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{
"code": "SASDV56",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Conformational signatures induced by ubiquitin modification in the amyloid-forming tau repeat domain.",
"publication": {
"title": "Conformational signatures induced by ubiquitin modification in the amyloid-forming tau repeat domain.",
"author_list": "Viola G, Trivellato D, Laitaoja M, Jänis J, Felli IC, D'Onofrio M, Mollica L, Giachin G, Assfalg M",
"journal": "Proc Natl Acad Sci U S A",
"doi": "10.1073/pnas.2425831122",
"pmid": "40198698",
"published_date": "2025 Apr 15"
},
"status": "released",
"submitted_date": "2024-08-13",
"released_date": "2025-03-21"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDV56.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDV56.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV56_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV56_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDV56_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV56_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDV56.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 6M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"beam_geometry": null,
"type_of_source": "X-ray synchrotron",
"point_source": null,
"line_collimation": null,
"sample_path_length": null,
"line_collimation_slitlength": null,
"line_collimation_integrationwidth": null,
"xray_energy": null,
"beam_profile_ah": null,
"beam_profile_al": null
},
"sample": {
"molecule": [
{
"long_name": "Isoform Tau-F of Microtubule-associated protein tau (C291A, K311C, K317C, C322A)",
"short_name": "tau4RD domain",
"sequence": "MQTAPVPMPDLKNVKSKIGSTENLKHQPGGGKVQIINKKLDLSNVQSKAGSKDNIKHV\r\nPGGGSVQIVYCPVDLSCVTSKAGSLGNIHHKPGGGQVEVKSEKLDFKDRVQSKIGSLDNITHVPGGGNKKIE",
"organism": "Homo sapiens",
"uniprot_code": "P10636",
"uniprot_range_first": 244,
"uniprot_range_last": 372,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MAEPRQEFEVMEDHAGTYGLGDRKDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPG\nSETSDAKSTPTAEDVTAPLVDEGAPGKQAAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAG\nHVTQARMVSKSKDGTGSDDKKAKGADGKTKIATPRGAAPPGQKGQANATRIPAKTPPAPK\nTPPSSGEPPKSGDRSGYSSPGSPGTPGSRSRTPSLPTPPTREPKKVAVVRTPPKSPSSAK\nSRLQTAPVPMPDLKNVKSKIGSTENLKHQPGGGKVQIINKKLDLSNVQSKCGSKDNIKHV\nPGGGSVQIVYKPVDLSKVTSKCGSLGNIHHKPGGGQVEVKSEKLDFKDRVQSKIGSLDNI\nTHVPGGGNKKIETHKLTFRENAKAKTDHGAEIVYKSPVVSGDTSPRHLSNVSSTGSIDMV\nDSPQLATLADEVSASLAKQGL",
"mw": 13.7,
"total_mw": 13.7,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Tau4RD (Q244-E372 plus initial methionine) with C291A, C322A, K311C, K317C mutations referred to as tau4RDΔC(311/317C)"
},
{
"long_name": "Polyubiquitin-B",
"short_name": null,
"sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP\r\nDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGC",
"organism": "Fukomys damarensis",
"uniprot_code": "A0A091E260",
"uniprot_range_first": 1,
"uniprot_range_last": 77,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN\nIQKESTLHLVLRLRGGC",
"mw": 8.668,
"total_mw": 8.668,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "The semisynthetic ubiquitination reaction was performed without major modifications to the already outlined protocol. Briefly, Ub-SH was activated with 5,5′-dithiobis(2-nitrobenzoic acid) (DTNB) and incubated with each tau mutant in a 1:4 tau:Ub molar ratio. The desired proteoform was then purified through ion exchange chromatography exploiting a linear gradient of NaCl."
}
],
"buffer": {
"name": "100 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 6.8,
"deuteration": null
},
"purity_method": null,
"name": "Microtubule-associated protein tau, lysine-rich four-repeat domain 4RD synthetically linked to Ubiquitin at tau residue C317",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "ESRF",
"address": "Grenoble, France",
"full_name": "European Synchrotron Radiation Facility",
"webpage": "http://www.esrf.eu/"
}
],
"contributor_name": "Gabriele",
"contributor_surname": "Giachin",
"orcid": "https://orcid.org/0000-0001-7550-0307"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2023-03-17",
"storage_temperature": 10.0,
"cell_temperature": 20.0,
"exposure_time": 0.05,
"number_of_frames": 20,
"wavelength": 0.123972,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 3.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.09,
"s_max": 3.998,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDV56_fit1_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDV56_fit1_model1.pdb",
"model_mw": 10.58,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 388
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDV56_fit1_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.045,
"p_value": 0.28,
"fit_residual_plot": "SASDV56_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDV56_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_tVYO25T.log",
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDV56_fit2_model1_img.png",
"software": "AMBER",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDV56_fit2_model1.pdb",
"model_mw": 22.3,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 9
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDV56_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.272,
"p_value": 0.0013,
"fit_residual_plot": "SASDV56_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDV56_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/crysol_summary_LdowpMg.txt",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of microtubule-associated protein tau (lysine-rich four-repeat domain 4RD) synthetically linked to ubiquitin at tau amino acid C317 in 100 mM NaCl, pH 6.8 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123972 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.00 mg/ml was measured at 20°C. 20 successive 0.050 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 20.66,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 25.8,
"porod_mw_error": null,
"pddf_i0": 0.0499,
"pddf_i0_error": null,
"guinier_i0": 0.0489423,
"guinier_i0_error": null,
"pddf_rg": 3.598,
"pddf_rg_error": null,
"guinier_rg": 3.34,
"guinier_rg_error": 0.046,
"pddf_dmax": 13.3,
"pddf_dmax_error": null,
"porod_volume": 41.3,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 12,
"guinier_point_last": 104,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDV56_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-04-10T13:15:30.028980+02:00",
"bragg_peak": []
}
