data_30355 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of de novo macrocycle Design8.1 ; _BMRB_accession_number 30355 _BMRB_flat_file_name bmr30355.str _Entry_type original _Submission_date 2017-10-24 _Accession_date 2017-10-24 _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" 46 "13C chemical shifts" 25 "15N chemical shifts" 9 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-01-02 original BMRB . stop_ _Original_release_date 2018-01-02 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 DDPT(DPR)(DAR)Q(DGN) _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 956.976 _Mol_thiol_state 'not present' _Details 'Head to tail cyclic between position 1 and 8' ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence ; DDPTXXQX ; loop_ _Residue_seq_code _Residue_label 1 ASP 2 ASP 3 PRO 4 THR 5 DPR 6 DAR 7 GLN 8 DGN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DGN _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-GLUTAMINE _BMRB_code DGN _PDB_code DGN _Standard_residue_derivative . _Molecular_mass 146.144 _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 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? OE1 OE1 O . 0 . ? NE2 NE2 N . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HXT HXT H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HE21 HE21 H . 0 . ? HE22 HE22 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 OXT HXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? DOUB CD OE1 ? ? SING CD NE2 ? ? SING NE2 HE21 ? ? SING NE2 HE22 ? ? stop_ save_ 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_DAR _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-ARGININE _BMRB_code DAR _PDB_code DAR _Standard_residue_derivative . _Molecular_mass 175.209 _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 . ? NE NE N . 0 . ? CZ CZ C . 0 . ? NH1 NH1 N . 0 . ? NH2 NH2 N . 1 . ? C C C . 0 . ? O O 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 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HE HE H . 0 . ? HH11 HH11 H . 0 . ? HH12 HH12 H . 0 . ? HH21 HH21 H . 0 . ? HH22 HH22 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 CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD NE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING NE CZ ? ? SING NE HE ? ? SING CZ NH1 ? ? DOUB CZ NH2 ? ? SING NH1 HH11 ? ? SING NH1 HH12 ? ? SING NH2 HH21 ? ? SING NH2 HH22 ? ? 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 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 unlabeled peptide, 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 SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 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 gromacs _Version . loop_ _Vendor _Address _Electronic_address Abraham . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details 'TCI Cryoprobe' 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_4 _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' 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' '2D 1H-15N HSQC' '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 ASP H H 9.098 0.00 . 2 1 1 ASP HA H 4.558 0.01 . 3 1 1 ASP HB2 H 2.812 0.00 . 4 1 1 ASP HB3 H 2.919 0.01 . 5 1 1 ASP CA C 53.135 0.00 . 6 1 1 ASP CB C 37.463 0.11 . 7 1 1 ASP N N 125.699 0.00 . 8 2 2 ASP H H 7.846 0.00 . 9 2 2 ASP HA H 4.804 0.01 . 10 2 2 ASP HB2 H 2.845 0.01 . 11 2 2 ASP HB3 H 3.207 0.01 . 12 2 2 ASP CA C 50.620 0.00 . 13 2 2 ASP CB C 38.017 0.06 . 14 2 2 ASP N N 121.477 0.00 . 15 3 3 PRO HA H 4.205 0.07 . 16 3 3 PRO HB2 H 1.962 0.01 . 17 3 3 PRO HB3 H 2.256 0.01 . 18 3 3 PRO HG2 H 2.079 0.12 . 19 3 3 PRO HG3 H 2.079 0.12 . 20 3 3 PRO HD2 H 3.904 0.01 . 21 3 3 PRO HD3 H 3.909 0.00 . 22 3 3 PRO CA C 64.365 0.00 . 23 3 3 PRO CB C 32.303 0.09 . 24 3 3 PRO CG C 27.219 0.00 . 25 3 3 PRO CD C 50.741 0.02 . 26 4 4 THR H H 7.571 0.00 . 27 4 4 THR HA H 4.459 0.01 . 28 4 4 THR HB H 3.981 0.01 . 29 4 4 THR HG2 H 1.084 0.01 . 30 4 4 THR CA C 59.420 0.00 . 31 4 4 THR CB C 69.226 0.00 . 32 4 4 THR CG2 C 21.223 0.00 . 33 4 4 THR N N 115.145 0.00 . 34 5 5 DPR CA C 62.773 0.00 . 35 5 5 DPR CB C 31.912 0.00 . 36 5 5 DPR CD C 50.877 0.02 . 37 5 5 DPR CG C 28.362 0.00 . 38 5 5 DPR HA H 4.292 0.15 . 39 5 5 DPR HB2 H 2.148 0.10 . 40 5 5 DPR HD2 H 3.647 0.01 . 41 5 5 DPR HD3 H 3.813 0.01 . 42 5 5 DPR HG2 H 1.952 0.09 . 43 6 6 DAR H H 7.811 0.02 . 44 6 6 DAR N N 120.633 0.00 . 45 6 6 DAR CA C 58.079 0.00 . 46 6 6 DAR CB C 30.415 0.00 . 47 6 6 DAR CD C 43.355 0.00 . 48 6 6 DAR CG C 27.370 0.05 . 49 6 6 DAR HA H 4.067 0.07 . 50 6 6 DAR HB2 H 1.734 0.02 . 51 6 6 DAR HB3 H 1.813 0.01 . 52 6 6 DAR HD2 H 3.176 0.01 . 53 6 6 DAR HE H 7.088 0.00 . 54 6 6 DAR HG2 H 1.517 0.01 . 55 6 6 DAR HG3 H 1.708 0.03 . 56 6 6 DAR NE N 116.271 0.00 . 57 7 7 GLN H H 7.651 0.00 . 58 7 7 GLN HA H 4.488 0.01 . 59 7 7 GLN HB2 H 1.921 0.01 . 60 7 7 GLN HB3 H 2.085 0.00 . 61 7 7 GLN HG2 H 2.163 0.01 . 62 7 7 GLN HG3 H 2.262 0.01 . 63 7 7 GLN HE21 H 7.457 0.00 . 64 7 7 GLN HE22 H 6.886 0.00 . 65 7 7 GLN CA C 54.308 0.00 . 66 7 7 GLN CB C 30.558 0.03 . 67 7 7 GLN CG C 33.566 0.15 . 68 7 7 GLN N N 119.460 0.00 . 69 7 7 GLN NE2 N 112.397 0.00 . 70 8 8 DGN H H 8.286 0.00 . 71 8 8 DGN N N 122.744 0.00 . 72 8 8 DGN CA C 57.325 0.00 . 73 8 8 DGN CB C 29.355 2.62 . 74 8 8 DGN CG C 33.536 0.00 . 75 8 8 DGN HA H 4.032 0.01 . 76 8 8 DGN HB2 H 1.912 0.03 . 77 8 8 DGN HE21 H 7.523 0.00 . 78 8 8 DGN HE22 H 6.900 0.00 . 79 8 8 DGN HG2 H 2.266 0.00 . 80 8 8 DGN NE2 N 112.519 0.00 . stop_ save_