data_9A9R # _entry.id 9A9R # loop_ _atom_type.symbol C H N O S # loop_ _audit_author.name _audit_author.pdbx_ordinal "Bonucci, A." 1 "Wang, T." 2 "Baroudi, H." 3 "Etienne, E." 4 "Gerbaud, G." 5 "Mileo, E." 6 "Yamato, T." 7 "Gontero, B." 8 "Launay, H." 9 "Belle, V." 10 "Receveur-Brechot, V." 11 # 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 1.28 http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic mmcif_pdbx.dic 5.403 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 9A9R _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2025-04-08 # 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 2025-11-05 # _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 9A9R pdb_00009a9r 10.2210/pdb9a9r/pdb # 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 "C3 H7 N O2" 89.094 ALA . ALANINE . "L-peptide linking" "C6 H15 N4 O2 1" 175.212 ARG . ARGININE . "L-peptide linking" "C4 H8 N2 O3" 132.119 ASN . ASPARAGINE . "L-peptide linking" "C4 H7 N O4" 133.103 ASP . "ASPARTIC ACID" . "L-peptide linking" "C3 H7 N O2 S" 121.154 CYS . CYSTEINE . "L-peptide linking" "C5 H10 N2 O3" 146.146 GLN . GLUTAMINE . "L-peptide linking" "C5 H9 N O4" 147.13 GLU . "GLUTAMIC ACID" . "L-peptide linking" "C2 H5 N O2" 75.067 GLY . GLYCINE . "peptide linking" "C6 H13 N O2" 131.175 ILE . ISOLEUCINE . "L-peptide linking" "C6 H13 N O2" 131.175 LEU . LEUCINE . "L-peptide linking" "C6 H15 N2 O2 1" 147.198 LYS . LYSINE . "L-peptide linking" "C5 H11 N O2 S" 149.208 MET . METHIONINE . "L-peptide linking" "C9 H11 N O2" 165.192 PHE . PHENYLALANINE . "L-peptide linking" "C5 H9 N O2" 115.132 PRO . PROLINE . "L-peptide linking" "C3 H7 N O3" 105.093 SER . SERINE . "L-peptide linking" "C4 H9 N O3" 119.12 THR . THREONINE . "L-peptide linking" "C11 H12 N2 O2" 204.229 TRP . TRYPTOPHAN . "L-peptide linking" "C9 H11 N O3" 181.191 TYR . TYROSINE . "L-peptide linking" "C5 H11 N O2" 117.148 VAL . VALINE . "L-peptide linking" # _citation.country . _citation.id 1 _citation.journal_abbrev "Febs J." _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 10.1111/febs.70187 _citation.pdbx_database_id_PubMed 40674273 _citation.title "Hidden protein disorder: Deciphering the structural organisation and dynamics of a non-canonical CP12 from the diatom Thalassiosira pseudonana" _citation.year 2025 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal 1 "Bonucci, A." 1 1 "Wang, T." 2 1 "Baroudi, H." 3 1 "Etienne, E." 4 1 "Gerbaud, G." 5 1 "Mileo, E." 6 1 "Parsiegla, G." 7 1 "Yamato, T." 8 1 "Gontero, B." 9 1 "Launay, H." 10 1 "Belle, V." 11 1 "Receveur-Brechot, V." 12 # _entity.details . _entity.formula_weight 20148.852 _entity.id 1 _entity.pdbx_description "CP12 domain-containing protein" _entity.pdbx_number_of_molecules 2 _entity.src_method MAN _entity.type POLYMER # _entity_poly.entity_id 1 _entity_poly.nstd_chirality . _entity_poly.nstd_linkage NO _entity_poly.nstd_monomer NO _entity_poly.pdbx_seq_one_letter_code AAIEAALDASKKFGSTSSEARVLWDIVEEMDASDNSVASKAPIVDSEYEAKVKSLCQMLTKTKAELDQVKALADDLKGVKLASPSVGSSAPDDSVMKEALAAARAATEEFGQSSPQARLAWETVEEIAASPVDIRAPLDEESLIELIEGSEALEKFQAALGSR _entity_poly.pdbx_seq_one_letter_code_can AAIEAALDASKKFGSTSSEARVLWDIVEEMDASDNSVASKAPIVDSEYEAKVKSLCQMLTKTKAELDQVKALADDLKGVKLASPSVGSSAPDDSVMKEALAAARAATEEFGQSSPQARLAWETVEEIAASPVDIRAPLDEESLIELIEGSEALEKFQAALGSR _entity_poly.pdbx_sequence_evidence_code . _entity_poly.pdbx_strand_id B,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 . ALA 1 1 . ALA 2 1 . ILE 3 1 . GLU 4 1 . ALA 5 1 . ALA 6 1 . LEU 7 1 . ASP 8 1 . ALA 9 1 . SER 10 1 . LYS 11 1 . LYS 12 1 . PHE 13 1 . GLY 14 1 . SER 15 1 . THR 16 1 . SER 17 1 . SER 18 1 . GLU 19 1 . ALA 20 1 . ARG 21 1 . VAL 22 1 . LEU 23 1 . TRP 24 1 . ASP 25 1 . ILE 26 1 . VAL 27 1 . GLU 28 1 . GLU 29 1 . MET 30 1 . ASP 31 1 . ALA 32 1 . SER 33 1 . ASP 34 1 . ASN 35 1 . SER 36 1 . VAL 37 1 . ALA 38 1 . SER 39 1 . LYS 40 1 . ALA 41 1 . PRO 42 1 . ILE 43 1 . VAL 44 1 . ASP 45 1 . SER 46 1 . GLU 47 1 . TYR 48 1 . GLU 49 1 . ALA 50 1 . LYS 51 1 . VAL 52 1 . LYS 53 1 . SER 54 1 . LEU 55 1 . CYS 56 1 . GLN 57 1 . MET 58 1 . LEU 59 1 . THR 60 1 . LYS 61 1 . THR 62 1 . LYS 63 1 . ALA 64 1 . GLU 65 1 . LEU 66 1 . ASP 67 1 . GLN 68 1 . VAL 69 1 . LYS 70 1 . ALA 71 1 . LEU 72 1 . ALA 73 1 . ASP 74 1 . ASP 75 1 . LEU 76 1 . LYS 77 1 . GLY 78 1 . VAL 79 1 . LYS 80 1 . LEU 81 1 . ALA 82 1 . SER 83 1 . PRO 84 1 . SER 85 1 . VAL 86 1 . GLY 87 1 . SER 88 1 . SER 89 1 . ALA 90 1 . PRO 91 1 . ASP 92 1 . ASP 93 1 . SER 94 1 . VAL 95 1 . MET 96 1 . LYS 97 1 . GLU 98 1 . ALA 99 1 . LEU 100 1 . ALA 101 1 . ALA 102 1 . ALA 103 1 . ARG 104 1 . ALA 105 1 . ALA 106 1 . THR 107 1 . GLU 108 1 . GLU 109 1 . PHE 110 1 . GLY 111 1 . GLN 112 1 . SER 113 1 . SER 114 1 . PRO 115 1 . GLN 116 1 . ALA 117 1 . ARG 118 1 . LEU 119 1 . ALA 120 1 . TRP 121 1 . GLU 122 1 . THR 123 1 . VAL 124 1 . GLU 125 1 . GLU 126 1 . ILE 127 1 . ALA 128 1 . ALA 129 1 . SER 130 1 . PRO 131 1 . VAL 132 1 . ASP 133 1 . ILE 134 1 . ARG 135 1 . ALA 136 1 . PRO 137 1 . LEU 138 1 . ASP 139 1 . GLU 140 1 . GLU 141 1 . SER 142 1 . LEU 143 1 . ILE 144 1 . GLU 145 1 . LEU 146 1 . ILE 147 1 . GLU 148 1 . GLY 149 1 . SER 150 1 . GLU 151 1 . ALA 152 1 . LEU 153 1 . GLU 154 1 . LYS 155 1 . PHE 156 1 . GLN 157 1 . ALA 158 1 . ALA 159 1 . LEU 160 1 . GLY 161 1 . SER 162 1 . ARG 163 # _ihm_chemical_component_descriptor.auth_name MTSL _ihm_chemical_component_descriptor.chemical_name (1-Oxyl-2,2,5,5-tetramethylpyrroline-3-methyl)methanethiosulfonate _ihm_chemical_component_descriptor.common_name MTSL _ihm_chemical_component_descriptor.details . _ihm_chemical_component_descriptor.id 1 _ihm_chemical_component_descriptor.inchi 1S/C10H18NO3S2/c1-9(2)6-8(7-15-16(5,13)14)10(3,4)11(9)12/h6H,7H2,1-5H3 _ihm_chemical_component_descriptor.inchi_key BLSCGBLQCTWVPO-UHFFFAOYSA-N _ihm_chemical_component_descriptor.smiles CC1(C=C(C(N1[O])(C)C)CSS(=O)(=O)C)C _ihm_chemical_component_descriptor.smiles_canonical . # loop_ _ihm_dataset_external_reference.dataset_list_id _ihm_dataset_external_reference.file_id _ihm_dataset_external_reference.id 1 1 1 2 8 2 1 2 3 1 3 4 1 4 5 1 5 6 3 10 7 # _ihm_dataset_group.application modeling _ihm_dataset_group.details . _ihm_dataset_group.id 1 _ihm_dataset_group.name . # loop_ _ihm_dataset_group_link.dataset_list_id _ihm_dataset_group_link.group_id 1 1 2 1 3 1 # loop_ _ihm_dataset_list.data_type _ihm_dataset_list.database_hosted _ihm_dataset_list.details _ihm_dataset_list.id "EPR data" NO "Five distance distribution of spin pairs" 1 "SAS data" YES "SASDBD database with accession code: SASDXG3" 2 "De Novo model" NO "AlphaFold2.1.1-Multimer predicted structure" 3 # _ihm_dataset_related_db_reference.accession_code SASDXG3 _ihm_dataset_related_db_reference.dataset_list_id 2 _ihm_dataset_related_db_reference.db_name SASBDB _ihm_dataset_related_db_reference.details . _ihm_dataset_related_db_reference.id 1 _ihm_dataset_related_db_reference.version . # loop_ _ihm_derived_distance_restraint.dataset_list_id _ihm_derived_distance_restraint.distance_lower_limit _ihm_derived_distance_restraint.distance_lower_limit_esd _ihm_derived_distance_restraint.distance_threshold_esd _ihm_derived_distance_restraint.distance_threshold_mean _ihm_derived_distance_restraint.distance_upper_limit _ihm_derived_distance_restraint.distance_upper_limit_esd _ihm_derived_distance_restraint.feature_id_1 _ihm_derived_distance_restraint.feature_id_2 _ihm_derived_distance_restraint.group_conditionality _ihm_derived_distance_restraint.group_id _ihm_derived_distance_restraint.id _ihm_derived_distance_restraint.mic_value _ihm_derived_distance_restraint.probability _ihm_derived_distance_restraint.random_exclusion_fraction _ihm_derived_distance_restraint.restraint_type 1 . . . 68 . . 1 2 . 1 1 . . . harmonic 1 . . . 43 . . 3 4 . 1 2 . . . harmonic 1 . . . 32 . . 5 6 . 1 3 . . . harmonic 1 . . . 64 . . 7 8 . 1 4 . . . harmonic 1 . . . 25 . . 9 10 . 1 5 . . . harmonic # _ihm_entity_poly_segment.comp_id_begin ALA _ihm_entity_poly_segment.comp_id_end ARG _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 163 # _ihm_epr_restraint.chi_value 0.88 _ihm_epr_restraint.dataset_list_id 1 _ihm_epr_restraint.details "The average chi value of normalized root mean-square difference between the experimental and simulated distributions of five spin pairs was provided." _ihm_epr_restraint.fitting_method "restrained-ensemble MD simulation using DEER/EPR data" _ihm_epr_restraint.fitting_method_citation_id . _ihm_epr_restraint.fitting_particle_type "paired electrons of the probe" _ihm_epr_restraint.fitting_software_id 3 _ihm_epr_restraint.fitting_state . _ihm_epr_restraint.model_id 1 _ihm_epr_restraint.ordinal_id 1 # loop_ _ihm_external_files.content_type _ihm_external_files.details _ihm_external_files.file_format _ihm_external_files.file_path _ihm_external_files.file_size_bytes _ihm_external_files.id _ihm_external_files.reference_id "Input data or restraints" "EPR data - distance distribution of spin pairs attached on residue 39" Other tp-CP12/S39C_DEER_n230_distr.dat . 