data_19177 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; [Asp2,11]RTD-1 ; _BMRB_accession_number 19177 _BMRB_flat_file_name bmr19177.str _Entry_type original _Submission_date 2013-04-19 _Accession_date 2013-04-19 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; High resolution NMR solution structure of a theta-defensin analogue containing the RGD integrin-binding sequence. 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 Bochen Alexander . . 3 Rosengren 'K. Johan' . . 4 Kessler Horst . . 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" 101 "13C chemical shifts" 51 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-02-05 update author 'update entry citation, etc.' 2014-02-03 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 19175 [Asp2]RTD-1 19176 [Asp11]RTD-1 stop_ save_ ############################# # Citation for this entry # ############################# save_RGD_peptides _Saveframe_category entry_citation _Citation_full . _Citation_title 'The Cyclic Cystine Ladder of Theta-Defensins as a Stable, Bifunctional Scaffold: A Proof-of-Concept Study Using the Integrin-Binding RGD Motif' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24382674 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Conibear Anne C. . 2 Bochen Alexander . . 3 Rosengren 'K. Johan' . . 4 Stupar Petar . . 5 Wang Conan . . 6 Kessler Horst . . 7 Craik David J. . stop_ _Journal_abbreviation ChemBioChem _Journal_volume 15 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 451 _Page_last 459 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name [Asp2,11]RTD-1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label [Asp2,11]RTD-1 $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 2094.525 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence GDCRCLCRRGDCRCICTR loop_ _Residue_seq_code _Residue_label 1 GLY 2 ASP 3 CYS 4 ARG 5 CYS 6 LEU 7 CYS 8 ARG 9 ARG 10 GLY 11 ASP 12 CYS 13 ARG 14 CYS 15 ILE 16 CYS 17 THR 18 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-06-22 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 2M79 [asp2,11]rtd-1 100.00 18 100.00 100.00 2.18e-01 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 'Rhesus monkey' 9544 Eukaryota Metazoa Macacca mulata 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 $entity 'chemical synthesis' . . . . . 'Solid phase peptide synthesis' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_H2O-D2Osample _Saveframe_category sample _Sample_type solution _Details '0.9 mM, pH 4' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 0.9 mM 'natural abundance' DSS 10 ug 'natural abundance' stop_ save_ save_D2Osample _Saveframe_category sample _Sample_type solution _Details '0.5 mM, pH 3' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 0.5 mM 'natural abundance' DSS 10 ug '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_Bruker_Av500 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_Bruker_Av600 _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 3 . 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 [Asp2,11]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 H H 8.610 0.010 1 2 1 1 GLY HA2 H 4.141 0.015 2 3 1 1 GLY HA3 H 3.672 0.004 2 4 1 1 GLY CA C 45.317 0.000 1 5 2 2 ASP H H 7.937 0.003 1 6 2 2 ASP HA H 4.970 0.001 1 7 2 2 ASP HB2 H 3.012 0.015 2 8 2 2 ASP HB3 H 2.760 0.019 2 9 2 2 ASP CA C 51.923 0.000 1 10 2 2 ASP CB C 38.973 0.000 1 11 3 3 CYS H H 8.868 0.014 1 12 3 3 CYS HA H 5.385 0.009 1 13 3 3 CYS HB2 H 3.062 0.000 2 14 3 3 CYS HB3 H 2.664 0.000 2 15 3 3 CYS CA C 55.799 0.000 1 16 3 3 CYS CB C 46.371 0.000 1 17 4 4 ARG H H 8.619 0.008 1 18 4 4 ARG HA H 4.672 0.007 1 19 4 4 ARG HB2 H 1.850 0.002 2 20 4 4 ARG HB3 H 1.850 0.002 2 21 4 4 ARG HG2 H 1.656 0.003 2 22 4 4 ARG HG3 H 1.594 0.007 2 23 4 4 ARG HD2 H 3.224 0.005 2 24 4 4 ARG HD3 H 3.224 0.005 2 25 4 4 ARG HE H 7.319 0.000 1 26 4 4 ARG CA C 55.052 0.000 1 27 4 4 ARG CB C 32.195 0.000 1 28 4 4 ARG CG C 27.177 0.000 1 29 4 4 ARG CD C 43.165 0.000 1 