{ "code": "SASDVT5", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "The structure and function of the DNA binding domain of class B MpARF2 share more traits with class A AtARF5 than to that of class B AtARF1.", "publication": { "title": "The structure and function of the DNA binding domain of class B MpARF2 share more traits with class A AtARF5 than to that of class B AtARF1.", "author_list": "Crespo I, Malfois M, Rienstra J, Tarrés-Solé A, van den Berg W, Weijers D, Boer DR", "journal": "Structure", "doi": "10.1016/j.str.2025.02.006", "pmid": "40086441", "published_date": "2025 Mar 7" }, "status": "released", "submitted_date": "2024-08-01", "released_date": "2024-12-09" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVT5.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVT5.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVT5_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVT5_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVT5_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVT5_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVT5.sascif", "experiment": { "instrument": { "detector": { "type": "CCD", "name": "ADSC Quantum 210r", "resolution": null }, "name": "ALBA", "city": "Cerdanyola del Vallès, Barcelona", "country": "Spain", "beamline_name": "BL11 - NCD", "beam_geometry": "", "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": "Auxin response factor", "short_name": "MpARF3", "sequence": "TGLDPQLWHACAGGMVQLPPVGAKVIYFPQGHGEQAATPPEFPRMMGPQ\r\nGTIGCRVVSVSFLADTETDEVYARIRLQPLEREAAMSIADSTLDADGGPS\r\nSPPPEKPASFAKTLTQSDANNGGGFSVPRYCAETIFPPLDYSIDPPVQTV\r\nLAKDVHGERWKFRHIYRGTPRRHLLTTGWSTFVNQKKLVAGDAIVFLRTA\r\nSGELCVGVRRSMRGTGGADSSTWSGGSSTSHHRPNRWEVKGTESFSDFLG\r\nNDSAAGGGSVSSAGSAAGPGGPRAGPGGSNSGPGIGIPGPSTTSSFARNR\r\nARVTAQSVLEAASLAVQGQPFEVVYYPRASTAEFCVKAQAVKAALDHTWF\r\nPGMRFKMAFETEDSSRISWFMGTISAVQPADSLWPKSPWRVLQVTWDEPD\r\nLLQGVSRVSPWQVELVSTLPGNSYSQSM", "organism": "Marchantia polymorpha", "uniprot_code": "A0A0G3FJH3", "uniprot_range_first": 52, "uniprot_range_last": 470, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MPGPSPGCGTMSGTNIKMEKSEESMGGGGKGWGGGRDRDSSSDGGGGSGENTGLDPQLWH\nACAGGMVQLPPVGAKVIYFPQGHGEQAATPPEFPRMMGPQGTIGCRVVSVSFLADTETDE\nVYARIRLQPLEREAAMSIADSTLDADGGPSSPPPEKPASFAKTLTQSDANNGGGFSVPRY\nCAETIFPPLDYSIDPPVQTVLAKDVHGERWKFRHIYRGTPRRHLLTTGWSTFVNQKKLVA\nGDAIVFLRTASGELCVGVRRSMRGTGGADSSTWSGGSSTSHHRPNRWEVKGTESFSDFLG\nNDSAAGGGSVSSAGSAAGPGGPRAGPGGSNSGPGIGIPGPSTTSSFARNRARVTAQSVLE\nAASLAVQGQPFEVVYYPRASTAEFCVKAQAVKAALDHTWFPGMRFKMAFETEDSSRISWF\nMGTISAVQPADSLWPKSPWRVLQVTWDEPDLLQGVSRVSPWQVELVSTLPMQLPPFSLPK\nKKLRAAQPSDMNMQGQGLMGMPITLPSVFGQINPWAHGLTMEEVTAGMQGARHDRVFGLA\nLSEKFRPGKLPGGFFSAAEGYYPDHAGRGGGGEPHLSAFPLQDRASNISSLISSLGSVPP\nSGDHGSAGALLVPAGSWSGGSANNKSASTQLVLFGQAINTDSNKSQPQHSGGSSCDGPSL\nQHLKEESSGKRKDSPSESNQNENFERGQKYMSGSLSNGKQSDLIVGEFQKWVPGLDKERG\nAGEKLAASPEILQSPQGAW", "mw": 45.502, "total_mw": 45.502, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "The protein construct used for SAXS contains an additional eight non-native amino acid C-terminal extension (GNSYSQSM)." } ], "buffer": { "name": "20 mM Tris-HCl, 150 mM NaCl, 1 mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Marchantia polymorpha Auxin Response Factor 3", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Barcelona, Spain", "full_name": "ALBA - Cells", "webpage": "https://www.cells.es" } ], "contributor_name": "Isidro", "contributor_surname": "Crespo", "orcid": "https://orcid.org/0000-0001-7698-1720" } ], "concentration_method": null, "concentration_unit": null, "date": "2019-12-03", "storage_temperature": 4.0, "cell_temperature": 20.0, "exposure_time": 0.5, "number_of_frames": 20, "wavelength": 0.1, "sample_detector_distance": 2.56, "concentration_min": null, "concentration_max": 3.5, "sample_volume": null, "flow_rate": null, "s_min": 0.236, "s_max": 5.82, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVT5_fit1_model1_img.png", "software": "GASBOR", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "GASBOR 2.3i (r10552)", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVT5_fit1_model1.pdb", "model_mw": null, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/Mp3sM-35.log", "symmetry": "P1", "comment": null, "user": 1088 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVT5_fit1_fixed_fit_img.png", "software": "GASBOR", "chi_square_value": 0.98, "p_value": 0.0, "fit_residual_plot": "SASDVT5_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVT5_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Mp3sM-35.log", "software_version": "GASBOR 2.3i (r10552)", "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVT5_fit2_model1_img.png", "software": "SwissModel", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVT5_fit2_model1.pdb", "model_mw": 44.44, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/report.html", "symmetry": null, "comment": null, "user": 1088 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVT5_fit2_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 0.747, "p_value": 0.0, "fit_residual_plot": "SASDVT5_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVT5_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/3_5mgmlAverage69-2000_MpARF3_Mp2base.log", "software_version": "ATSAS 3.3.0 (r14945)", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "CAUTION: Dmax appears underestimated.", "experiment_description": "Synchrotron SAXS data from solutions of M. polymorpha auxin response factor 3 in 20 mM Tris-HCl, 150 mM NaCl, 1 mM DTT, pH 8 were collected on the BL11 - NCD beam line at ALBA (Cerdanyola del Vallès, Barcelona, Spain) using a ADSC Quantum 210r detector at a sample-detector distance of 2.6 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.50 mg/ml was measured at 20°C. 20 successive 0.500 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": "arbitrary", "experimental_mw": 42.64, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 36.9, "porod_mw_error": null, "pddf_i0": 1.593, "pddf_i0_error": null, "guinier_i0": 1.69425, "guinier_i0_error": null, "pddf_rg": 2.375, "pddf_rg_error": null, "guinier_rg": 2.6, "guinier_rg_error": 0.018, "pddf_dmax": 6.16, "pddf_dmax_error": null, "porod_volume": 59.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 92, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVT5_datloglog_img.png", "symmetry": null, "last_modified": "2025-03-20T11:11:00.318393+01:00", "bragg_peak": [] }