1 1 "Input data or restraints" "EPR data - distance distribution of spin pairs attached on residue 46" Other tp-CP12/S46C_DEER_tris_distr.dat . 2 1 "Input data or restraints" "EPR data - distance distribution of spin pairs attached on residue 56" Other tp-CP12/S56C_DEER_distr.dat . 3 1 "Input data or restraints" "EPR data - distance distribution of spin pairs attached on residue 83" Other tp-CP12/S83C_Deer_t2_6000_n173_distr.dat . 4 1 "Input data or restraints" "EPR data - distance distribution of spin pairs attached on residue 150" Other tp-CP12/S150C_DEER_distr.dat . 5 1 "Modeling or post-processing output" " Average theoretical SAXS data of structural ensembles" TXT tp-CP12/Average-SAXS-1435reMD.fit . 6 1 "Modeling or post-processing output" "plot of average SAXS curve of the 1435 SAXS theoretical curves obtained from the individual crysol fits and experimental SAXS data" PNG tp-CP12/Average-fit.BMP . 7 1 "Input data or restraints" "Experimental SAXS data" Other tp-CP12/Cp12Thaps-OK-SAXS.dat . 8 1 "Modeling or post-processing output" " 1435 sampled PDB files that fit both SAXS and SDSL-EPR experimental data" PDB tp-CP12/pdbs-reMD.7z . 9 1 "Input data or restraints" "AlphaFold2.1.1-Multimer predicted structure" PDB tp-CP12/S56-Superpo-Shape.pdb . 10 1 # _ihm_external_reference_info.associated_url https://zenodo.org/records/15178979/files/tp-CP12.zip _ihm_external_reference_info.details . _ihm_external_reference_info.reference 10.5281/zenodo.15117282 _ihm_external_reference_info.reference_id 1 _ihm_external_reference_info.reference_provider Zenodo _ihm_external_reference_info.reference_type DOI _ihm_external_reference_info.refers_to Archive # loop_ _ihm_feature_list.details _ihm_feature_list.entity_type _ihm_feature_list.feature_id _ihm_feature_list.feature_type . polymer 1 residue . polymer 2 residue . polymer 3 residue . polymer 4 residue . polymer 5 residue . polymer 6 residue . polymer 7 residue . polymer 8 residue . polymer 9 residue . polymer 10 residue # _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 . _ihm_model_representation.id 1 _ihm_model_representation.name . # loop_ _ihm_model_representation_details.description _ihm_model_representation_details.entity_asym_id _ihm_model_representation_details.entity_description _ihm_model_representation_details.entity_id _ihm_model_representation_details.entity_poly_segment_id _ihm_model_representation_details.id _ihm_model_representation_details.model_granularity _ihm_model_representation_details.model_mode _ihm_model_representation_details.model_object_count _ihm_model_representation_details.model_object_primitive _ihm_model_representation_details.representation_id _ihm_model_representation_details.starting_model_id . B "CP12 domain-containing protein" 1 1 1 by-atom flexible . atomistic 1 1 . A "CP12 domain-containing protein" 1 1 2 by-atom flexible . atomistic 1 2 # _ihm_modeling_protocol.details "A short version: CP12 mutant genes from T. pseudonana were synthesized and cloned into pET-28a vectors with N-terminal His-tags and thrombin cleavage sites. Expressed in E. coli BL21-C41(DE3), proteins were purified by Ni-NTA chromatography, thrombin cleavage, and size exclusion chromatography. Purified proteins were concentrated, flash-frozen, and quantified by UV absorbance. For spin labeling, reduced CP12 variants were incubated with MTSL and purified. Labeling efficiency was verified by EPR. EPR spectra were acquired at room temperature and 100 K using Bruker Elexsys systems, with SimLabel used for cw-EPR simulations. DEER data were analyzed with DeerAnalysis2019. SAXS data were processed using CRYSOL3.2.1 and compared to spinl-abel-free models. AlphaFold2.1.1-Multimer predicted CP12 homodimer structures, refined via PyMOL and YASARA. Restrained MD simulations were performed in AMBER20 (ff19SB, OPC water, PME electrostatics), with CA-CA restraints matching DEER distances. All-atom reMD was conducted using NAMD and CHARMM36m with 