data_30146 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Solution Structure of Designed Peptide NC_cEE_D1 ; _BMRB_accession_number 30146 _BMRB_flat_file_name bmr30146.str _Entry_type original _Submission_date 2016-07-19 _Accession_date 2016-07-19 _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" 112 "13C chemical shifts" 62 "15N chemical shifts" 14 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-02-22 update BMRB 'update entry citation' 2016-09-16 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 30138 'Designed Peptide NC_HEE_D1' 30140 'Designed Peptide NC_EHE_D1' 30141 'Designed Peptide NC_EEH_D2' 30142 'Designed Peptide NC_EEH_D1' 30143 'Designed Peptide NC_cHH_D1' 30144 'Designed Peptide NC_cHh_DL_D1' 30145 'Designed Peptide NC_cHHH_D1' stop_ _Original_release_date 2016-09-16 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Accurate de novo design of hyperstable constrained peptides. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27626386 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bhardwaj G. . . 2 Mulligan V. K. . 3 Bahl C. D. . 4 Gilmore J. M. . 5 Harvey P. J. . 6 Cheneval O. . . 7 Buchko G. W. . 8 Pulavarti S. V. . 9 Kaas Q. . . 10 Eletsky A. . . 11 Huang P. S. . 12 Johnsen W. A. . 13 Greisen P. J. . 14 Rocklin G. J. . 15 Song Y. . . 16 Linsky T. W. . 17 Watkins A. . . 18 Rettie S. A. . 19 Xu X. . . 20 Carter L. P. . 21 Bonneau R. . . 22 Olson J. M. . 23 Coutsias E. . . 24 Correnti C. E. . 25 Szyperski T. . . 26 Craik D. J. . 27 Baker D. . . stop_ _Journal_abbreviation Nature _Journal_volume 538 _Journal_issue 7625 _Journal_ASTM NATUAS _Journal_ISSN 1476-4687 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 329 _Page_last 335 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Designed peptide NC_cEE_D1' _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 2083.544 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence ; PVTWCVRIXPTVRCTVRX ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 VAL 3 THR 4 TRP 5 CYS 6 VAL 7 ARG 8 ILE 9 DPR 10 PRO 11 THR 12 VAL 13 ARG 14 CYS 15 THR 16 VAL 17 ARG 18 DPR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DPR _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-PROLINE _BMRB_code DPR _PDB_code DPR _Standard_residue_derivative . _Molecular_mass 115.130 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HXT HXT H . 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 CD ? ? SING N H ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD HD2 ? ? SING CD HD3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? 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_1 . 32630 . . . . 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 '1.0 mg/mL design peptide NC_cEE_D1, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.0 mg/mL 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '1.0 mg/mL design peptide NC_cEE_D1, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.0 mg/mL 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _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_ save_software_2 _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_3 _Saveframe_category software _Name CcpNMR _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing 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-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-15N_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_2D_ECOSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ECOSY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3.0 0.1 pH pressure 1 . . temperature 298 0.1 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 protons' ppm 0.000 internal indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.000 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' '2D ECOSY' stop_ loop_ _Sample_label $sample_1 $sample_2 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 PRO HA H 4.549 0.003 1 2 1 1 PRO HB2 H 2.179 0.000 2 3 1 1 PRO HB3 H 2.246 0.004 2 4 1 1 PRO HG2 H 1.967 0.000 2 5 1 1 PRO HG3 H 2.105 0.005 2 6 1 1 PRO HD2 H 3.763 0.005 2 7 1 1 PRO HD3 H 4.014 0.002 2 8 1 1 PRO CA C 63.690 0.000 1 9 1 1 PRO CB C 32.385 0.003 1 10 1 1 PRO CG C 26.328 0.050 1 11 1 1 PRO CD C 50.406 0.000 1 12 2 2 VAL H H 7.681 0.004 1 13 2 2 VAL HA H 4.354 0.002 1 14 2 2 VAL HB H 2.175 0.002 1 15 2 2 VAL HG1 H 0.969 0.003 1 16 2 2 VAL HG2 H 0.828 0.005 1 17 2 2 VAL CA C 61.736 0.000 1 18 2 2 VAL CB C 34.330 0.000 1 19 2 2 VAL CG1 C 21.144 0.000 1 20 2 2 VAL CG2 C 21.161 0.000 1 21 2 2 VAL N N 121.272 0.000 1 22 3 3 THR H H 8.541 0.002 1 23 3 3 THR HA H 4.911 0.005 1 24 3 3 THR HB H 3.956 0.002 1 25 3 3 THR HG2 H 1.119 0.001 1 26 3 3 THR CA C 62.050 0.000 1 27 3 3 THR CB C 70.041 0.000 1 28 3 3 THR CG2 C 21.974 0.000 1 29 3 3 THR N N 122.162 0.000 1 30 4 4 TRP H H 9.042 0.004 1 31 4 4 TRP HA H 5.013 0.002 1 32 4 4 TRP HB2 H 3.067 0.006 2 33 4 4 TRP HB3 H 3.271 0.006 2 34 4 4 TRP HD1 H 7.088 0.001 1 35 4 4 TRP HE1 H 10.081 0.000 1 36 4 4 TRP HE3 H 7.541 0.000 1 37 4 4 TRP HZ2 H 7.453 0.001 1 38 4 4 TRP HZ3 H 7.074 0.000 1 39 4 4 TRP HH2 H 7.192 0.002 1 40 4 4 TRP CA C 56.065 0.000 1 41 4 4 TRP CB C 31.330 0.001 1 42 4 4 TRP N N 129.057 0.000 1 43 5 5 CYS H H 8.782 0.004 1 44 5 5 CYS HA H 5.507 0.002 1 45 5 5 CYS HB2 H 2.535 0.008 2 46 5 5 CYS HB3 H 2.890 0.009 2 47 5 5 CYS CA C 55.339 0.000 1 48 5 5 CYS CB C 47.044 0.002 1 49 5 5 CYS N N 124.001 0.000 1 50 6 6 VAL H H 8.695 0.002 1 51 6 6 VAL HA H 4.393 0.002 1 52 6 6 VAL HB H 1.957 0.004 1 53 6 6 VAL HG1 H 0.884 0.004 1 54 6 6 VAL HG2 H 0.883 0.004 1 55 6 6 VAL CA C 59.919 0.000 1 56 6 6 VAL CB C 35.296 0.004 1 57 6 6 VAL CG1 C 20.031 0.000 1 58 6 6 VAL CG2 C 20.767 0.000 1 59 6 6 VAL N N 120.515 0.000 1 60 7 7 ARG H H 8.586 0.002 1 61 7 7 ARG HA H 4.843 0.008 1 62 7 7 ARG HB2 H 1.669 0.003 2 63 7 7 ARG HB3 H 1.812 0.002 2 64 7 7 ARG HG2 H 1.477 0.004 2 65 7 7 ARG HG3 H 1.533 0.004 2 66 7 7 ARG HD2 H 3.118 0.004 2 67 7 7 ARG HD3 H 3.198 0.002 2 68 7 7 ARG HE H 7.265 0.002 1 69 7 7 ARG CA C 55.501 0.000 1 70 7 7 ARG CB C 30.931 0.021 1 71 7 7 ARG CG C 27.808 0.002 1 72 7 7 ARG CD C 43.061 0.035 1 73 7 7 ARG N N 125.296 0.000 1 74 8 8 ILE H H 8.742 0.003 1 75 8 8 ILE HA H 4.573 0.002 1 76 8 8 ILE HB H 1.767 0.003 1 77 8 8 ILE HG12 H 1.089 0.003 1 78 8 8 ILE HG13 H 1.429 0.004 1 79 8 8 ILE HG2 H 0.870 0.002 1 80 8 8 ILE HD1 H 0.819 0.002 1 81 8 8 ILE CA C 58.141 0.000 1 82 8 8 ILE CB C 38.742 0.000 1 83 8 8 ILE CG1 C 26.867 0.003 1 84 8 8 ILE CG2 C 17.557 0.000 1 85 8 8 ILE CD1 C 13.283 0.000 1 86 8 8 ILE N N 127.841 0.000 1 87 9 9 DPR CB C 30.431 0.005 1 88 9 9 DPR CD C 51.048 0.000 1 89 9 9 DPR CG C 27.783 0.003 1 90 9 9 DPR HA H 4.756 