data_30470 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Solution structure of Rivi3 ; _BMRB_accession_number 30470 _BMRB_flat_file_name bmr30470.str _Entry_type original _Submission_date 2018-05-21 _Accession_date 2018-05-21 _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 Harvey P. J. . 2 Craik D. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 169 "13C chemical shifts" 69 "15N chemical shifts" 23 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-04-09 original BMRB . stop_ _Original_release_date 2018-06-18 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Discovery, structure and biological activities of novel cyclotides from Rinorea virgata and Rinorea bengalensis ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Niyomploy P. . . 2 Chan L. Y. . 3 Harvey P. J. . 4 Poth A. G. . 5 Colgrave M. L. . 6 Craik D. J. . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Rivi3 _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 3139.782 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; GLPICGETCLLGKCYTPGCS CRRPVCYKN ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 LEU 3 PRO 4 ILE 5 CYS 6 GLY 7 GLU 8 THR 9 CYS 10 LEU 11 LEU 12 GLY 13 LYS 14 CYS 15 TYR 16 THR 17 PRO 18 GLY 19 CYS 20 SER 21 CYS 22 ARG 23 ARG 24 PRO 25 VAL 26 CYS 27 TYR 28 LYS 29 ASN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . 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 'Rinorea virgata' 1343662 Eukaryota Viridiplantae Rinorea virgata 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 '2.0 mg/mL NA peptide, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2.0 mg/mL 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name TOPSPIN _Version 3.5 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection 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 CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name CNS _Version . 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_NMR_spectrometer_1 _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 $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-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _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 pH 4.1 . pH pressure 1 . atm temperature 298 . 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 C 13 'methyl carbons' ppm 0.00 internal indirect . . . 0.25144953 DSS H 1 'methyl carbons' ppm 0.00 internal direct . . . 1.0 DSS N 15 'methyl carbons' ppm 0.00 internal indirect . . . 