data_30320 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; De Novo Design of Covalently Constrained Meso-size Protein Scaffolds with Unique Tertiary Structures ; _BMRB_accession_number 30320 _BMRB_flat_file_name bmr30320.str _Entry_type original _Submission_date 2017-08-01 _Accession_date 2017-08-01 _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 Wu H. . . 2 Wu Y. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 166 "13C chemical shifts" 58 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-11-22 update BMRB 'update entry citation' 2017-09-28 original author 'original release' stop_ _Original_release_date 2017-09-27 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28973862 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dang Bobo . . 2 Wu Haifan . . 3 Mulligan 'Vikram Khipple' K. . 4 Mravic Marco . . 5 Wu Yibing . . 6 Lemmin Thomas . . 7 Ford Alexander . . 8 Silva Daniel-Adriano A. . 9 Baker David . . 10 DeGrado William F. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_name_full 'Proceedings of the National Academy of Sciences of the United States of America' _Journal_volume 114 _Journal_issue 41 _Journal_ISSN 1091-6490 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 10852 _Page_last 10857 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name '38-mer peptide' _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 4058.436 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 38 _Mol_residue_sequence ; SPEERAQLLTAAEKADELGC PEERAQLLTAAEKADELG ; loop_ _Residue_seq_code _Residue_label 1 SER 2 PRO 3 GLU 4 GLU 5 ARG 6 ALA 7 GLN 8 LEU 9 LEU 10 THR 11 ALA 12 ALA 13 GLU 14 LYS 15 ALA 16 ASP 17 GLU 18 LEU 19 GLY 20 CYS 21 PRO 22 GLU 23 GLU 24 ARG 25 ALA 26 GLN 27 LEU 28 LEU 29 THR 30 ALA 31 ALA 32 GLU 33 LYS 34 ALA 35 ASP 36 GLU 37 LEU 38 GLY 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 . 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 '0.7 mM non-labeled 1, 95% H2O/5% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.7 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_3 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceII _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 50 1 mM pH 4.0 . pH pressure 1 . atm temperature 298 0.5 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 water C 13 protons ppm 4.77 internal indirect . . . 