{ "code": "SASDXV8", "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/SASDXV8.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDXV8.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXV8_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXV8_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDXV8_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXV8_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDXV8.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, 1 mM BaCl2", "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 Vof Bifunctional hemolysin/adenylate cyclase, 1 mM BaCl2", "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": "2024-08-01", "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": 5.025, "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/SASDXV8_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/SASDXV8_fit1_fixed_fit_img.png", "software": "DENSS", "chi_square_value": 1.5844, "p_value": 0.0002, "fit_residual_plot": "SASDXV8_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXV8_fit1.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": 21.2, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 20.0, "porod_mw_error": null, "pddf_i0": 118.9, "pddf_i0_error": null, "guinier_i0": 117.636, "guinier_i0_error": null, "pddf_rg": 3.15, "pddf_rg_error": null, "guinier_rg": 2.978, "guinier_rg_error": 0.111, "pddf_dmax": 13.1, "pddf_dmax_error": null, "porod_volume": 32.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 22, "guinier_point_last": 60, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDXV8_datloglog_img.png", "symmetry": null, "last_modified": "2025-10-16T14:20:57.487343+02:00", "bragg_peak": [] }