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{
"code": "SASDXZ8",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Ion-selective conformational stabilization of a disordered repeats-in-toxin protein domain.",
"publication": {
"title": "Ion-selective conformational stabilization of a disordered repeats-in-toxin protein domain.",
"author_list": "Gudinas AP, Shambharkar GM, Chang MP, Fernández D, Matsui T, Mai DJ",
"journal": "Biophys J",
"doi": "10.1016/j.bpj.2025.10.014",
"pmid": "41088755",
"published_date": "2025 Oct 13"
},
"status": "released",
"submitted_date": "2025-09-05",
"released_date": "2025-10-16"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDXZ8.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDXZ8.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXZ8_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXZ8_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDXZ8_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXZ8_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDXZ8.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus3 X 1M",
"resolution": 0.172
},
"name": "Stanford Synchrotron Radiation Lightsource (SSRL)",
"city": "Menlo Park, CA",
"country": "USA",
"beamline_name": "BL4-2",
"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": "Repeats-in-toxin domain Block V of adenylate cyclase toxin",
"short_name": "RTX Block V",
"sequence": "MRGSHHHHHHGSHMELGASGSARDDVLIGDAGANVLNGLAGNDVLSGGAGDDVLLGDEGSDLLSGDAGNDDLFGGQGDDTYLFGVGYGHDTIYESGGGHDTIRINAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAMAQYPDEFTSLEKLN*",
"organism": "Bordetella pertussis",
"uniprot_code": "P0DKX7",
"uniprot_range_first": 1529,
"uniprot_range_last": 1680,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MQQSHQAGYANAADRESGIPAAVLDGIKAVAKEKNATLMFRLVNPHSTSLIAEGVATKGL\nGVHAKSSDWGLQAGYIPVNPNLSKLFGRAPEVIARADNDVNSSLAHGHTAVDLTLSKERL\nDYLRQAGLVTGMADGVVASNHAGYEQFEFRVKETSDGRYAVQYRRKGGDDFEAVKVIGNA\nAGIPLTADIDMFAIMPHLSNFRDSARSSVTSGDSVTDYLARTRRAASEATGGLDRERIDL\nLWKIARAGARSAVGTEARRQFRYDGDMNIGVITDFELEVRNALNRRAHAVGAQDVVQHGT\nEQNNPFPEADEKIFVVSATGESQMLTRGQLKEYIGQQRGEGYVFYENRAYGVAGKSLFDD\nGLGAAPGVPSGRSKFSPDVLETVPASPGLRRPSLGAVERQDSGYDSLDGVGSRSFSLGEV\nSDMAAVEAAELEMTRQVLHAGARQDDAEPGVSGASAHWGQRALQGAQAVAAAQRLVHAIA\nLMTQFGRAGSTNTPQEAASLSAAVFGLGEASSAVAETVSGFFRGSSRWAGGFGVAGGAMA\nLGGGIAAAVGAGMSLTDDAPAGQKAAAGAEIALQLTGGTVELASSIALALAAARGVTSGL\nQVAGASAGAAAGALAAALSPMEIYGLVQQSHYADQLDKLAQESSAYGYEGDALLAQLYRD\nKTAAEGAVAGVSAVLSTVGAAVSIAAAASVVGAPVAVVTSLLTGALNGILRGVQQPIIEK\nLANDYARKIDELGGPQAYFEKNLQARHEQLANSDGLRKMLADLQAGWNASSVIGVQTTEI\nSKSALELAAITGNADNLKSVDVFVDRFVQGERVAGQPVVLDVAAGGIDIASRKGERPALT\nFITPLAAPGEEQRRRTKTGKSEFTTFVEIVGKQDRWRIRDGAADTTIDLAKVVSQLVDAN\nGVLKHSIKLDVIGGDGDDVVLANASRIHYDGGAGTNTVSYAALGRQDSITVSADGERFNV\nRKQLNNANVYREGVATQTTAYGKRTENVQYRHVELARVGQLVEVDTLEHVQHIIGGAGND\nSITGNAHDNFLAGGSGDDRLDGGAGNDTLVGGEGQNTVIGGAGDDVFLQDLGVWSNQLDG\nGAGVDTVKYNVHQPSEERLERMGDTGIHADLQKGTVEKWPALNLFSVDHVKNIENLHGSR\nLNDRIAGDDQDNELWGHDGNDTIRGRGGDDILRGGLGLDTLYGEDGNDIFLQDDETVSDD\nIDGGAGLDTVDYSAMIHPGRIVAPHEYGFGIEADLSREWVRKASALGVDYYDNVRNVENV\nIGTSMKDVLIGDAQANTLMGQGGDDTVRGGDGDDLLFGGDGNDMLYGDAGNDTLYGGLGD\nDTLEGGAGNDWFGQTQAREHDVLRGGDGVDTVDYSQTGAHAGIAAGRIGLGILADLGAGR\nVDKLGEAGSSAYDTVSGIENVVGTELADRITGDAQANVLRGAGGADVLAGGEGDDVLLGG\nDGDDQLSGDAGRDRLYGEAGDDWFFQDAANAGNLLDGGDGRDTVDFSGPGRGLDAGAKGV\nFLSLGKGFASLMDEPETSNVLRNIENAVGSARDDVLIGDAGANVLNGLAGNDVLSGGAGD\nDVLLGDEGSDLLSGDAGNDDLFGGQGDDTYLFGVGYGHDTIYESGGGHDTIRINAGADQL\nWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAMAQYPD\nPGAAAAAPPAARVPDTLMQSLAVNWR",
"mw": 19.1,