25 MTSL spin labels per site (CYR1). Simulations used Langevin dynamics at 303 K with 2 ns production runs. Harmonic restraints were imposed toward DEER distributions using a 100 kcal/mol-Angstrom squared force constant. Final structure ensembles were generated by removing spin labels and validated via SAXS profile fitting. (For more details, see modelling details.txt file at DOI: 10.5281/zenodo.15117282)" _ihm_modeling_protocol.id 1 _ihm_modeling_protocol.num_steps 1 _ihm_modeling_protocol.protocol_name modeling # loop_ _ihm_modeling_protocol_details.dataset_group_id _ihm_modeling_protocol_details.description _ihm_modeling_protocol_details.ensemble_flag _ihm_modeling_protocol_details.id _ihm_modeling_protocol_details.multi_scale_flag _ihm_modeling_protocol_details.multi_state_flag _ihm_modeling_protocol_details.num_models_begin _ihm_modeling_protocol_details.num_models_end _ihm_modeling_protocol_details.ordered_flag _ihm_modeling_protocol_details.protocol_id _ihm_modeling_protocol_details.script_file_id _ihm_modeling_protocol_details.software_id _ihm_modeling_protocol_details.step_id _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 'AlphaFold modelling: Structure prediction for the CP12 homodimer was performed using AlphaFold v2.1.1-Multimer (AF2) and the default databases The sequence of mature CP12 was used in the AF2 input file for multiple sequence alignments (MSAs) lookup and structural template matching. The predicted local distance difference test score (pLDDT,) was used to estimate the per-residue confidence of the models. The percentages of the secondary structure elements of the models were assessed using YASARA View22. Modification of the selected AF2 model was performed using PyMOL by a rotation around N-Ca bond of residue I134 and by respecting the Ramachandran plot. Structure prediction of T. pseudonana PRK was performed using AlphaFold3 webserver (Abramson, J et al. Accurate structure prediction of biomolecular interactions with AlphaFold3. Nature (2024) based on the sequence provided by UNIPROT (entry B8BZ40) devoid of the first 15 residues, which are predicted with a score of 0.96 to form the chloroplast transit peptide by HECTAR v1.3 (https://webtools.sb-roscoff.fr/root?tool_id=abims_hectar HECTAR: A Method to Predict Subcellular Targeting in Heterokonts", Gschloessl et al., BMC Bioinformatics, 2008 (PubMed ID 18811941)) specifically trained for heterokonts.' NO 1 NO NO . . NO 1 . 1 1 . "ab initio modeling" . 1 1 "Harmonic restrained MD simulations were run with the Amber 20 package based on the modified AF2 model. The Amber ff19SB force field was used for the protein, which was immersed into a cubic periodic box filled with water solvent molecules modeled by the OPC model with the LEaP program of AmberTools20. All charged residues were considered in their standard protonation state at pH = 7.0. We added 28 sodium ions to neutralize the simulation box and the total number of atoms became 178352. Nonbonded particle-particle interactions were considered with a distance cutoff of 9 � and the long-range electrostatic interactions were treated with the particle mesh Ewald (PME) method. After minimization, heating, and equilibration of the simulation system, several rounds of MD simulations were conducted imposing harmonic restraints on the CA-CA distances across the dimer for respective spin-labeled residues S39, S46, S56, S83, and C150 with a spring force of 30 kcal/(mol��2). Each round ran for 100ps with time step of 2 fs at T = 300 K and P = 1 atm. The trajectories and snapshots were saved every 1 ps. The initial/target distances for each CA atom pair were 73 �/68 � for S39, 57 � /43 � for S46, 26 �/ 32 � for S56, 51 �/64 � for S83, 12 �/25 � for C150, respectively. " NO 2 NO NO 1 1 NO 1 . 2 2 "harmonic restrained MD simulations " sampling . 1 1 "The following reMD simulations were run by using a modified version of NAMD 2 with all-atom CHARMM36m protein force field. 