data_30365 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of de novo macrocycle design7.3a ; _BMRB_accession_number 30365 _BMRB_flat_file_name bmr30365.str _Entry_type original _Submission_date 2017-10-25 _Accession_date 2017-10-25 _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 Shortridge M. D. . 2 Hosseinzadeh P. . . 3 Pardo-Avila F. . . 4 Varani G. . . 5 Baker D. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 41 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-01-05 original BMRB . stop_ _Original_release_date 2018-01-03 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Comprehensive computational design of ordered peptide macrocycles. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 29242347 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hosseinzadeh P. . . 2 Bhardwaj G. . . 3 Mulligan V. K. . 4 Shortridge M. D. . 5 Craven T. W. . 6 Pardo-Avila F. . . 7 Rettie S. A. . 8 Kim D. E. . 9 Silva D. A. . 10 Ibrahim Y. M. . 11 Webb I. K. . 12 Cort J. R. . 13 Adkins J. N. . 14 Varani G. . . 15 Baker D. . . stop_ _Journal_abbreviation Science _Journal_volume 358 _Journal_issue 6369 _Journal_ASTM SCIEAS _Journal_ISSN 1095-9203 _Journal_CSD 0038 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1461 _Page_last 1466 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name QDP(DPR)K(2TL)(DAS) _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 800.833 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence ; QDPXKXX ; loop_ _Residue_seq_code _Residue_label 1 GLN 2 ASP 3 PRO 4 DPR 5 LYS 6 DTH 7 DAS 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_ save_chem_comp_DTH _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-THREONINE _BMRB_code DTH _PDB_code DTH _Standard_residue_derivative . _Molecular_mass 119.119 _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 . ? CG2 CG2 C . 0 . ? OG1 OG1 O . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HB HB H . 0 . ? HG21 HG21 H . 0 . ? HG22 HG22 H . 0 . ? HG23 HG23 H . 0 . ? HG1 HG1 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 HN2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG2 ? ? SING CB OG1 ? ? SING CB HB ? ? SING CG2 HG21 ? ? SING CG2 HG22 ? ? SING CG2 HG23 ? ? SING OG1 HG1 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DAS _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common 'D-ASPARTIC ACID' _BMRB_code DAS _PDB_code DAS _Standard_residue_derivative . _Molecular_mass 133.103 _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 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? OD1 OD1 O . 0 . ? OD2 OD2 O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD2 HD2 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 C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG OD1 ? ? SING CG OD2 ? ? SING OD2 HD2 ? ? 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 Human 9606 Eukaryota Metazoa Homo sapiens 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 '5 mg/mL Design 7.3a, 5 % v/v [U-2H] glycerol, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 5 mg/mL 'natural abundance' glycerol 5 '% v/v' [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name gromacs _Version 2016.1 loop_ _Vendor _Address _Electronic_address Abraham . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 . 'Not defined' pH 5.5 . pH pressure 1 . atm temperature 278 . 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' 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 GLN H H 9.157 0.00 . 2 1 1 GLN HA H 4.317 0.00 . 3 1 1 GLN HB2 H 1.815 0.00 . 4 1 1 GLN HB3 H 1.815 0.00 . 5 1 1 GLN HG2 H 2.305 0.00 . 6 1 1 GLN HG3 H 2.305 0.00 . 7 2 2 ASP H H 8.171 0.02 . 8 2 2 ASP HA H 5.227 0.00 . 9 2 2 ASP HB2 H 2.824 0.00 . 10 2 2 ASP HB3 H 2.979 0.00 . 11 3 3 PRO HA H 4.530 0.00 . 12 3 3 PRO HB2 H 2.096 0.01 . 13 3 3 PRO HB3 H 1.934 0.00 . 14 3 3 PRO HG2 H 2.280 0.00 . 15 3 3 PRO HG3 H 1.802 0.00 . 16 3 3 PRO HD2 H 3.747 0.00 . 17 3 3 PRO HD3 H 4.119 0.00 . 18 4 4 DPR HA H 4.651 0.00 . 19 4 4 DPR HB3 H 2.009 0.01 . 20 4 4 DPR HD2 H 3.826 0.00 . 21 4 4 DPR HD3 H 3.559 0.00 . 22 4 4 DPR HG2 H 2.209 0.00 . 23 4 4 DPR HG3 H 1.736 0.00 . 24 5 5 LYS H H 8.042 0.00 . 25 5 5 LYS HA H 4.432 0.00 . 26 5 5 LYS HB2 H 1.662 0.00 . 27 5 5 LYS HB3 H 1.662 0.00 . 28 5 5 LYS HG2 H 1.822 0.00 . 29 5 5 LYS HG3 H 1.822 0.00 . 30 5 5 LYS HD2 H 1.306 0.00 . 31 5 5 LYS HD3 H 1.389 0.00 . 32 5 5 LYS HE2 H 2.930 0.00 . 33 5 5 LYS HE3 H 2.930 0.00 . 34 5 5 LYS HZ H 7.548 0.01 . 35 6 6 DTH H H 8.242 0.02 . 36 6 6 DTH HA H 4.632 0.00 . 37 6 6 DTH HB H 4.162 0.00 . 38 6 6 DTH HG21 H 1.018 0.00 . 39 7 7 DAS H H 8.566 0.00 . 40 7 7 DAS HA H 4.481 0.00 . 41 7 7 DAS HB3 H 2.830 0.00 . stop_ save_