data_9A8B # _entry.id 9A8B # loop_ _atom_type.symbol C H N O # loop_ _audit_author.name _audit_author.pdbx_ordinal "Moyer, A.P." 1 "Baker, D." 2 "Ramelot, T.A." 3 "Montelione, G.T." 4 # loop_ _audit_conform.dict_location _audit_conform.dict_name _audit_conform.dict_version https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ihm_ext.dic mmcif_ihm_ext.dic 1.27 http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic mmcif_pdbx.dic 5.399 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 9A8B _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2024-03-08 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2024-08-21 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 9A8B pdb_00009a8b 10.2210/pdb9a8b/pdb PDB-Dev PDBDEV_00000376 PDBDEV_00000376 ? # loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type "C2 H4 O" 44.053 ACE . "ACETYL GROUP" . non-polymer "C H5 N" 31.058 NME . METHYLAMINE . non-polymer "C5 H9 N O2" 115.132 PRO . PROLINE . "L-peptide linking" "C9 H11 N O2" 165.192 ZTR . "[2-(aminomethyl)phenyl]acetic acid" . non-polymer # _citation.country . _citation.id 1 _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_id_ASTM . _citation.journal_id_CSD . _citation.journal_id_ISSN . _citation.journal_issue . _citation.journal_volume . _citation.page_first . _citation.page_last . _citation.pdbx_database_id_DOI 10.1021/jacs.4c04991 _citation.pdbx_database_id_PubMed . _citation.title "Enumerative Discovery of Non-Canonical Polypeptide Secondary Structures" _citation.year 2024 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal 1 "Moyer, A.P." 1 1 "Ramelot, T.A." 2 1 "Curti, M." 3 1 "Eastman, M.A." 4 1 "Kang, A." 5 1 "Bera, A.K." 6 1 "Tejero, R." 7 1 "Salveson, P.J." 8 1 "Curutchet, C." 9 1 "Romero, E." 10 1 "Montelione, G.T." 11 1 "Baker, D." 12 # _entity.details "solid phase peptide synthesis" _entity.formula_weight 1196.407 _entity.id 1 _entity.pdbx_description "ACE-ZTR-PRO-ZTR-PRO-ZTR-PRO-ZTR-PRO-NME peptide" _entity.pdbx_number_of_molecules 1 _entity.src_method SYN _entity.type POLYMER # _entity_poly.entity_id 1 _entity_poly.nstd_chirality . _entity_poly.nstd_linkage NO _entity_poly.nstd_monomer YES _entity_poly.pdbx_seq_one_letter_code (ACE)(ZTR)P(ZTR)P(ZTR)P(ZTR)P(NME) _entity_poly.pdbx_seq_one_letter_code_can XXPXPXPXPX _entity_poly.pdbx_sequence_evidence_code . _entity_poly.pdbx_strand_id A _entity_poly.type polypeptide(L) # loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 . ACE 1 1 . ZTR 2 1 . PRO 3 1 . ZTR 4 1 . PRO 5 1 . ZTR 6 1 . PRO 7 1 . ZTR 8 1 . PRO 9 1 . NME 10 # _ihm_dataset_group.application validation _ihm_dataset_group.details . _ihm_dataset_group.id 2 _ihm_dataset_group.name . # loop_ _ihm_dataset_group_link.dataset_list_id _ihm_dataset_group_link.group_id 2 2 3 2 4 2 # loop_ _ihm_dataset_list.data_type _ihm_dataset_list.database_hosted _ihm_dataset_list.details _ihm_dataset_list.id "NMR data" YES "BMRB ID 52499" 2 Other NO "CD spectra" 3 "NMR data" YES "BMRB ID 52504" 4 # loop_ _ihm_dataset_related_db_reference.accession_code _ihm_dataset_related_db_reference.dataset_list_id _ihm_dataset_related_db_reference.db_name _ihm_dataset_related_db_reference.details _ihm_dataset_related_db_reference.id _ihm_dataset_related_db_reference.version 52499 2 BMRB "1x DPR2 chemical shifts and NMR FID data" 1 . 