0.10132912 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 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 1H-15N HSQC' '2D 1H-13C HSQC aliphatic' 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 GLY H H 8.736 0.002 1 2 1 1 GLY HA2 H 3.541 0.002 2 3 1 1 GLY HA3 H 4.203 0.003 2 4 1 1 GLY CA C 45.472 0.013 1 5 1 1 GLY N N 101.578 0.000 1 6 2 2 LEU H H 8.130 0.002 1 7 2 2 LEU HA H 5.206 0.001 1 8 2 2 LEU HB2 H 1.473 0.003 2 9 2 2 LEU HB3 H 1.917 0.002 2 10 2 2 LEU HG H 1.709 0.000 1 11 2 2 LEU HD1 H 0.999 0.008 2 12 2 2 LEU HD2 H 0.997 0.006 2 13 2 2 LEU CB C 45.398 0.013 1 14 2 2 LEU CD1 C 25.575 0.000 1 15 2 2 LEU CD2 C 24.509 0.000 1 16 2 2 LEU N N 121.306 0.000 1 17 3 3 PRO HA H 4.745 0.007 1 18 3 3 PRO HB2 H 1.222 0.001 2 19 3 3 PRO HB3 H 2.235 0.002 2 20 3 3 PRO HG2 H 2.018 0.014 2 21 3 3 PRO HG3 H 2.170 0.006 2 22 3 3 PRO HD2 H 3.773 0.009 2 23 3 3 PRO HD3 H 3.773 0.009 2 24 3 3 PRO CB C 27.567 0.004 1 25 3 3 PRO CG C 27.312 0.007 1 26 3 3 PRO CD C 49.943 0.000 1 27 4 4 ILE H H 7.931 0.004 1 28 4 4 ILE HA H 4.689 0.004 1 29 4 4 ILE HB H 2.281 0.002 1 30 4 4 ILE HG12 H 1.149 0.002 2 31 4 4 ILE HG13 H 1.199 0.006 2 32 4 4 ILE HG2 H 0.927 0.001 1 33 4 4 ILE HD1 H 0.815 0.001 1 34 4 4 ILE CB C 38.034 0.000 1 35 4 4 ILE CG1 C 25.937 0.007 1 36 4 4 ILE CD1 C 17.537 0.000 1 37 4 4 ILE N N 115.664 0.000 1 38 5 5 CYS H H 8.064 0.001 1 39 5 5 CYS HA H 4.400 0.002 1 40 5 5 CYS HB2 H 3.086 0.005 2 41 5 5 CYS HB3 H 3.375 0.003 2 42 5 5 CYS CA C 59.728 0.000 1 43 5 5 CYS CB C 49.193 0.020 1 44 5 5 CYS N N 119.701 0.000 1 45 6 6 GLY H H 8.617 0.002 1 46 6 6 GLY HA2 H 3.713 0.004 2 47 6 6 GLY HA3 H 3.827 0.002 2 48 6 6 GLY CA C 46.534 0.000 1 49 6 6 GLY N N 110.490 0.000 1 50 7 7 GLU H H 7.169 0.001 1 51 7 7 GLU HA H 4.700 0.006 1 52 7 7 GLU HB2 H 1.823 0.006 2 53 7 7 GLU HB3 H 1.895 0.004 2 54 7 7 GLU HG2 H 2.374 0.005 2 55 7 7 GLU HG3 H 2.474 0.002 2 56 7 7 GLU CB C 32.642 0.007 1 57 7 7 GLU CG C 35.659 0.010 1 58 7 7 GLU N N 117.189 0.000 1 59 8 8 THR H H 8.603 0.002 1 60 8 8 THR HA H 4.693 0.004 1 61 8 8 THR HB H 4.460 0.002 1 62 8 8 THR HG2 H 1.265 0.001 1 63 8 8 THR CB C 71.367 0.000 1 64 8 8 THR CG2 C 21.592 0.000 1 65 8 8 THR N N 116.689 0.000 1 66 9 9 CYS H H 8.484 0.001 1 67 9 9 CYS HA H 5.199 0.001 1 68 9 9 CYS HB2 H 2.575 0.006 2 69 9 9 CYS HB3 H 3.145 0.005 2 70 9 9 CYS CB C 49.758 0.040 1 71 9 9 CYS N N 116.458 0.000 1 72 10 10 LEU H H 8.808 0.002 1 73 10 10 LEU HA H 4.024 0.002 1 74 10 10 LEU HB2 H 1.679 0.000 2 75 10 10 LEU HB3 H 1.722 0.006 2 76 10 10 LEU HD1 H 0.991 0.010 2 77 10 10 LEU HD2 H 0.963 0.006 2 78 10 10 LEU CA C 58.671 0.000 1 79 10 10 LEU CB C 41.722 0.008 1 80 10 10 LEU CD1 C 22.634 0.000 1 81 10 10 LEU N N 124.801 0.000 1 82 11 11 LEU H H 8.157 0.002 1 83 11 11 LEU HA H 4.560 0.003 1 84 11 11 LEU HB2 H 1.734 0.002 2 85 11 11 LEU HB3 H 1.831 0.004 2 86 11 11 LEU HG H 1.614 0.002 1 87 11 11 LEU HD1 H 0.953 0.000 2 88 11 11 LEU HD2 H 0.870 0.000 2 89 11 11 LEU CA C 54.519 0.000 1 90 11 11 LEU CB C 40.978 0.009 1 91 11 11 LEU CG C 27.240 0.000 1 92 11 11 LEU CD2 C 22.665 0.000 1 93 11 11 LEU N N 115.480 0.000 1 94 12 12 GLY H H 7.786 0.002 1 95 12 12 GLY HA2 H 3.806 