30 5 5 CYS H H 9.041 0.003 1 31 5 5 CYS HA H 5.482 0.013 1 32 5 5 CYS HB2 H 2.658 0.000 2 33 5 5 CYS HB3 H 3.047 0.002 2 34 5 5 CYS CA C 55.522 0.000 1 35 5 5 CYS CB C 47.261 0.000 1 36 6 6 LEU H H 8.701 0.001 1 37 6 6 LEU HA H 4.678 0.000 1 38 6 6 LEU HB2 H 1.568 0.003 2 39 6 6 LEU HB3 H 1.568 0.003 2 40 6 6 LEU HG H 1.565 0.000 1 41 6 6 LEU HD1 H 0.924 0.000 2 42 6 6 LEU HD2 H 0.924 0.000 2 43 6 6 LEU CA C 54.684 0.000 1 44 6 6 LEU CB C 44.113 0.000 1 45 6 6 LEU CG C 27.25 0.000 1 46 6 6 LEU CD1 C 24.468 0.000 1 47 6 6 LEU CD2 C 24.468 0.000 1 48 7 7 CYS H H 9.050 0.001 1 49 7 7 CYS HA H 5.453 0.001 1 50 7 7 CYS HB2 H 2.751 0.001 2 51 7 7 CYS HB3 H 3.093 0.002 2 52 7 7 CYS CA C 55.342 0.000 1 53 7 7 CYS CB C 47.558 0.000 1 54 8 8 ARG H H 8.589 0.006 1 55 8 8 ARG HA H 4.528 0.007 1 56 8 8 ARG HB2 H 1.824 0.000 2 57 8 8 ARG HB3 H 1.824 0.000 2 58 8 8 ARG HG2 H 1.653 0.006 2 59 8 8 ARG HG3 H 1.559 0.004 2 60 8 8 ARG HD2 H 3.238 0.001 2 61 8 8 ARG HD3 H 3.238 0.001 2 62 8 8 ARG HE H 7.265 0.001 1 63 8 8 ARG CA C 55.593 0.000 1 64 8 8 ARG CB C 32.226 0.000 1 65 8 8 ARG CG C 27.260 0.000 1 66 8 8 ARG CD C 43.140 0.000 1 67 9 9 ARG H H 9.392 0.010 1 68 9 9 ARG HA H 3.931 0.003 1 69 9 9 ARG HB2 H 2.039 0.002 2 70 9 9 ARG HB3 H 1.893 0.000 2 71 9 9 ARG HG2 H 1.635 0.007 2 72 9 9 ARG HG3 H 1.635 0.007 2 73 9 9 ARG HD2 H 3.255 0.002 2 74 9 9 ARG HD3 H 3.255 0.002 2 75 9 9 ARG HE H 7.257 0.000 1 76 9 9 ARG CA C 57.006 0.000 1 77 9 9 ARG CB C 28.248 0.000 1 78 9 9 ARG CG C 27.633 0.000 1 79 9 9 ARG CD C 43.252 0.000 1 80 10 10 GLY H H 8.630 0.004 1 81 10 10 GLY HA2 H 4.146 0.001 2 82 10 10 GLY HA3 H 3.664 0.002 2 83 10 10 GLY CA C 45.322 0.000 1 84 11 11 ASP H H 7.920 0.007 1 85 11 11 ASP HA H 4.984 0.017 1 86 11 11 ASP HB2 H 2.993 0.017 2 87 11 11 ASP HB3 H 2.755 0.013 2 88 11 11 ASP CA C 52.034 0.000 1 89 11 11 ASP CB C 39.254 0.000 1 90 12 12 CYS H H 8.880 0.001 1 91 12 12 CYS HA H 5.378 0.015 1 92 12 12 CYS HB2 H 3.041 0.000 2 93 12 12 CYS HB3 H 2.679 0.000 2 94 12 12 CYS CA C 55.664 0.000 1 95 12 12 CYS CB C 46.305 0.000 1 96 13 13 ARG H H 8.714 0.007 1 97 13 13 ARG HA H 4.689 0.009 1 98 13 13 ARG HB2 H 1.838 0.002 2 99 13 13 ARG HB3 H 1.838 0.002 2 100 13 13 ARG HG2 H 1.664 0.004 2 101 13 13 ARG HG3 H 1.664 0.004 2 102 13 13 ARG HD2 H 3.220 0.004 2 103 13 13 ARG HD3 H 3.220 0.004 2 104 13 13 ARG HE H 7.279 0.000 1 105 13 13 ARG CA C 54.375 0.000 1 106 13 13 ARG CB C 31.976 0.000 1 107 13 13 ARG CG C 26.901 0.000 1 108 13 13 ARG CD C 43.016 0.000 1 109 14 14 CYS H H 9.053 0.007 1 110 14 14 CYS HA H 5.493 0.002 1 111 14 14 CYS HB2 H 2.641 0.000 2 112 14 14 CYS HB3 H 3.069 0.001 2 113 14 14 CYS CA C 55.681 0.000 1 114 14 14 CYS CB C 47.761 0.000 1 115 15 15 ILE H H 8.778 0.001 1 116 15 15 ILE HA H 4.395 0.001 1 117 15 15 ILE HB H 1.851 0.008 1 118 15 15 ILE HG12 H 1.167 0.002 2 119 15 15 ILE HG13 H 1.167 0.002 2 120 15 15 ILE HG2 H 0.913 0.009 1 121 15 15 ILE HD1 H 0.901 0.001 1 122 15 15 ILE CA C 60.346 0.000 1 123 15 15 ILE CB C 40.268 0.000 1 124 15 15 ILE CG1 C 27.244 0.000 1 125 15 15 ILE CG2 C 17.312 0.000 1 126 15 15 ILE CD1 C 12.936 0.000 1 127 16 16 CYS H H 9.122 0.001 1 128 16 16 CYS HA H 5.499 0.010 1 129 16 16 CYS HB2 H 2.728 0.001 2 130 16 16 CYS HB3 H 3.120 0.002 2 131 16 16 CYS CA C 55.542 0.000 1 132 16 16 CYS CB C 47.634 0.000 1 133 17 17 THR H H 8.617 0.005 1 134 17 17 THR HA H 4.449 0.008 1 135 17 17 THR HB H 4.133 0.001 1 136 17 17 THR HG2 H 1.229 0.004 1 137 17 17 THR CA C 61.182 0.000 1 138 17 17 THR CB C 70.161 0.000 1 139 17 17 THR CG2 C 21.252 0.000 1 140 18 18 ARG H H 9.400 0.003 1 141 18 18 ARG HA H 3.924 0.002 1 142 18 18 ARG HB2 H 2.034 0.000 2 143 18 18 ARG HB3 H 1.883 0.001 2 144 18 18 ARG HG2 H 1.657 0.003 2 145 18 18 ARG HG3 H 1.657 0.003 2 146 18 18 ARG HD2 H 3.247 0.003 2 147 18 18 ARG HD3 H 3.247 0.003 2 148 18 18 ARG HE H 7.258 0.000 1 149 18 18 ARG CA C 57.243 0.000 1 150 18 18 ARG CB C 28.403 0.000 1 151 18 18 ARG CG C 27.492 0.000 1 152 18 18 ARG CD C 43.398 0.000 1 stop_ save_