25 copies of all-atom MTSL (CYR1 in CHARMM-GUI) spin labels were attached to residues S39, S46, S56, S83 and C150, respectively, with reMD Prepper in vacuum for saving the computational resources. The force field of all-atom CYR1 spin label is provided by CHARMM-GUI. Spatial overlap among the 25 copies of CYR1 spin labels was allowed by neglecting the interactions among them. Five independent all-atom reMD simulations were conducted at 303.15 K with different random number seeds using Langevin dynamics with a damping coefficient of 5 ps-1. Before each reMD production run, we performed minimization and equilibration, during which only sidechain atoms were relaxed, keeping the backbone atom positions with harmonic restraints of 2 kcal/(mol��2) imposed on them. For these structural refinement, we switched off the harmonic restraints imposed on the backbone atoms, and conducted production runs of reMD simulations for 2 ns with a time step of 0.5 fs. The long-range electrostatic interactions were treated with the particle mesh Ewald (PME) method and the nonbonded interactions were truncated at a 10 � distance cutoff. The distance distributions of each spin label pair were restrained with a force constant of 100 kcal/(mol��2) toward the experimental distance distribution histograms with a bin width of 0.025 nm. The atomic coordinates of each reMD production run were saved every 1ps. Since each spin label has 25 copies, a total number of 625 distances for each spin label pair were obtained from a single snapshot of trajectories and a total of 1, 250, 000 data points were yielded for every spin label pair from one single reMD production run. " YES 3 NO NO 1 1435 YES 1 . 3 3 " restrained-ensemble MD simulation " sampling . 1 1 "The saved atomic coordinates of reMD productions were then removed of CYR1 spin-labels, and then used as an ensemble of structures to simulate the SAXS data." NO 4 NO NO . . NO 1 . 4 4 . . . 1 1 "DEER distance distributions were extracted from raw experimental data using DeerAnalysis2019 software" NO 5 NO NO . . NO 1 . 5 5 . . . 1 # loop_ _ihm_poly_probe_conjugate.ambiguous_stoichiometry_flag _ihm_poly_probe_conjugate.chem_comp_descriptor_id _ihm_poly_probe_conjugate.dataset_list_id _ihm_poly_probe_conjugate.details _ihm_poly_probe_conjugate.id _ihm_poly_probe_conjugate.position_id _ihm_poly_probe_conjugate.probe_id _ihm_poly_probe_conjugate.probe_stoichiometry . 1 1 . 1 1 1 . . 1 1 . 2 2 1 . . 1 1 . 3 3 1 . . 1 1 . 4 4 1 . . 1 1 . 5 5 1 . # loop_ _ihm_poly_probe_position.comp_id _ihm_poly_probe_position.description _ihm_poly_probe_position.entity_description _ihm_poly_probe_position.entity_id _ihm_poly_probe_position.id _ihm_poly_probe_position.mod_res_chem_comp_descriptor_id _ihm_poly_probe_position.modification_flag _ihm_poly_probe_position.mut_res_chem_comp_id _ihm_poly_probe_position.mutation_flag _ihm_poly_probe_position.seq_id SER . . 1 1 1 YES CYS YES 39 SER . . 1 2 1 YES CYS YES 46 CYS . . 1 3 1 YES . NO 56 SER . . 1 4 1 YES CYS YES 83 SER . . 1 5 1 YES CYS YES 150 # loop_ _ihm_poly_residue_feature.asym_id _ihm_poly_residue_feature.comp_id_begin _ihm_poly_residue_feature.comp_id_end _ihm_poly_residue_feature.entity_id _ihm_poly_residue_feature.feature_id _ihm_poly_residue_feature.interface_residue_flag _ihm_poly_residue_feature.ordinal_id _ihm_poly_residue_feature.rep_atom _ihm_poly_residue_feature.residue_range_granularity _ihm_poly_residue_feature.seq_id_begin _ihm_poly_residue_feature.seq_id_end B SER SER 1 1 YES 1 CA by-residue 39 39 A SER SER 1 2 YES 2 CA by-residue 39 39 B SER SER 1 3 YES 3 CA by-residue 46 46 A SER SER 1 4 YES 4 CA by-residue 46 46 B CYS CYS 1 5 YES 5 CA by-residue 56 56 A CYS CYS 1 6 YES 6 CA by-residue 56 56 B SER SER 1 7 YES 7 CA by-residue 83 83 A SER SER 1 8 YES 8 CA by-residue 83 83 B SER SER 1 9 YES 9 CA by-residue 150 150 A SER SER 1 10 YES 10 CA by-residue 150 150 # _ihm_probe_list.probe_chem_comp_descriptor_id 1 _ihm_probe_list.probe_id 1 _ihm_probe_list.probe_link_type covalent _ihm_probe_list.probe_name MTSL _ihm_probe_list.probe_origin extrinsic _ihm_probe_list.reactive_probe_chem_comp_descriptor_id . _ihm_probe_list.reactive_probe_flag . _ihm_probe_list.reactive_probe_name . # _ihm_sas_restraint.chi_value 3.86 _ihm_sas_restraint.dataset_list_id 2 _ihm_sas_restraint.details . _ihm_sas_restraint.fitting_atom_type . _ihm_sas_restraint.fitting_method . _ihm_sas_restraint.fitting_state Single _ihm_sas_restraint.id 1 _ihm_sas_restraint.model_id 1 _ihm_sas_restraint.profile_segment_flag . _ihm_sas_restraint.radius_of_gyration . _ihm_sas_restraint.struct_assembly_id 1 # loop_ _ihm_starting_model_details.asym_id _ihm_starting_model_details.dataset_list_id _ihm_starting_model_details.description _ihm_starting_model_details.entity_description _ihm_starting_model_details.entity_id _ihm_starting_model_details.entity_poly_segment_id _ihm_starting_model_details.starting_model_auth_asym_id _ihm_starting_model_details.starting_model_id _ihm_starting_model_details.starting_model_sequence_offset _ihm_starting_model_details.starting_model_source B 3 . "CP12 domain-containing protein" 1 1 B 1 0 "ab initio model" A 3 . "CP12 domain-containing protein" 1 1 A 2 0 "ab initio model" # _ihm_struct_assembly.description "Chloroplastic protein CP12 modeled using EPR and SAX with starting models from AlphaFold." _ihm_struct_assembly.id 1 _ihm_struct_assembly.name "Chloroplastic protein CP12 " # loop_ _ihm_struct_assembly_details.assembly_id _ihm_struct_assembly_details.asym_id _ihm_struct_assembly_details.entity_description _ihm_struct_assembly_details.entity_id _ihm_struct_assembly_details.entity_poly_segment_id _ihm_struct_assembly_details.id _ihm_struct_assembly_details.parent_assembly_id 1 B "CP12 domain-containing protein" 1 1 1 1 1 A "CP12 domain-containing protein" 1 1 2 1 # loop_ _software.citation_id _software.classification _software.description _software.location _software.name _software.pdbx_ordinal _software.type _software.version . "model building" . https://cosmic-cryoem.org/tools/alphafoldmultimer/ "AlphaFold Multimer" 1 program 2.1.1 . refinement . http://ambermd.org/ Amber 2 program 20 . refinement . http://www.ks.uiuc.edu/Research/namd/ "modified version of NAMD" 3 program 2 . "data collection" . https://www.embl-hamburg.de/biosaxs/crysol.html CRYSOL 4 program 3.1 . other fitting https://epr.ethz.ch/software/older-versions/old_deeranalysis.html DeerAnalysis 5 program 2019 # _struct.entry_id 9A9R _struct.pdbx_CASP_flag . _struct.pdbx_descriptor . _struct.pdbx_details . _struct.pdbx_model_details "This model is produced from a restrained Amber/MD simulation starting from a AlphaFold2.1.1-multimer predicted structure." _struct.pdbx_model_type_details . _struct.pdbx_structure_determination_methodology integrative _struct.title "Chloroplastic protein CP12 from the diatom Thalassiosira pseudonana (tp-CP12, homodimer)" # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _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 . 1 A . . . . . . . 1 B . . . . . . # _struct_ref.db_code B8BQS1_THAPS _struct_ref.db_name UNP _struct_ref.details . _struct_ref.entity_id 1 _struct_ref.id 1 _struct_ref.pdbx_align_begin 35 _struct_ref.pdbx_align_end . _struct_ref.pdbx_db_accession B8BQS1 _struct_ref.pdbx_db_isoform . _struct_ref.pdbx_seq_one_letter_code . # _struct_ref_seq.align_id 1 _struct_ref_seq.db_align_beg 35 _struct_ref_seq.db_align_end 197 _struct_ref_seq.ref_id 1 _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.seq_align_end 163 # 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 B 1 1 ALA 164 164 ALA ALA B . B 1 2 ALA 165 165 ALA ALA B . B 1 3 ILE 166 166 ILE ILE B . B 1 4 GLU 167 167 GLU GLU B . B 1 5 ALA 168 168 ALA ALA B . B 1 6 ALA 169 169 ALA ALA B . B 1 7 LEU 170 170 LEU LEU B . B 1 8 ASP 171 171 ASP ASP B . B 1 9 ALA 172 172 ALA ALA B . B 1 10 SER 173 173 SER SER B . B 1 11 LYS 174 174 LYS LYS B . B 1 12 LYS 175 175 LYS LYS B . B 1 13 PHE 176 176 PHE PHE B . B 1 14 GLY 177 177 GLY GLY B . B 1 15 SER 178 178 SER SER B . B 1 16 THR 179 179 THR THR B . B 1 17 SER 180 180 SER SER B . B 1 18 SER 181 181 SER SER B . B 1 19 GLU 182 182 GLU GLU B . B 1 20 ALA 183 183 ALA ALA B . B 1 21 ARG 184 184 ARG ARG B . B 1 22 VAL 185 185 VAL VAL B . B 1 23 LEU 186 186 LEU LEU B . B 1 24 TRP 187 187 TRP TRP B . B 1 25 ASP 188 188 ASP ASP B . B 1 26 ILE 189 189 ILE ILE B . B 1 27 VAL 190 190 VAL VAL B . B 1 28 GLU 191 191 GLU GLU B . B 1 29 GLU 192 192 GLU GLU B . B 1 30 MET 193 193 MET MET B . B 1 31 ASP 194 194 ASP ASP B . B 1 32 ALA 195 195 ALA ALA B . B 1 33 SER 196 196 SER SER B . B 1 34 ASP 197 197 ASP ASP B . B 1 35 ASN 198 198 ASN ASN B . B 1 36 SER 199 199 SER SER B . B 1 37 VAL 200 200 VAL VAL B . B 1 38 ALA 201 201 ALA ALA B . B 1 39 SER 202 202 SER SER B . B 1 40 LYS 203 203 LYS LYS B . B 1 41 ALA 204 204 ALA ALA B . B 1 42 PRO 205 205 PRO PRO B . B 1 43 ILE 206 206 ILE ILE B . B 1 44 VAL 207 207 VAL VAL B . B 1 45 ASP 208 208 ASP ASP B . B 1 46 