0.003 2 96 12 12 GLY HA3 H 4.289 0.002 2 97 12 12 GLY CA C 46.286 0.000 1 98 12 12 GLY N N 105.194 0.000 1 99 13 13 LYS H H 7.618 0.002 1 100 13 13 LYS HA H 4.590 0.003 1 101 13 13 LYS HB2 H 1.472 0.005 2 102 13 13 LYS HB3 H 1.472 0.005 2 103 13 13 LYS HG2 H 0.973 0.003 2 104 13 13 LYS HG3 H 1.019 0.006 2 105 13 13 LYS HD2 H 1.531 0.002 2 106 13 13 LYS HD3 H 1.531 0.002 2 107 13 13 LYS HE2 H 2.788 0.001 2 108 13 13 LYS HE3 H 2.788 0.001 2 109 13 13 LYS HZ H 7.478 0.001 1 110 13 13 LYS CB C 35.912 0.000 1 111 13 13 LYS CD C 28.951 0.000 1 112 13 13 LYS CE C 42.150 0.000 1 113 13 13 LYS N N 119.910 0.000 1 114 14 14 CYS H H 8.351 0.004 1 115 14 14 CYS HA H 4.614 0.006 1 116 14 14 CYS HB2 H 2.641 0.007 2 117 14 14 CYS HB3 H 3.164 0.002 2 118 14 14 CYS CB C 44.375 0.042 1 119 14 14 CYS N N 121.925 0.000 1 120 15 15 TYR H H 11.594 0.002 1 121 15 15 TYR HA H 4.363 0.004 1 122 15 15 TYR HB2 H 2.827 0.008 2 123 15 15 TYR HB3 H 3.141 0.010 2 124 15 15 TYR HD1 H 7.208 0.005 1 125 15 15 TYR HD2 H 7.208 0.005 1 126 15 15 TYR HE1 H 6.773 0.000 1 127 15 15 TYR HE2 H 6.773 0.000 1 128 15 15 TYR CA C 59.625 0.000 1 129 15 15 TYR CB C 39.592 0.024 1 130 15 15 TYR N N 126.695 0.000 1 131 16 16 THR H H 10.018 0.019 1 132 16 16 THR HA H 4.349 0.002 1 133 16 16 THR HB H 4.350 0.002 1 134 16 16 THR HG2 H 1.353 0.001 1 135 16 16 THR CA C 62.627 0.000 1 136 16 16 THR CB C 69.144 0.000 1 137 16 16 THR CG2 C 21.478 0.000 1 138 16 16 THR N N 126.019 0.000 1 139 17 17 PRO HA H 4.227 0.004 1 140 17 17 PRO HB2 H 1.898 0.002 2 141 17 17 PRO HB3 H 2.321 0.001 2 142 17 17 PRO HG2 H 2.029 0.001 2 143 17 17 PRO HG3 H 2.167 0.004 2 144 17 17 PRO HD2 H 3.719 0.002 2 145 17 17 PRO HD3 H 4.172 0.002 2 146 17 17 PRO CA C 64.466 0.000 1 147 17 17 PRO CB C 31.927 0.036 1 148 17 17 PRO CG C 27.790 0.013 1 149 17 17 PRO CD C 51.562 0.004 1 150 18 18 GLY H H 8.717 0.002 1 151 18 18 GLY HA2 H 3.709 0.001 2 152 18 18 GLY HA3 H 4.150 0.004 2 153 18 18 GLY CA C 45.334 0.049 1 154 18 18 GLY N N 111.099 0.000 1 155 19 19 CYS H H 7.698 0.002 1 156 19 19 CYS HA H 5.418 0.002 1 157 19 19 CYS HB2 H 2.593 0.006 2 158 19 19 CYS HB3 H 3.845 0.001 2 159 19 19 CYS CA C 58.037 0.000 1 160 19 19 CYS CB C 49.615 0.000 1 161 20 20 SER H H 9.619 0.002 1 162 20 20 SER HA H 4.676 0.004 1 163 20 20 SER HB2 H 3.760 0.005 2 164 20 20 SER HB3 H 3.794 0.017 2 165 20 20 SER CB C 65.655 0.007 1 166 20 20 SER N N 117.405 0.000 1 167 21 21 CYS H H 8.858 0.002 1 168 21 21 CYS HA H 4.685 0.003 1 169 21 21 CYS HB2 H 2.918 0.003 2 170 21 21 CYS HB3 H 2.963 0.002 2 171 21 21 CYS CB C 41.517 0.041 1 172 22 22 ARG H H 9.104 0.002 1 173 22 22 ARG HA H 4.612 0.003 1 174 22 22 ARG HB2 H 1.787 0.005 2 175 22 22 ARG HB3 H 1.787 0.005 2 176 22 22 ARG HG2 H 1.406 0.004 2 177 22 22 ARG HG3 H 1.473 0.001 2 178 22 22 ARG HD2 H 2.528 0.001 2 179 22 