{ "code": "SASDVD6", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "Integrated structural model of the palladin-actin complex using XL-MS, docking, NMR, and SAXS.", "publication": { "title": "Integrated structural model of the palladin-actin complex using XL-MS, docking, NMR, and SAXS.", "author_list": "Sargent R, Liu DH, Yadav R, Glennenmeier D, Bradford C, Urbina N, Beck MR", "journal": "Protein Sci", "doi": "10.1002/pro.70122", "pmid": "40248864", "published_date": "2025 May" }, "status": "released", "submitted_date": "2024-08-22", "released_date": "2024-08-29" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVD6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVD6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVD6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVD6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVD6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVD6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVD6.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Rayonix MX225-HE", "resolution": null }, "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": "Palladin", "short_name": "Ig4WT", "sequence": "TVQERFFRPHFLQAPGDLTVQEGKLCRMDCKVSGLPTPDLSWQLDGKPIRPDSAHKMLVRENGVHSLIIEPVTSRDAGIYTCIATNRAGQNSFNLELVVAAKEAHK", "organism": "Mus musculus", "uniprot_code": "Q9ET54", "uniprot_range_first": 1154, "uniprot_range_last": 1257, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MSETSSHDSFYDSLSDVQEEGKSADFFPGLSAFLSQEEINKSLDLARRAIDSSETEDFDS\nEKEISQIFSKSPISLCETPSHEEPKSGKQTSSERPQDSRRAPVQPLTGDQAERITSPGSK\nRKPGVSPLLASPSYIRSLRKAEKRGAKNPNPSSKPKTAQQSKAGPQSQLCDKAASFIEEL\nTSIFREAAKPRNRSPNGESSSPDSGYLSPKNQPSALMSASASQSPTADQLDQLEMDAEVK\nQAQGSLCYQAHQASEETLPLAHIPHPQPQKARHLPTAPRFIQKLRSQEVAEGSRVYLECR\nVTGNPTPRVRWFCEGKELYNSPDVQIHCESGELHTLVIAEAFEDDTGRYTCLATNPSGSD\nSTSAEVFIEGASSTDSDSESLSFISKAGAMPQAQKKTTSVSLTIGSSAPKTGVTTAVIQP\nLSVPVQQAHSATSYLCRPDGTTMGCLLPVFTKELQNTAASEGQVVVLECRVRGAPPLQVQ\nWFRQGSEIQDSPDFRILQKKPRSTAEPEEICTLVIAESFPEDAGIFTCSATNDYGSVTST\nAQLVITSANNENCSYDSTGEPNSDHFQHFPPPPPILETGSYELASQKPSEIQQVNSPNLG\nFSMAALQMQFNTAERETNGVHPSHGVNGLINGKAYGNKSPPTPTALLSPTKEPPPLLAKP\nKLDPLKLQQLQNQVRLEQEACAWPPAPPGVPCNSSSSGSSAPPSPPFPPPPPAFPELAAC\nASPVPSEPMSALASRATAMQSSGSFNYARPKQFIAAQNLGPASGLPTPTSSPSSSSLPSP\nLSPTPRPFGRAPGPPFVEPEAMWGPSSPSPPPPPPPVFSPSAAYPVPDVFPLPPPPPPLP\nSSTSHCASPARFGPSQTPAAFLSALLPSQPPPVAVNALGLPKGVTPAGFPKKSSRTARIA\nSDEEIQGTKDAVIQDLERKLRFKEDLLNNGQPRLTYEERMARRLLGADSANVFNIQEPEE\nTAANQDAGAPRASVGGPLDGQKEYKVSSCEQRLISEIEYRLERSPVDESGDEVQDPDVPV\nENATAPFFEMKLKHYKIFEGMPVTFTCRVAGNPKPKIYWFKDGKQISPKSDHYTIQRDLD\nGTCSLHTTASTLDDDGNYTIMAANPQGRVSCTGRLMVQAVNQRGRSPRSPSGHPHARRPR\nSRSRDSGDENEPIQERFFRPHFLQAPGDLTVQEGKLCRMDCKVSGLPTPDLSWQLDGKPI\nRPDSAHKMLVRENGVHSLIIEPVTSRDAGIYTCIATNRAGQNSFNLELVVAAKEAHKAPV\nFMEKLQNTGVADGYPVRLECRVSGVPPPQIFWKKENESLTHSTERVSMHQDNHGYICLLI\nQGATKEDAGWYTVSAKNEAGIVSCTARLDVYTQWHQQPQTTKPKKVRPSASRYAALSDQG\nLDIKAAFQPEASPSHLTLNSGLVESEDL", "mw": 11.768, "total_mw": 11.768, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "The protein construct used for SAXS contains two additional non-native amino acids at the N-terminus (TV). The protein fragment encompasses the Ig-like C2-type 4 domain (Ig4WT)." } ], "buffer": { "name": "20 mM HEPES pH 7.4, 1 mM DTT, 100 mM NaCl", "concentration_unit": null, "comment": "HEPES storage buffer", "additive": null, "concentration": null, "pka": null, "ph": null, "deuteration": null }, "purity_method": null, "name": "The Ig-like C2-type 4 domain (Ig4WT) of Palladin", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": null, "full_name": "Wichita State University", "webpage": null } ], "contributor_name": "Rachel", "contributor_surname": "Sargent", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2023-08-29", "storage_temperature": 4.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 12, "wavelength": 0.113, "sample_detector_distance": 1.246, "concentration_min": 0.5, "concentration_max": 10.0, "sample_volume": null, "flow_rate": null, "s_min": 0.104, "s_max": 7.383, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVD6_fit1_model1_img.png", "software": "SASREF", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "2.8.2", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVD6_fit1_model1.pdb", "model_mw": 10.78, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/4WTsasref.log", "symmetry": null, "comment": null, "user": 1106 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVD6_fit1_fixed_fit_img.png", "software": "SASREF", "chi_square_value": 13.52, "p_value": 0.0, "fit_residual_plot": "SASDVD6_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVD6_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/4WTsasref.log", "software_version": "2.8.2", "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVD6_fit2_model1_img.png", "software": "SASREF", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVD6_fit2_model1.pdb", "model_mw": 10.78, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 1106 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVD6_fit2_fixed_fit_img.png", "software": "FoXS", "chi_square_value": 10.603084, "p_value": 0.0, "fit_residual_plot": "SASDVD6_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVD6_fit2.fit", "fit_log": null, "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "NOTE: Amino acid sequence discrepancies are noted between on aligning the model and the submitted amino acid sequence.", "experiment_description": "Synchrotron SAXS data from solutions of the Ig-like C2-type 4 domain (Ig4WT) of palladin in 20 mM HEPES pH 7.4, 1 mM DTT, 100 mM NaCl were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL; Menlo Park, CA, USA) using a Rayonix MX225-HE detector at a sample-detector distance of 1.2 m and at a wavelength of λ = 0.113 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 10 mg/ml were measured at 20°C. 12 successive 1 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 10.2, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 11.3, "porod_mw_error": null, "pddf_i0": 0.003862, "pddf_i0_error": null, "guinier_i0": 0.00382275, "guinier_i0_error": null, "pddf_rg": 1.77, "pddf_rg_error": null, "guinier_rg": 1.691, "guinier_rg_error": 0.082, "pddf_dmax": 6.78, "pddf_dmax_error": null, "porod_volume": 18.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 10, "guinier_point_last": 87, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVD6_datloglog_img.png", "symmetry": null, "last_modified": "2025-04-28T15:41:13.044270+02:00", "bragg_peak": [] }