ARG HD3 H 3.282 0.010 1 138 18 18 ARG CA C 57.366 0.010 1 139 18 18 ARG CB C 28.321 0.010 1 140 18 18 ARG CD C 43.338 0.010 1 stop_ save_