SER 209 209 SER SER B . B 1 47 GLU 210 210 GLU GLU B . B 1 48 TYR 211 211 TYR TYR B . B 1 49 GLU 212 212 GLU GLU B . B 1 50 ALA 213 213 ALA ALA B . B 1 51 LYS 214 214 LYS LYS B . B 1 52 VAL 215 215 VAL VAL B . B 1 53 LYS 216 216 LYS LYS B . B 1 54 SER 217 217 SER SER B . B 1 55 LEU 218 218 LEU LEU B . B 1 56 CYS 219 219 CYS CYS B . B 1 57 GLN 220 220 GLN GLN B . B 1 58 MET 221 221 MET MET B . B 1 59 LEU 222 222 LEU LEU B . B 1 60 THR 223 223 THR THR B . B 1 61 LYS 224 224 LYS LYS B . B 1 62 THR 225 225 THR THR B . B 1 63 LYS 226 226 LYS LYS B . B 1 64 ALA 227 227 ALA ALA B . B 1 65 GLU 228 228 GLU GLU B . B 1 66 LEU 229 229 LEU LEU B . B 1 67 ASP 230 230 ASP ASP B . B 1 68 GLN 231 231 GLN GLN B . B 1 69 VAL 232 232 VAL VAL B . B 1 70 LYS 233 233 LYS LYS B . B 1 71 ALA 234 234 ALA ALA B . B 1 72 LEU 235 235 LEU LEU B . B 1 73 ALA 236 236 ALA ALA B . B 1 74 ASP 237 237 ASP ASP B . B 1 75 ASP 238 238 ASP ASP B . B 1 76 LEU 239 239 LEU LEU B . B 1 77 LYS 240 240 LYS LYS B . B 1 78 GLY 241 241 GLY GLY B . B 1 79 VAL 242 242 VAL VAL B . B 1 80 LYS 243 243 LYS LYS B . B 1 81 LEU 244 244 LEU LEU B . B 1 82 ALA 245 245 ALA ALA B . B 1 83 SER 246 246 SER SER B . B 1 84 PRO 247 247 PRO PRO B . B 1 85 SER 248 248 SER SER B . B 1 86 VAL 249 249 VAL VAL B . B 1 87 GLY 250 250 GLY GLY B . B 1 88 SER 251 251 SER SER B . B 1 89 SER 252 252 SER SER B . B 1 90 ALA 253 253 ALA ALA B . B 1 91 PRO 254 254 PRO PRO B . B 1 92 ASP 255 255 ASP ASP B . B 1 93 ASP 256 256 ASP ASP B . B 1 94 SER 257 257 SER SER B . B 1 95 VAL 258 258 VAL VAL B . B 1 96 MET 259 259 MET MET B . B 1 97 LYS 260 260 LYS LYS B . B 1 98 GLU 261 261 GLU GLU B . B 1 99 ALA 262 262 ALA ALA B . B 1 100 LEU 263 263 LEU LEU B . B 1 101 ALA 264 264 ALA ALA B . B 1 102 ALA 265 265 ALA ALA B . B 1 103 ALA 266 266 ALA ALA B . B 1 104 ARG 267 267 ARG ARG B . B 1 105 ALA 268 268 ALA ALA B . B 1 106 ALA 269 269 ALA ALA B . B 1 107 THR 270 270 THR THR B . B 1 108 GLU 271 271 GLU GLU B . B 1 109 GLU 272 272 GLU GLU B . B 1 110 PHE 273 273 PHE PHE B . B 1 111 GLY 274 274 GLY GLY B . B 1 112 GLN 275 275 GLN GLN B . B 1 113 SER 276 276 SER SER B . B 1 114 SER 277 277 SER SER B . B 1 115 PRO 278 278 PRO PRO B . B 1 116 GLN 279 279 GLN GLN B . B 1 117 ALA 280 280 ALA ALA B . B 1 118 ARG 281 281 ARG ARG B . B 1 119 LEU 282 282 LEU LEU B . B 1 120 ALA 283 283 ALA ALA B . B 1 121 TRP 284 284 TRP TRP B . B 1 122 GLU 285 285 GLU GLU B . B 1 123 THR 286 286 THR THR B . B 1 124 VAL 287 287 VAL VAL B . B 1 125 GLU 288 288 GLU GLU B . B 1 126 GLU 289 289 GLU GLU B . B 1 127 ILE 290 290 ILE ILE B . B 1 128 ALA 291 291 ALA ALA B . B 1 129 ALA 292 292 ALA ALA B . B 1 130 SER 293 293 SER SER B . B 1 131 PRO 294 294 PRO PRO B . B 1 132 VAL 295 295 VAL VAL B . B 1 133 ASP 296 296 ASP ASP B . B 1 134 ILE 297 297 ILE ILE B . B 1 135 ARG 298 298 ARG ARG B . B 1 136 ALA 299 299 ALA ALA B . B 1 137 PRO 300 300 PRO PRO B . B 1 138 LEU 301 301 LEU LEU B . B 1 139 ASP 302 302 ASP ASP B . B 1 140 GLU 303 303 GLU GLU B . B 1 141 GLU 304 304 GLU GLU B . B 1 142 SER 305 305 SER SER B . B 1 143 LEU 306 306 LEU LEU B . B 1 144 ILE 307 307 ILE ILE B . B 1 145 GLU 308 308 GLU GLU B . B 1 146 LEU 309 309 LEU LEU B . B 1 147 ILE 310 310 ILE ILE B . B 1 148 GLU 311 311 GLU GLU B . B 1 149 GLY 312 312 GLY GLY B . B 1 150 SER 313 313 SER SER B . B 1 151 GLU 314 314 GLU GLU B . B 1 152 ALA 315 315 ALA ALA B . B 1 153 LEU 316 316 LEU LEU B . B 1 154 GLU 317 317 GLU GLU B . B 1 155 LYS 318 318 LYS LYS B . B 1 156 PHE 319 319 PHE PHE B . B 1 157 GLN 320 320 GLN GLN B . B 1 158 ALA 321 321 ALA ALA B . B 1 159 ALA 322 322 ALA ALA B . B 1 160 LEU 323 323 LEU LEU B . B 1 161 GLY 324 324 GLY GLY B . B 1 162 SER 325 325 SER SER B . B 1 163 ARG 326 326 ARG ARG B . A 1 1 ALA 1 1 ALA ALA A . A 1 2 ALA 2 2 ALA ALA A . A 1 3 ILE 3 3 ILE ILE A . A 1 4 GLU 4 4 GLU GLU A . A 1 5 ALA 5 5 ALA ALA A . A 1 6 ALA 6 6 ALA ALA A . A 1 7 LEU 7 7 LEU LEU A . A 1 8 ASP 8 8 ASP ASP A . A 1 9 ALA 9 9 ALA ALA A . A 1 10 SER 10 10 SER SER A . A 1 11 LYS 11 11 LYS LYS A . A 1 12 LYS 12 12 LYS LYS A . A 1 13 PHE 13 13 PHE PHE A . A 1 14 GLY 14 14 GLY GLY A . A 1 15 SER 15 15 SER SER A . A 1 16 THR 16 16 THR THR A . A 1 17 SER 17 17 SER SER A . A 1 18 SER 18 18 SER SER A . A 1 19 GLU 19 19 GLU GLU A . A 1 20 ALA 20 20 ALA ALA A . A 1 21 ARG 21 21 ARG ARG A . A 1 22 VAL 22 