data_30333 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Capped-strapped peptide ; _BMRB_accession_number 30333 _BMRB_flat_file_name bmr30333.str _Entry_type original _Submission_date 2017-08-13 _Accession_date 2017-08-13 _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 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 80 "13C chemical shifts" 30 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-02-15 original BMRB . stop_ _Original_release_date 2017-08-29 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; An ideal alpha-helix by bridging capping motifs in a short peptide ; _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 Wu H. . . 2 Acharyya A. . . 3 Wu Y. . . 4 Liu L. . . 5 Jo H. . . 6 Gai F. . . 7 DeGrado W. F. . 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 'Capped-strapped peptide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 entity_2 $entity_B0I 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 1445.716 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence ; XTPRQARAARAAXCX ; loop_ _Residue_seq_code _Residue_label 1 H00 2 THR 3 PRO 4 ARG 5 GLN 6 ALA 7 ARG 8 ALA 9 ALA 10 ARG 11 ALA 12 ALA 13 DAL 14 CYS 15 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DAL _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-ALANINE _BMRB_code DAL _PDB_code DAL _Standard_residue_derivative . _Molecular_mass 89.093 _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 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB1 HB1 H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 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 H ? ? SING N H2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB HB1 ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_H00 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common '4-sulfanylbutanoic acid' _BMRB_code H00 _PDB_code H00 _Standard_residue_derivative . _Molecular_mass 120.170 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? SD SD S . 0 . ? C C C . 0 . ? O O O . 0 . ? HA1 HA1 H . 0 . ? HA2 HA2 H . 0 . ? HB1 HB1 H . 0 . ? HB2 HB2 H . 0 . ? HG1 HG1 H . 0 . ? HG2 HG2 H . 0 . ? H1 H1 H . 0 . ? OXT OXT O . 0 . ? H2 H2 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 CA C ? ? SING CA CB ? ? DOUB C O ? ? SING CB CG ? ? SING CG SD ? ? SING CA HA1 ? ? SING CA HA2 ? ? SING CB HB1 ? ? SING CB HB2 ? ? SING CG HG1 ? ? SING CG HG2 ? ? SING SD H1 ? ? SING C OXT ? ? SING OXT H2 ? ? stop_ save_ save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _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 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 HN1 ? ? SING N HN2 ? ? stop_ save_ ############# # Ligands # ############# save_B0I _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "entity_B0I (3,3'-dimethyl-1,1'-biphenyl)" _BMRB_code B0I _PDB_code B0I _Molecular_mass 182.261 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons CB1 CB1 C . 