0.251449528 water H 1 protons ppm 4.77 internal direct . . . 1 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 NOESY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC' 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 SER H H 8.07 0.05 1 2 1 1 SER HA H 4.97 0.05 1 3 1 1 SER CB C 63.45 0.20 1 4 2 2 PRO HA H 4.28 0.05 1 5 2 2 PRO HB2 H 1.98 0.05 1 6 2 2 PRO HB3 H 2.38 0.05 1 7 2 2 PRO HG2 H 2.13 0.05 1 8 2 2 PRO HG3 H 2.05 0.05 1 9 2 2 PRO HD2 H 3.92 0.05 1 10 2 2 PRO HD3 H 3.79 0.05 1 11 2 2 PRO CA C 64.98 0.20 1 12 2 2 PRO CB C 31.96 0.20 1 13 2 2 PRO CD C 50.78 0.20 1 14 3 3 GLU H H 8.58 0.05 1 15 3 3 GLU HA H 4.20 0.05 1 16 3 3 GLU HB2 H 2.04 0.05 1 17 3 3 GLU HB3 H 2.07 0.05 1 18 3 3 GLU HG2 H 2.43 0.05 1 19 3 3 GLU HG3 H 2.46 0.05 1 20 3 3 GLU CA C 58.70 0.20 1 21 3 3 GLU CB C 28.16 0.20 1 22 4 4 GLU H H 7.89 0.05 1 23 4 4 GLU HA H 4.17 0.05 1 24 4 4 GLU HG2 H 2.41 0.05 1 25 4 4 GLU HG3 H 2.45 0.05 1 26 4 4 GLU CA C 58.03 0.20 1 27 5 5 ARG H H 8.15 0.05 1 28 5 5 ARG HA H 3.95 0.05 1 29 5 5 ARG HB2 H 1.82 0.05 1 30 5 5 ARG HB3 H 1.92 0.05 1 31 5 5 ARG HG2 H 1.56 0.05 1 32 5 5 ARG HG3 H 1.71 0.05 1 33 5 5 ARG HD2 H 3.12 0.05 1 34 5 5 ARG HD3 H 3.20 0.05 1 35 5 5 ARG HE H 7.27 0.05 1 36 5 5 ARG CB C 30.08 0.20 1 37 6 6 ALA H H 8.05 0.05 1 38 6 6 ALA HA H 4.14 0.05 1 39 6 6 ALA CA C 54.66 0.20 1 40 6 6 ALA CB C 18.38 0.20 1 41 7 7 GLN H H 7.93 0.05 1 42 7 7 GLN HA H 4.13 0.05 1 43 7 7 GLN HG2 H 2.41 0.05 1 44 7 7 GLN HG3 H 2.52 0.05 1 45 7 7 GLN HE21 H 7.44 0.05 1 46 7 7 GLN HE22 H 6.81 0.05 1 47 8 8 LEU H H 8.11 0.05 1 48 8 8 LEU HA H 4.19 0.05 1 49 8 8 LEU HB2 H 1.75 0.05 1 50 8 8 LEU HB3 H 1.83 0.05 1 51 8 8 LEU HG H 1.55 0.05 1 52 8 8 LEU HD1 H 0.83 0.05 2 53 8 8 LEU HD2 H 0.87 0.05 2 54 8 8 LEU CB C 42.18 0.20 1 55 9 9 LEU H H 8.24 0.05 1 56 9 9 LEU HA H 4.18 0.05 1 57 9 9 LEU HB2 H 1.74 0.05 1 58 9 9 LEU HB3 H 1.83 0.05 1 59 9 9 LEU HG H 1.55 0.05 1 60 9 9 LEU HD1 H 0.81 0.05 2 61 9 9 LEU HD2 H 0.86 0.05 2 62 9 9 LEU CA C 57.23 0.20 1 63 9 9 LEU CB C 41.82 0.20 1 64 10 10 THR H H 8.10 0.05 1 65 10 10 THR HA H 4.31 0.05 1 66 10 10 THR HB H 4.08 0.05 1 67 10 10 THR CB C 69.30 0.20 1 68 11 11 ALA H H 8.11 0.05 1 69 11 11 ALA HA H 4.13 0.05 1 70 11 11 ALA CA C 54.84 0.20 1 71 11 11 ALA CB C 18.08 0.20 1 72 12 12 ALA H H 8.44 0.05 1 73 12 12 ALA HA H 4.06 0.05 1 74 12 12 ALA CA C 54.84 0.20 1 75 12 12 