"total_mw": 19.1,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
}
],
"buffer": {
"name": "50 mM Tris, 5 mM DTT , 3 mM CaCl2",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Repeats-in-toxin domain Block V of Bifunctional hemolysin/adenylate cyclase, 3 mM CaCl2",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Stanford, California, USA",
"full_name": "Stanford University",
"webpage": "https://www.stanford.edu/"
}
],
"contributor_name": "Alana",
"contributor_surname": "Gudinas",
"orcid": "https://orcid.org/0000-0003-2859-7868"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2024-12-12",
"storage_temperature": 23.0,
"cell_temperature": 21.9,
"exposure_time": 2.0,
"number_of_frames": 1,
"wavelength": 0.1127,
"sample_detector_distance": 1.7,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.066,
"s_max": 5.071,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": null,
"software": "DENSS",
"pdb_link": [],
"model_title": null,
"type_of_model": "density",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDXZ8_fit1_model1.mrc",
"model_mw": null,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 1267
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXZ8_fit1_fixed_fit_img.png",
"software": "DENSS",
"chi_square_value": 1.1316,
"p_value": 0.0035,
"fit_residual_plot": "SASDXZ8_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXZ8_fit1.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXZ8_fit2_model1_img.png",
"software": "REFMAC",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDXZ8_fit2_model1.pdb",
"model_mw": 18.44,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 1267
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXZ8_fit2_fixed_fit_img.png",
"software": "FoXS",
"chi_square_value": 9.950144,
"p_value": 0.0,
"fit_residual_plot": "SASDXZ8_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXZ8_fit2.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXZ8_fit3_model1_img.png",
"software": "AlphaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDXZ8_fit3_model1.cif",
"model_mw": null,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 1267
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXZ8_fit3_fixed_fit_img.png",
"software": "FoXS",
"chi_square_value": 2.742818,
"p_value": 0.0,
"fit_residual_plot": "SASDXZ8_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXZ8_fit3.fit",
"fit_log": null,
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Disordered repeats-in-toxin domain Block V of Bifunctional hemolysin/adenylate cyclase in 50 mM Tris, 5 mM DTT, pH 7.5 were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL) storage ring (Menlo Park, CA, USA) using a Pilatus3 X 1M detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.1127 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 10.00 mg/ml was measured at 21.9°C. 500 frames were collected with an exposure time of 2 seconds. 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": "arbitrary",
"experimental_mw": 14.82,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 23.0,
"porod_mw_error": null,
"pddf_i0": 8.953,
"pddf_i0_error": null,
"guinier_i0": 8.85828,
"guinier_i0_error": null,
"pddf_rg": 2.06,
"pddf_rg_error": null,
"guinier_rg": 1.964,
"guinier_rg_error": 0.046,
"pddf_dmax": 8.8,
"pddf_dmax_error": null,
"porod_volume": 38.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 24,
"guinier_point_last": 113,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDXZ8_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-10-16T14:21:55.410833+02:00",
"bragg_peak": []
}