0 . ? CG1 CG1 C . 0 . ? CD1 CD1 C . 0 . ? CD2 CD2 C . 0 . ? CE1 CE1 C . 0 . ? CE2 CE2 C . 0 . ? CZ1 CZ1 C . 0 . ? CB2 CB2 C . 0 . ? CG2 CG2 C . 0 . ? CD3 CD3 C . 0 . ? CD4 CD4 C . 0 . ? CE3 CE3 C . 0 . ? CE4 CE4 C . 0 . ? CZ2 CZ2 C . 0 . ? HB11 HB11 H . 0 . ? HB12 HB12 H . 0 . ? H1 H1 H . 0 . ? HD1 HD1 H . 0 . ? HD2 HD2 H . 0 . ? HE2 HE2 H . 0 . ? HZ1 HZ1 H . 0 . ? HB22 HB22 H . 0 . ? H2 H2 H . 0 . ? HB21 HB21 H . 0 . ? HD3 HD3 H . 0 . ? HD4 HD4 H . 0 . ? HE4 HE4 H . 0 . ? HZ2 HZ2 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 DOUB CE2 CZ1 ? ? SING CE2 CD2 ? ? SING CZ1 CE1 ? ? DOUB CZ2 CE4 ? ? SING CZ2 CE3 ? ? SING CE4 CD4 ? ? DOUB CD2 CG1 ? ? SING CE1 CE3 ? ? DOUB CE1 CD1 ? ? DOUB CE3 CD3 ? ? DOUB CD4 CG2 ? ? SING CD3 CG2 ? ? SING CG2 CB2 ? ? SING CG1 CD1 ? ? SING CG1 CB1 ? ? SING CB1 HB11 ? ? SING CB1 HB12 ? ? SING CB1 H1 ? ? SING CD1 HD1 ? ? SING CD2 HD2 ? ? SING CE2 HE2 ? ? SING CZ1 HZ1 ? ? SING CB2 HB22 ? ? SING CB2 H2 ? ? SING CB2 HB21 ? ? SING CD3 HD3 ? ? SING CD4 HD4 ? ? SING CE4 HE4 ? ? SING CZ2 HZ2 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_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 '0.6 mM Capped-strapped peptide A37, 95% H2O/5% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.6 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 'data analysis' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_software_4 _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_ ######################### # 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 . mM pH 4.0 . pH pressure 1 . atm temperature 308 . 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 'methyl protons' ppm 4.65 internal indirect . . . 0.25144953 water H 1 protons ppm 4.65 internal direct . . . 1.0 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_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 H00 HA1 H 2.53 0.05 1 2 1 1 H00 HA2 H 2.74 0.05 1 3 1 1 H00 HB1 H 1.95 0.05 1 4 1 1 H00 HB2 H 2.08 0.05 1 5 1 1 H00 HG1 H 2.27 0.05 1 6 1 1 H00 HG2 H 2.41 0.05 1 7 2 2 THR H H 8.57 0.05 1 8 2 2 THR HA H 4.63 0.05 1 9 2 2 THR HB H 4.73 0.05 1 10 2 2 THR HG2 H 1.33 0.05 1 11 2 2 THR CG2 C 21.84 0.20 1 12 3 3 PRO HA H 4.29 0.05 1 13 3 3 PRO HB2 H 1.95 0.05 1 14 3 3 PRO HB3 H 2.39 0.05 1 15 3 3 PRO HG2 H 2.22 0.05 1 16 3 3 PRO HG3 H 2.03 0.05 1 17 3 3 PRO HD2 H 3.94 0.05 1 18 3 3 PRO HD3 H 3.94 0.05 1 19 3 3 PRO CA C 65.95 0.20 1 20 3 3 PRO CB C 31.77 0.20 1 21 3 3 PRO CG C 28.22 0.20 1 22 3 3 PRO CD C 50.31 0.20 1 23 4 4 ARG H H 7.97 0.05 1 24 4 4 ARG HA H 3.97 0.05 1 