0.005 1 91 9 9 DPR HB2 H 2.291 0.006 2 92 9 9 DPR HB3 H 1.923 0.001 2 93 9 9 DPR HD2 H 3.879 0.003 2 94 9 9 DPR HD3 H 3.550 0.007 2 95 9 9 DPR HG2 H 2.144 0.008 2 96 9 9 DPR HG3 H 2.022 0.003 2 97 10 10 PRO HA H 4.560 0.003 1 98 10 10 PRO HB2 H 2.182 0.002 2 99 10 10 PRO HB3 H 2.224 0.000 2 100 10 10 PRO HG2 H 1.970 0.003 2 101 10 10 PRO HG3 H 2.092 0.000 2 102 10 10 PRO HD2 H 3.728 0.005 2 103 10 10 PRO HD3 H 4.033 0.005 2 104 10 10 PRO CA C 63.657 0.000 1 105 10 10 PRO CB C 32.446 0.000 1 106 10 10 PRO CG C 26.277 0.000 1 107 10 10 PRO CD C 50.328 0.003 1 108 11 11 THR H H 7.837 0.002 1 109 11 11 THR HA H 4.546 0.005 1 110 11 11 THR HB H 4.113 0.002 1 111 11 11 THR HG2 H 1.173 0.002 1 112 11 11 THR CA C 61.407 0.000 1 113 11 11 THR CB C 71.005 0.000 1 114 11 11 THR CG2 C 21.560 0.000 1 115 11 11 THR N N 116.368 0.000 1 116 12 12 VAL H H 8.556 0.003 1 117 12 12 VAL HA H 4.647 0.003 1 118 12 12 VAL HB H 1.888 0.004 1 119 12 12 VAL HG1 H 0.828 0.010 1 120 12 12 VAL HG2 H 0.816 0.008 1 121 12 12 VAL CA C 61.420 0.000 1 122 12 12 VAL CB C 33.682 0.000 1 123 12 12 VAL CG2 C 21.803 0.000 1 124 12 12 VAL N N 124.094 0.000 1 125 13 13 ARG H H 8.869 0.002 1 126 13 13 ARG HA H 4.719 0.006 1 127 13 13 ARG HB2 H 1.674 0.004 2 128 13 13 ARG HB3 H 1.794 0.004 2 129 13 13 ARG HG2 H 1.485 0.004 2 130 13 13 ARG HG3 H 1.633 0.004 2 131 13 13 ARG HD2 H 3.165 0.001 1 132 13 13 ARG HD3 H 3.165 0.001 1 133 13 13 ARG HE H 7.143 0.002 1 134 13 13 ARG CA C 54.669 0.000 1 135 13 13 ARG CB C 32.671 0.000 1 136 13 13 ARG CG C 26.931 0.021 1 137 13 13 ARG CD C 43.257 0.000 1 138 13 13 ARG N N 127.843 0.000 1 139 14 14 CYS H H 9.189 0.004 1 140 14 14 CYS HA H 5.714 0.002 1 141 14 14 CYS HB2 H 2.620 0.007 2 142 14 14 CYS HB3 H 2.996 0.002 2 143 14 14 CYS CA C 55.572 0.000 1 144 14 14 CYS CB C 46.943 0.001 1 145 14 14 CYS N N 125.462 0.000 1 146 15 15 THR H H 9.181 0.004 1 147 15 15 THR HA H 4.541 0.002 1 148 15 15 THR HB H 3.795 0.004 1 149 15 15 THR HG2 H 1.184 0.004 1 150 15 15 THR CA C 61.045 0.000 1 151 15 15 THR CB C 71.358 0.000 1 152 15 15 THR CG2 C 21.297 0.000 1 153 15 15 THR N N 119.140 0.000 1 154 16 16 VAL H H 8.622 0.001 1 155 16 16 VAL HA H 4.601 0.004 1 156 16 16 VAL HB H 2.000 0.002 1 157 16 16 VAL HG1 H 0.937 0.005 1 158 16 16 VAL HG2 H 0.935 0.004 1 159 16 16 VAL CA C 62.152 0.000 1 160 16 16 VAL CB C 32.980 0.000 1 161 16 16 VAL CG1 C 20.716 0.000 1 162 16 16 VAL CG2 C 21.315 0.000 1 163 16 16 VAL N N 124.989 0.000 1 164 17 17 ARG H H 9.140 0.003 1 165 17 17 ARG HA H 4.916 0.004 1 166 17 17 ARG HB2 H 1.729 0.002 2 167 17 17 ARG HB3 H 1.801 0.003 2 168 17 17 ARG HG2 H 1.522 0.007 2 169 17 17 ARG HG3 H 1.584 0.004 2 170 17 17 ARG HD2 H 3.013 0.002 2 171 17 17 ARG HD3 H 3.065 0.002 2 172 17 17 ARG HE H 7.037 0.002 1 173 17 17 ARG CA C 52.650 0.000 1 174 17 17 ARG CB C 31.342 0.008 1 175 17 17 ARG CG C 26.873 0.000 1 176 17 17 ARG CD C 43.606 0.001 1 177 17 17 ARG N N 129.082 0.000 1 178 18 18 DPR CA C 61.041 0.000 1 179 18 18 DPR CB C 30.435 0.015 1 180 18 18 DPR CD C 50.905 0.028 1 181 18 18 DPR CG C 27.785 0.000 1 182 18 18 DPR HA H 4.742 0.006 1 183 18 18 DPR HB2 H 2.292 0.000 2 184 18 18 DPR HB3 H 1.939 0.000 2 185 18 18 DPR HD2 H 3.844 0.012 2 186 18 18 DPR HD3 H 3.575 0.003 2 187 18 18 DPR HG2 H 2.154 0.000 2 188 18 18 DPR HG3 H 2.010 0.000 2 stop_ save_