52504 4 BMRB "10x DPR2 chemical shifts and NMR FID data" 2 . # _ihm_entity_poly_segment.comp_id_begin ACE _ihm_entity_poly_segment.comp_id_end NME _ihm_entity_poly_segment.entity_id 1 _ihm_entity_poly_segment.id 1 _ihm_entity_poly_segment.seq_id_begin 1 _ihm_entity_poly_segment.seq_id_end 10 # _ihm_model_group.details . _ihm_model_group.id 1 _ihm_model_group.name . # _ihm_model_group_link.group_id 1 _ihm_model_group_link.model_id 1 # _ihm_model_list.assembly_id 1 _ihm_model_list.model_id 1 _ihm_model_list.model_name . _ihm_model_list.protocol_id 1 _ihm_model_list.representation_id 1 # _ihm_model_representation.details "No starting models were used" _ihm_model_representation.id 1 _ihm_model_representation.name . # _ihm_model_representation_details.description . _ihm_model_representation_details.entity_asym_id A _ihm_model_representation_details.entity_description ACE-ZTR-PRO-ZTR-PRO-ZTR-PRO-ZTR-PRO-NME _ihm_model_representation_details.entity_id 1 _ihm_model_representation_details.entity_poly_segment_id 1 _ihm_model_representation_details.id 1 _ihm_model_representation_details.model_granularity by-atom _ihm_model_representation_details.model_mode flexible _ihm_model_representation_details.model_object_count . _ihm_model_representation_details.model_object_primitive atomistic _ihm_model_representation_details.representation_id 1 _ihm_model_representation_details.starting_model_id . # loop_ _ihm_modeling_post_process.analysis_id _ihm_modeling_post_process.dataset_group_id _ihm_modeling_post_process.details _ihm_modeling_post_process.feature _ihm_modeling_post_process.feature_name _ihm_modeling_post_process.id _ihm_modeling_post_process.num_models_begin _ihm_modeling_post_process.num_models_end _ihm_modeling_post_process.protocol_id _ihm_modeling_post_process.script_file_id _ihm_modeling_post_process.software_id _ihm_modeling_post_process.step_id _ihm_modeling_post_process.struct_assembly_id _ihm_modeling_post_process.type 1 2 "In depth manual comparison of experimental and predicted NMR NOESY data" other "Created simulated 2D HH NOESY peak lists using the model structure as a guide" 1 . . 1 . 4 1 1 validation 2 2 "In depth manual comparison of experimental and predicted NMR NOESY data" other "Overlay simulated 2D HH NOESY peak lists with the experimental NMR data" 2 . . 1 . 5 2 1 validation # _ihm_modeling_protocol.details "De novo modeling was carried out without using any starting models or input data. Experimental data was used to validate the de novo models generated. " _ihm_modeling_protocol.id 1 _ihm_modeling_protocol.num_steps 1 _ihm_modeling_protocol.protocol_name modeling # _ihm_modeling_protocol_details.dataset_group_id . _ihm_modeling_protocol_details.description "Computational model produced with in-house monomer and dimer sampling protocols using AIMnet(SMD)-D4 for energy minimizations and scoring." _ihm_modeling_protocol_details.ensemble_flag NO _ihm_modeling_protocol_details.id 1 _ihm_modeling_protocol_details.multi_scale_flag NO _ihm_modeling_protocol_details.multi_state_flag NO _ihm_modeling_protocol_details.num_models_begin . _ihm_modeling_protocol_details.num_models_end . _ihm_modeling_protocol_details.ordered_flag NO _ihm_modeling_protocol_details.protocol_id 1 _ihm_modeling_protocol_details.script_file_id . _ihm_modeling_protocol_details.software_id 1 _ihm_modeling_protocol_details.step_id 1 _ihm_modeling_protocol_details.step_method . _ihm_modeling_protocol_details.step_name . _ihm_modeling_protocol_details.struct_assembly_description . _ihm_modeling_protocol_details.struct_assembly_id 1 # _ihm_struct_assembly.description "4x DPR2 dipeptide repeat of (AMPA, S-Proline)4 octamer computationally modeled using monomer and dimer sampling protocols, energy minimizations, and scoring, and validated using CD and NMR data." _ihm_struct_assembly.id 1 _ihm_struct_assembly.name "4x DPR2 dipeptide repeat of (AMPA, S-Proline)4 octamer" # _ihm_struct_assembly_details.assembly_id 1 _ihm_struct_assembly_details.asym_id A _ihm_struct_assembly_details.entity_description ACE-ZTR-PRO-ZTR-PRO-ZTR-PRO-ZTR-PRO-NME _ihm_struct_assembly_details.entity_id 1 _ihm_struct_assembly_details.entity_poly_segment_id 1 _ihm_struct_assembly_details.id 1 _ihm_struct_assembly_details.parent_assembly_id 1 # loop_ _software.citation_id _software.classification _software.description _software.location _software.name _software.pdbx_ordinal _software.type _software.version . "energy minimization and scoring" '"atoms-in-molecules" neural network potential trained by all atom DFT calculations, greatly increasing the computational speed. Includes implicit solvation energy (SMD method) and the empirical D4 dispersion corrections' https://github.com/aiqm/aimnet AIMNet 1 other AIMNet(SMD)-D4 . "initial conformation generator" "Cambridge Structural Database conformational search method for generation of conformers, which leverages data from small molecule crystal structures" http://confgen.net "Cambridge Structural Database (CSD) ConfGen" 2 other . . "code for model building" "algorithms for mathematical operations and scientific computing in Python" https://scipy.org/ SciPy 3 other . . "restraint analysis and structure quality assessment" . https://github.rpi.edu/RPIBioinformatics/PDBStat_public PDBStat 4 program 5.21 . "NMR data analysis" . https://sites.google.com/view/pokynmr Poky 5 program "build 20220114" # _struct.entry_id 9A8B _struct.pdbx_CASP_flag . _struct.pdbx_descriptor "4x DPR2 dipeptide repeat of (AMPA, S-Proline)4 octamer" _struct.pdbx_details . _struct.pdbx_model_details "Model produced with in-house monomer and dimer sampling protocols using AIMnet(SMD)-D4 for energy minimizations and scoring." _struct.pdbx_model_type_details "lowest energy model" _struct.pdbx_structure_determination_methodology integrative _struct.title "Dipeptide repeat designed model, 4x DPR2, verified with CD and NMR data." # _struct_asym.details . _struct_asym.entity_id 1 _struct_asym.id A _struct_asym.pdbx_PDB_id . _struct_asym.pdbx_alt_id . _struct_asym.pdbx_blank_PDB_chainid_flag . _struct_asym.pdbx_modified . _struct_asym.pdbx_order . _struct_asym.pdbx_type . # _struct_ref.db_code 9A8B _struct_ref.db_name PDB _struct_ref.details . _struct_ref.entity_id 1 _struct_ref.id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_align_end 10 _struct_ref.pdbx_db_accession 9A8B _struct_ref.pdbx_db_isoform . _struct_ref.pdbx_seq_one_letter_code . # _struct_ref_seq.align_id 1 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.db_align_end 10 _struct_ref_seq.ref_id 1 _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.seq_align_end 10 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code A 1 1 ACE 1 1 ACE ACE A . A 1 2 ZTR 2 2 ZTR ZTR A . A 1 3 PRO 3 3 PRO PRO A . A 1 4 ZTR 4 4 ZTR ZTR A . A 1 5 PRO 5 5 PRO PRO A . A 1 6 ZTR 6 6 ZTR ZTR A . A 1 7 PRO 7 7 PRO PRO A . A 1 8 ZTR 8 8 ZTR ZTR A . A 1 9 PRO 9 9 PRO PRO A . A 1 10 NME 1 1 NME NME A 0 # # loop_ # #