ALA CB C 18.08 0.20 1 76 13 13 GLU H H 7.92 0.05 1 77 13 13 GLU HA H 4.17 0.05 1 78 13 13 GLU CA C 57.75 0.20 1 79 14 14 LYS H H 7.94 0.05 1 80 14 14 LYS HA H 4.13 0.05 1 81 14 14 LYS HB2 H 1.85 0.05 1 82 14 14 LYS HB3 H 1.91 0.05 1 83 14 14 LYS HG2 H 1.47 0.05 1 84 14 14 LYS HG3 H 1.54 0.05 1 85 14 14 LYS CB C 32.24 0.20 1 86 15 15 ALA H H 7.99 0.05 1 87 15 15 ALA HA H 4.15 0.05 1 88 15 15 ALA CA C 54.09 0.20 1 89 15 15 ALA CB C 18.16 0.20 1 90 16 16 ASP H H 8.05 0.05 1 91 16 16 ASP HA H 4.49 0.05 1 92 16 16 ASP HB2 H 2.78 0.05 1 93 16 16 ASP HB3 H 2.94 0.05 1 94 16 16 ASP CA C 61.37 0.20 1 95 16 16 ASP CB C 39.65 0.20 1 96 17 17 GLU H H 8.06 0.05 1 97 17 17 GLU HA H 4.20 0.05 1 98 17 17 GLU HB2 H 2.12 0.05 1 99 17 17 GLU HB3 H 2.16 0.05 1 100 17 17 GLU HG2 H 2.45 0.05 1 101 17 17 GLU HG3 H 2.56 0.05 1 102 17 17 GLU CA C 57.69 0.20 1 103 17 17 GLU CB C 28.14 0.20 1 104 18 18 LEU H H 8.03 0.05 1 105 18 18 LEU HA H 4.34 0.05 1 106 18 18 LEU HB2 H 1.70 0.05 1 107 18 18 LEU HB3 H 1.73 0.05 1 108 18 18 LEU HG H 1.63 0.05 1 109 18 18 LEU HD1 H 0.86 0.05 2 110 18 18 LEU HD2 H 0.90 0.05 2 111 18 18 LEU CA C 55.37 0.20 1 112 18 18 LEU CB C 42.20 0.20 1 113 19 19 GLY H H 8.08 0.05 1 114 19 19 GLY HA2 H 4.02 0.05 1 115 19 19 GLY HA3 H 4.02 0.05 1 116 19 19 GLY CA C 45.75 0.20 1 117 20 20 CYS H H 8.05 0.05 1 118 20 20 CYS HA H 4.96 0.05 1 119 20 20 CYS HB2 H 2.94 0.05 1 120 20 20 CYS HB3 H 3.02 0.05 1 121 20 20 CYS CB C 27.71 0.20 1 122 21 21 PRO HA H 4.29 0.05 1 123 21 21 PRO HB2 H 1.99 0.05 1 124 21 21 PRO HB3 H 2.35 0.05 1 125 21 21 PRO HG2 H 2.08 0.05 1 126 21 21 PRO HG3 H 2.05 0.05 1 127 21 21 PRO HD2 H 3.86 0.05 1 128 21 21 PRO HD3 H 3.68 0.05 1 129 21 21 PRO CA C 64.98 0.20 1 130 21 21 PRO CB C 31.96 0.20 1 131 21 21 PRO CD C 50.98 0.20 1 132 22 22 GLU H H 8.72 0.05 1 133 22 22 GLU HA H 4.24 0.05 1 134 22 22 GLU CA C 58.70 0.20 1 135 22 22 GLU CB C 28.17 0.20 1 136 23 23 GLU H H 7.89 0.05 1 137 23 23 GLU HA H 4.17 0.05 1 138 23 23 GLU CA C 58.09 0.20 1 139 24 24 ARG H H 8.07 0.05 1 140 24 24 ARG HA H 3.97 0.05 1 141 24 24 ARG HB2 H 1.80 0.05 1 142 24 24 ARG HB3 H 1.93 0.05 1 143 24 24 ARG HG2 H 1.56 0.05 1 144 24 24 ARG HG3 H 1.71 0.05 1 145 24 24 ARG HD2 H 3.12 0.05 1 146 24 24 ARG HD3 H 3.19 0.05 1 147 24 24 ARG HE H 7.33 0.05 1 148 24 24 ARG CB C 30.08 0.20 1 149 25 25 ALA H H 8.10 0.05 1 150 25 25 ALA HA H 