22 VAL VAL A . A 1 23 LEU 23 23 LEU LEU A . A 1 24 TRP 24 24 TRP TRP A . A 1 25 ASP 25 25 ASP ASP A . A 1 26 ILE 26 26 ILE ILE A . A 1 27 VAL 27 27 VAL VAL A . A 1 28 GLU 28 28 GLU GLU A . A 1 29 GLU 29 29 GLU GLU A . A 1 30 MET 30 30 MET MET A . A 1 31 ASP 31 31 ASP ASP A . A 1 32 ALA 32 32 ALA ALA A . A 1 33 SER 33 33 SER SER A . A 1 34 ASP 34 34 ASP ASP A . A 1 35 ASN 35 35 ASN ASN A . A 1 36 SER 36 36 SER SER A . A 1 37 VAL 37 37 VAL VAL A . A 1 38 ALA 38 38 ALA ALA A . A 1 39 SER 39 39 SER SER A . A 1 40 LYS 40 40 LYS LYS A . A 1 41 ALA 41 41 ALA ALA A . A 1 42 PRO 42 42 PRO PRO A . A 1 43 ILE 43 43 ILE ILE A . A 1 44 VAL 44 44 VAL VAL A . A 1 45 ASP 45 45 ASP ASP A . A 1 46 SER 46 46 SER SER A . A 1 47 GLU 47 47 GLU GLU A . A 1 48 TYR 48 48 TYR TYR A . A 1 49 GLU 49 49 GLU GLU A . A 1 50 ALA 50 50 ALA ALA A . A 1 51 LYS 51 51 LYS LYS A . A 1 52 VAL 52 52 VAL VAL A . A 1 53 LYS 53 53 LYS LYS A . A 1 54 SER 54 54 SER SER A . A 1 55 LEU 55 55 LEU LEU A . A 1 56 CYS 56 56 CYS CYS A . A 1 57 GLN 57 57 GLN GLN A . A 1 58 MET 58 58 MET MET A . A 1 59 LEU 59 59 LEU LEU A . A 1 60 THR 60 60 THR THR A . A 1 61 LYS 61 61 LYS LYS A . A 1 62 THR 62 62 THR THR A . A 1 63 LYS 63 63 LYS LYS A . A 1 64 ALA 64 64 ALA ALA A . A 1 65 GLU 65 65 GLU GLU A . A 1 66 LEU 66 66 LEU LEU A . A 1 67 ASP 67 67 ASP ASP A . A 1 68 GLN 68 68 GLN GLN A . A 1 69 VAL 69 69 VAL VAL A . A 1 70 LYS 70 70 LYS LYS A . A 1 71 ALA 71 71 ALA ALA A . A 1 72 LEU 72 72 LEU LEU A . A 1 73 ALA 73 73 ALA ALA A . A 1 74 ASP 74 74 ASP ASP A . A 1 75 ASP 75 75 ASP ASP A . A 1 76 LEU 76 76 LEU LEU A . A 1 77 LYS 77 77 LYS LYS A . A 1 78 GLY 78 78 GLY GLY A . A 1 79 VAL 79 79 VAL VAL A . A 1 80 LYS 80 80 LYS LYS A . A 1 81 LEU 81 81 LEU LEU A . A 1 82 ALA 82 82 ALA ALA A . A 1 83 SER 83 83 SER SER A . A 1 84 PRO 84 84 PRO PRO A . A 1 85 SER 85 85 SER SER A . A 1 86 VAL 86 86 VAL VAL A . A 1 87 GLY 87 87 GLY GLY A . A 1 88 SER 88 88 SER SER A . A 1 89 SER 89 89 SER SER A . A 1 90 ALA 90 90 ALA ALA A . A 1 91 PRO 91 91 PRO PRO A . A 1 92 ASP 92 92 ASP ASP A . A 1 93 ASP 93 93 ASP ASP A . A 1 94 SER 94 94 SER SER A . A 1 95 VAL 95 95 VAL VAL A . A 1 96 MET 96 96 MET MET A . A 1 97 LYS 97 97 LYS LYS A . A 1 98 GLU 98 98 GLU GLU A . A 1 99 ALA 99 99 ALA ALA A . A 1 100 LEU 100 100 LEU LEU A . A 1 101 ALA 101 101 ALA ALA A . A 1 102 ALA 102 102 ALA ALA A . A 1 103 ALA 103 103 ALA ALA A . A 1 104 ARG 104 104 ARG ARG A . A 1 105 ALA 105 105 ALA ALA A . A 1 106 ALA 106 106 ALA ALA A . A 1 107 THR 107 107 THR THR A . A 1 108 GLU 108 108 GLU GLU A . A 1 109 GLU 109 109 GLU GLU A . A 1 110 PHE 110 110 PHE PHE A . A 1 111 GLY 111 111 GLY GLY A . A 1 112 GLN 112 112 GLN GLN A . A 1 113 SER 113 113 SER SER A . A 1 114 SER 114 114 SER SER A . A 1 115 PRO 115 115 PRO PRO A . A 1 116 GLN 116 116 GLN GLN A . A 1 117 ALA 117 117 ALA ALA A . A 1 118 ARG 118 118 ARG ARG A . A 1 119 LEU 119 119 LEU LEU A . A 1 120 ALA 120 120 ALA ALA A . A 1 121 TRP 121 121 TRP TRP A . A 1 122 GLU 122 122 GLU GLU A . A 1 123 THR 123 123 THR THR A . A 1 124 VAL 124 124 VAL VAL A . A 1 125 GLU 125 125 GLU GLU A . A 1 126 GLU 126 126 GLU GLU A . A 1 127 ILE 127 127 ILE ILE A . A 1 128 ALA 128 128 ALA ALA A . A 1 129 ALA 129 129 ALA ALA A . A 1 130 SER 130 130 SER SER A . A 1 131 PRO 131 131 PRO PRO A . A 1 132 VAL 132 132 VAL VAL A . A 1 133 ASP 133 133 ASP ASP A . A 1 134 ILE 134 134 ILE ILE A . A 1 135 ARG 135 135 ARG ARG A . A 1 136 ALA 136 136 ALA ALA A . A 1 137 PRO 137 137 PRO PRO A . A 1 138 LEU 138 138 LEU LEU A . A 1 139 ASP 139 139 ASP ASP A . A 1 140 GLU 140 140 GLU GLU A . A 1 141 GLU 141 141 GLU GLU A . A 1 142 SER 142 142 SER SER A . A 1 143 LEU 143 143 LEU LEU A . A 1 144 ILE 144 144 ILE ILE A . A 1 145 GLU 145 145 GLU GLU A . A 1 146 LEU 146 146 LEU LEU A . A 1 147 ILE 147 147 ILE ILE A . A 1 148 GLU 148 148 GLU GLU A . A 1 149 GLY 149 149 GLY GLY A . A 1 150 SER 150 150 SER SER A . A 1 151 GLU 151 151 GLU GLU A . A 1 152 ALA 152 152 ALA ALA A . A 1 153 LEU 153 153 LEU LEU A . A 1 154 GLU 154 154 GLU GLU A . A 1 155 LYS 155 155 LYS LYS A . A 1 156 PHE 156 156 PHE PHE A . A 1 157 GLN 157 157 GLN GLN A . A 1 158 ALA 158 158 ALA ALA A . A 1 159 ALA 159 159 ALA ALA A . A 1 160 LEU 160 160 LEU LEU A . A 1 161 GLY 161 161 GLY GLY A . A 1 162 SER 162 162 SER SER A . A 1 163 ARG 163 163 ARG ARG A . # # loop_ # #