25 4 4 ARG HB2 H 1.87 0.05 1 26 4 4 ARG HB3 H 1.87 0.05 1 27 4 4 ARG HG2 H 1.59 0.05 1 28 4 4 ARG HG3 H 1.73 0.05 1 29 4 4 ARG HD2 H 3.21 0.05 1 30 4 4 ARG HD3 H 3.21 0.05 1 31 4 4 ARG HE H 7.22 0.05 1 32 4 4 ARG CA C 59.50 0.20 1 33 4 4 ARG CB C 29.92 0.20 1 34 4 4 ARG CG C 27.55 0.20 1 35 5 5 GLN H H 7.64 0.05 1 36 5 5 GLN HA H 3.82 0.05 1 37 5 5 GLN HB2 H 2.18 0.05 1 38 5 5 GLN HB3 H 0.99 0.05 1 39 5 5 GLN HG2 H 2.34 0.05 1 40 5 5 GLN HG3 H 2.34 0.05 1 41 5 5 GLN HE21 H 6.84 0.05 1 42 5 5 GLN HE22 H 7.52 0.05 1 43 5 5 GLN CA C 58.82 0.20 1 44 5 5 GLN CB C 28.32 0.20 1 45 5 5 GLN CG C 34.98 0.20 1 46 6 6 ALA H H 8.48 0.05 1 47 6 6 ALA HA H 3.92 0.05 1 48 6 6 ALA HB H 1.31 0.05 1 49 6 6 ALA CA C 54.88 0.20 1 50 6 6 ALA CB C 17.94 0.20 1 51 7 7 ARG H H 7.95 0.05 1 52 7 7 ARG HA H 3.92 0.05 1 53 7 7 ARG HB2 H 1.89 0.05 1 54 7 7 ARG HB3 H 1.89 0.05 1 55 7 7 ARG HG2 H 1.58 0.05 1 56 7 7 ARG HG3 H 1.84 0.05 1 57 7 7 ARG HD2 H 3.16 0.05 1 58 7 7 ARG HD3 H 3.23 0.05 1 59 7 7 ARG HE H 7.28 0.05 1 60 7 7 ARG CA C 59.44 0.20 1 61 7 7 ARG CB C 30.26 0.20 1 62 7 7 ARG CG C 27.86 0.20 1 63 8 8 ALA H H 7.66 0.05 1 64 8 8 ALA HA H 4.12 0.05 1 65 8 8 ALA HB H 1.58 0.05 1 66 8 8 ALA CA C 54.74 0.20 1 67 8 8 ALA CB C 17.83 0.20 1 68 9 9 ALA H H 8.19 0.05 1 69 9 9 ALA HA H 2.98 0.05 1 70 9 9 ALA HB H 0.92 0.05 1 71 9 9 ALA CA C 54.55 0.20 1 72 9 9 ALA CB C 17.95 0.20 1 73 10 10 ARG H H 7.75 0.05 1 74 10 10 ARG HA H 4.05 0.05 1 75 10 10 ARG HB2 H 1.87 0.05 1 76 10 10 ARG HB3 H 1.87 0.05 1 77 10 10 ARG HG2 H 1.59 0.05 1 78 10 10 ARG HG3 H 1.76 0.05 1 79 10 10 ARG HD2 H 3.17 0.05 1 80 10 10 ARG HD3 H 3.21 0.05 1 81 10 10 ARG HE H 7.25 0.05 1 82 10 10 ARG CA C 58.95 0.20 1 83 10 10 ARG CB C 30.13 0.20 1 84 10 10 ARG CG C 27.57 0.20 1 85 11 11 ALA H H 7.79 0.05 1 86 11 11 ALA HA H 4.14 0.05 1 87 11 11 ALA HB H 1.48 0.05 1 88 11 11 ALA CA C 54.41 0.20 1 89 11 11 ALA CB C 18.07 0.20 1 90 12 12 ALA H H 7.54 0.05 1 91 12 12 ALA HA H 4.41 0.05 1 92 12 12 ALA HB H 1.66 0.05 1 93 12 12 ALA CA C 52.10 0.20 1 94 12 12 ALA CB C 20.12 0.20 1 95 13 13 DAL H H 7.53 0.05 1 96 13 13 DAL CA C 53.43 0.20 1 97 13 13 DAL CB C 19.59 0.20 1 98 13 13 DAL HA H 4.33 0.05 1 99 13 13 DAL HB1 H 1.49 0.05 1 100 13 13 DAL HB2 H 1.49 0.05 1 101 13 13 DAL HB3 H 1.49 0.05 1 102 14 14 CYS HA H 4.62 0.05 1 103 14 14 CYS HB2 H 2.79 0.05 1 104 14 14 CYS HB3 H 2.79 0.05 1 105 14 14 CYS CB C 35.58 0.20 1 106 15 15 NH2 HN1 H 8.13 0.05 1 stop_ save_ save_assigned_chemical_shifts_1_2 _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_2 _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 1 101 1 B0I HB12 H 3.64 0.05 1 2 101 1 B0I HB11 H 3.75 0.05 1 3 101 1 B0I HD1 H 7.29 0.05 1 4 101 1 B0I HD2 H 7.12 0.05 1 stop_ save_