4.14 0.05 1 151 25 25 ALA CA C 54.66 0.20 1 152 25 25 ALA CB C 18.38 0.20 1 153 26 26 GLN H H 7.95 0.05 1 154 26 26 GLN HA H 4.15 0.05 1 155 26 26 GLN HG2 H 2.41 0.05 1 156 26 26 GLN HG3 H 2.50 0.05 1 157 26 26 GLN HE21 H 7.46 0.05 1 158 26 26 GLN HE22 H 6.82 0.05 1 159 27 27 LEU H H 8.16 0.05 1 160 27 27 LEU HA H 4.19 0.05 1 161 27 27 LEU HB2 H 1.74 0.05 1 162 27 27 LEU HB3 H 1.81 0.05 1 163 27 27 LEU HG H 1.54 0.05 1 164 27 27 LEU HD1 H 0.82 0.05 2 165 27 27 LEU HD2 H 0.86 0.05 2 166 27 27 LEU CB C 42.18 0.20 1 167 28 28 LEU H H 8.28 0.05 1 168 28 28 LEU HA H 4.19 0.05 1 169 28 28 LEU HB2 H 1.73 0.05 1 170 28 28 LEU HB3 H 1.82 0.05 1 171 28 28 LEU HG H 1.54 0.05 1 172 28 28 LEU HD1 H 0.81 0.05 2 173 28 28 LEU HD2 H 0.86 0.05 2 174 28 28 LEU CA C 57.23 0.20 1 175 28 28 LEU CB C 41.82 0.20 1 176 29 29 THR H H 8.06 0.05 1 177 29 29 THR HA H 4.32 0.05 1 178 29 29 THR HB H 4.09 0.05 1 179 29 29 THR CB C 69.30 0.20 1 180 30 30 ALA H H 8.13 0.05 1 181 30 30 ALA HA H 4.14 0.05 1 182 30 30 ALA CA C 54.84 0.20 1 183 30 30 ALA CB C 18.34 0.20 1 184 31 31 ALA H H 8.43 0.05 1 185 31 31 ALA HA H 4.07 0.05 1 186 31 31 ALA CA C 54.71 0.20 1 187 31 31 ALA CB C 18.08 0.20 1 188 32 32 GLU H H 7.89 0.05 1 189 32 32 GLU HA H 4.17 0.05 1 190 32 32 GLU CA C 57.75 0.20 1 191 33 33 LYS H H 7.97 0.05 1 192 33 33 LYS HA H 4.12 0.05 1 193 33 33 LYS HB2 H 1.86 0.05 1 194 33 33 LYS HB3 H 1.90 0.05 1 195 33 33 LYS CB C 32.24 0.20 1 196 33 33 LYS CE C 42.18 0.20 1 197 34 34 ALA H H 8.00 0.05 1 198 34 34 ALA HA H 4.12 0.05 1 199 34 34 ALA CA C 54.09 0.20 1 200 34 34 ALA CB C 18.16 0.20 1 201 35 35 ASP H H 8.06 0.05 1 202 35 35 ASP HA H 4.47 0.05 1 203 35 35 ASP HB2 H 2.77 0.05 1 204 35 35 ASP HB3 H 2.98 0.05 1 205 35 35 ASP CA C 61.37 0.20 1 206 35 35 ASP CB C 39.58 0.20 1 207 36 36 GLU H H 8.10 0.05 1 208 36 36 GLU HA H 4.13 0.05 1 209 36 36 GLU HG2 H 2.47 0.05 1 210 36 36 GLU HG3 H 2.60 0.05 1 211 36 36 GLU CA C 58.16 0.20 1 212 36 36 GLU CB C 28.14 0.20 1 213 37 37 LEU H H 7.97 0.05 1 214 37 37 LEU HA H 4.30 0.05 1 215 37 37 LEU HB2 H 1.73 0.05 1 216 37 37 LEU HB3 H 1.76 0.05 1 217 37 37 LEU HG H 1.66 0.05 1 218 37 37 LEU HD1 H 0.87 0.05 2 219 37 37 LEU HD2 H 0.89 0.05 2 220 37 37 LEU CA C 55.38 0.20 1 221 38 38 GLY H H 8.08 0.05 1 222 38 38 GLY HA2 H 4.02 0.05 1 223 38 38 GLY HA3 H 4.02 0.05 1 224 38 38 GLY CA C 45.75 0.20 1 stop_ save_