data_30360 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of de novo macrocycle design10.2 ; _BMRB_accession_number 30360 _BMRB_flat_file_name bmr30360.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" 53 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-12-26 original BMRB . stop_ _Original_release_date 2017-12-21 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 E(DVA)DP(DGL)(DHI)(DPR)N(DAL)(DPR) _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 1105.133 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence ; EXDPXXXNXX ; loop_ _Residue_seq_code _Residue_label 1 GLU 2 DVA 3 ASP 4 PRO 5 DGL 6 DHI 7 DPR 8 ASN 9 DAL 10 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_ save_chem_comp_DGL _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common 'D-GLUTAMIC ACID' _BMRB_code DGL _PDB_code DGL _Standard_residue_derivative . _Molecular_mass 147.129 _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 . ? CD CD C . 0 . ? OE1 OE1 O . 0 . ? OE2 OE2 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 . ? HE2 HE2 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 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? DOUB CD OE1 ? ? SING CD OE2 ? ? SING OE2 HE2 ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DHI _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-HISTIDINE _BMRB_code DHI _PDB_code DHI _Standard_residue_derivative . _Molecular_mass 156.162 _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 . ? ND1 ND1 N . 1 . ? CD2 CD2 C . 0 . ? CE1 CE1 C . 0 . ? NE2 NE2 N . 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 . ? HD1 HD1 H . 0 . ? HD2 HD2 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 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 ? ? SING CG ND1 ? ? DOUB CG CD2 ? ? DOUB ND1 CE1 ? ? SING ND1 HD1 ? ? SING CD2 NE2 ? ? SING CD2 HD2 ? ? SING CE1 NE2 ? ? SING CE1 HE1 ? ? SING NE2 HE2 ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DVA _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-VALINE _BMRB_code DVA _PDB_code DVA _Standard_residue_derivative . _Molecular_mass 117.146 _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 . ? CG1 CG1 C . 0 . ? CG2 CG2 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 . ? HB HB H . 0 . ? HG11 HG11 H . 0 . ? HG12 HG12 H . 0 . ? HG13 HG13 H . 0 . ? HG21 HG21 H . 0 . ? HG22 HG22 H . 0 . ? HG23 HG23 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 CG1 ? ? SING CB CG2 ? ? SING CB HB ? ? SING CG1 HG11 ? ? SING CG1 HG12 ? ? SING CG1 HG13 ? ? SING CG2 HG21 ? ? SING CG2 HG22 ? ? SING CG2 HG23 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ 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_ #################### # 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 10.2, 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_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 800 _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_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _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 GLU H H 8.542 0.00 . 2 1 1 GLU HA H 4.471 0.00 . 3 1 1 GLU HB2 H 2.399 0.00 . 4 1 1 GLU HB3 H 1.903 0.00 . 5 1 1 GLU HG2 H 2.097 0.00 . 6 1 1 GLU HG3 H 2.097 0.00 . 7 2 2 DVA H H 8.304 0.00 . 8 2 2 DVA HA H 3.914 0.00 . 9 2 2 DVA HB H 2.026 0.00 . 10 2 2 DVA HG11 H 0.871 0.00 . 11 3 3 ASP H H 8.590 0.00 . 12 3 3 ASP HA H 4.904 0.00 . 13 3 3 ASP HB2 H 2.940 0.00 . 14 3 3 ASP HB3 H 2.680 0.00 . 15 4 4 PRO HA H 4.296 0.00 . 16 4 4 PRO HB2 H 1.897 0.00 . 17 4 4 PRO HB3 H 2.229 0.00 . 18 4 4 PRO HG2 H 1.970 0.00 . 19 4 4 PRO HG3 H 1.970 0.00 . 20 4 4 PRO HD2 H 3.695 0.00 . 21 4 4 PRO HD3 H 3.639 0.00 . 22 5 5 DGL H H 8.498 0.00 . 23 5 5 DGL HA H 4.166 0.00 . 24 5 5 DGL HB2 H 1.715 0.00 . 25 5 5 DGL HB3 H 2.277 0.00 . 26 5 5 DGL HG3 H 2.018 0.00 . 27 6 6 DHI H H 7.874 0.00 . 28 6 6 DHI HA H 5.033 0.00 . 29 6 6 DHI HB2 H 3.164 0.00 . 30 6 6 DHI HB3 H 3.068 0.00 . 31 6 6 DHI HD2 H 7.225 0.00 . 32 7 7 DPR HA H 4.303 0.00 . 33 7 7 DPR HB2 H 1.843 0.00 . 34 7 7 DPR HB3 H 2.204 0.00 . 35 7 7 DPR HD2 H 3.557 0.00 . 36 7 7 DPR HD3 H 3.519 0.00 . 37 7 7 DPR HG2 H 1.907 0.00 . 38 7 7 DPR HG3 H 1.977 0.00 . 39 8 8 ASN H H 8.610 0.00 . 40 8 8 ASN HA H 4.800 0.01 . 41 8 8 ASN HB2 H 2.623 0.00 . 42 8 8 ASN HB3 H 2.801 0.00 . 43 8 8 ASN HD21 H 7.600 0.00 . 44 8 8 ASN HD22 H 6.900 0.00 . 45 9 9 DAL H H 8.105 0.00 . 46 9 9 DAL HA H 4.637 0.00 . 47 9 9 DAL HB1 H 1.347 0.00 . 48 10 10 DPR HA H 4.412 0.00 . 49 10 10 DPR HB2 H 2.280 0.00 . 50 10 10 DPR HB3 H 1.889 0.00 . 51 10 10 DPR HD2 H 3.817 0.00 . 52 10 10 DPR HD3 H 3.615 0.00 . 53 10 10 DPR HG3 H 1.992 0.00 . stop_ save_