22 ARG HD3 H 2.811 0.001 2 180 22 22 ARG HE H 6.876 0.001 1 181 22 22 ARG CB C 28.908 0.000 1 182 22 22 ARG CG C 26.512 0.000 1 183 22 22 ARG CD C 43.323 0.049 1 184 22 22 ARG N N 133.822 0.000 1 185 23 23 ARG H H 8.388 0.001 1 186 23 23 ARG HA H 4.096 0.001 1 187 23 23 ARG HB2 H 1.791 0.006 2 188 23 23 ARG HB3 H 1.854 0.002 2 189 23 23 ARG HG2 H 1.483 0.003 2 190 23 23 ARG HG3 H 1.853 0.002 2 191 23 23 ARG HD2 H 3.213 0.001 2 192 23 23 ARG HD3 H 3.213 0.001 2 193 23 23 ARG HE H 7.221 0.002 1 194 23 23 ARG CA C 56.569 0.000 1 195 23 23 ARG CB C 31.266 0.005 1 196 23 23 ARG CG C 26.377 0.036 1 197 23 23 ARG CD C 43.794 0.000 1 198 23 23 ARG N N 125.667 0.000 1 199 24 24 PRO HA H 4.479 0.002 1 200 24 24 PRO HB2 H 1.984 0.001 2 201 24 24 PRO HB3 H 2.572 0.002 2 202 24 24 PRO HG2 H 1.787 0.005 2 203 24 24 PRO HG3 H 2.091 0.003 2 204 24 24 PRO HD2 H 3.558 0.002 2 205 24 24 PRO HD3 H 3.671 0.003 2 206 24 24 PRO CA C 65.702 0.000 1 207 24 24 PRO CB C 33.611 0.003 1 208 24 24 PRO CG C 24.386 0.002 1 209 24 24 PRO CD C 49.036 0.007 1 210 25 25 VAL H H 8.543 0.001 1 211 25 25 VAL HA H 4.250 0.002 1 212 25 25 VAL HB H 2.051 0.002 1 213 25 25 VAL HG1 H 0.933 0.001 2 214 25 25 VAL HG2 H 0.506 0.003 2 215 25 25 VAL CA C 62.937 0.000 1 216 25 25 VAL CB C 34.834 0.000 1 217 25 25 VAL CG1 C 22.170 0.000 1 218 25 25 VAL CG2 C 21.574 0.000 1 219 25 25 VAL N N 129.515 0.000 1 220 26 26 CYS H H 7.695 0.002 1 221 26 26 CYS HA H 4.973 0.003 1 222 26 26 CYS HB2 H 2.870 0.007 2 223 26 26 CYS HB3 H 3.161 0.005 2 224 26 26 CYS CA C 55.789 0.000 1 225 26 26 CYS CB C 44.195 0.000 1 226 27 27 TYR H H 9.556 0.003 1 227 27 27 TYR HA H 5.005 0.005 1 228 27 27 TYR HB2 H 2.518 0.003 2 229 27 27 TYR HB3 H 2.862 0.001 2 230 27 27 TYR HD1 H 6.743 0.002 1 231 27 27 TYR HD2 H 6.743 0.002 1 232 27 27 TYR HE1 H 6.809 0.002 1 233 27 27 TYR HE2 H 6.809 0.002 1 234 27 27 TYR CA C 57.367 0.000 1 235 27 27 TYR CB C 43.078 0.000 1 236 27 27 TYR N N 123.462 0.000 1 237 28 28 LYS H H 9.225 0.001 1 238 28 28 LYS HA H 4.683 0.004 1 239 28 28 LYS HB2 H 1.709 0.004 2 240 28 28 LYS HB3 H 1.894 0.004 2 241 28 28 LYS HG2 H 1.305 0.029 2 242 28 28 LYS HG3 H 1.357 0.031 2 243 28 28 LYS HD2 H 1.653 0.004 2 244 28 28 LYS HD3 H 1.653 0.004 2 245 28 28 LYS HE2 H 2.919 0.004 2 246 28 28 LYS HE3 H 2.919 0.004 2 247 28 28 LYS HZ H 7.609 0.001 1 248 28 28 LYS CB C 35.161 0.010 1 249 28 28 LYS CG C 25.005 0.010 1 250 28 28 LYS CD C 29.607 0.000 1 251 28 28 LYS CE C 42.257 0.000 1 252 28 28 LYS N N 122.858 0.000 1 253 29 29 ASN H H 9.437 0.001 1 254 29 29 ASN HA H 4.388 0.001 1 255 29 29 ASN HB2 H 2.905 0.004 2 256 29 29 ASN HB3 H 3.121 0.004 2 257 29 29 ASN HD21 H 7.542 0.002 2 258 29 29 ASN HD22 H 6.966 0.002 2 259 29 29 ASN CA C 54.545 0.000 1 260 29 29 ASN CB C 37.508 0.008 1 261 29 29 ASN ND2 N 112.639 0.000 1 stop_ save_