{ "code": "SASDX82", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Activation and dimerization of the relaxase from the Bacillus subtilis conjugative plasmid pLS20 by DNA-induced cross-over of the catalytic residue", "publication": null, "status": "released", "submitted_date": "2025-03-11", "released_date": "2025-09-19" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDX82.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDX82.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX82_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX82_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDX82_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX82_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDX82.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": "Relaxase", "short_name": null, "sequence": "MDSPGVVLVSKYVSGKSTKFSKYVNYINRDEAVRTEKFQTYNVNKLDGYNQYMGNPEKSSGIFTQHKDSLSPVEKNQLKEIFRQAQKNDSVMWQDVISFDNKWLEERGIYNSQTGWVNEGAIQNSIRKGMEVLLREEQLEQSGVWSAAIHYNTDNIHVHIALVEPNPTKEYGVFTNKKTGEVYQARRGNRKLKTLDKMKSKVANTLMDRDKELSKISQLIHDRIAPKGLKFQVDKLAAALEHHHHHH", "organism": "Bacillus subtilis subsp. natto", "uniprot_code": "E9RJ23", "uniprot_range_first": 1, "uniprot_range_last": 232, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MDSPGVVLVSKYVSGKSTKFSKYVNYINRDEAVRTEKFQTYNVNKLDGYNQYMGNPEKSS\r\nGIFTQHKDSLSPVEKNQLKEIFRQAQKNDSVMWQDVISFDNKWLEERGIYNSQTGWVNEG\r\nAIQNSIRKGMEVLLREEQLEQSGVWSAAIHYNTDNIHVHIALVEPNPTKEYGVFTNKKTG\r\nEVYQARRGNRKLKTLDKMKSKVANTLMDRDKELSKISQLIHDRIAPKGLKFQPRLDTYMT\r\nKMYNHIYENLPEDMRLWKYNNNALNNIRPEIDSVITMYIQKYHPEDYKELDQSLKEEMEF\r\nRKSVYGDGPKQVERYKEYRKNKHKELYTKLGNSMLKEMAEIRRRESQSKQMNRSGTYAPS\r\nSVSNRQWDTKGRRIKRSDINKIKHALDKDYQSMKNMRKYQQMQYEMEQSR", "mw": 28.502, "total_mw": 28.502, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "The protein construct used for SAXS contains an additional non-native 15 amino acid C-terminal extension including a polyhistidine tag (VDKLAAALEHHHHHH)." } ], "buffer": { "name": "20 mM Tris, 300 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": "N-terminal domain of relaxase from Bacillus subtilis conjugative plasmid pLS20", "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": 25.0, "exposure_time": 0.1, "number_of_frames": 20, "wavelength": 0.1, "sample_detector_distance": 2.56, "concentration_min": null, "concentration_max": 5.0, "sample_volume": null, "flow_rate": null, "s_min": 0.21, "s_max": 5.82, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDX82_fit1_model1_img.png", "software": "Phenix", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDX82_fit1_model1.pdb", "model_mw": 25.03, "bead_radius": null, "log": null, "symmetry": "Monomer", "comment": "Monomer", "user": 1088 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDX82_fit1_fixed_fit_img.png", "software": "OLIGOMER", "chi_square_value": 0.89, "p_value": 0.0, "fit_residual_plot": "SASDX82_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDX82_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/oligomer_OpjE7AF.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "pLS20: https://doi.org/10.1093/nargab/lqab096", "experiment_description": "Synchrotron SAXS data from solutions of the N-terminal domain of relaxase in 20 mM Tris, 300 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 5.00 mg/ml was measured at 25°C. 20 successive 0.100 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": 26.45, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 39.9, "porod_mw_error": null, "pddf_i0": 1.875, "pddf_i0_error": null, "guinier_i0": 1.91399, "guinier_i0_error": null, "pddf_rg": 2.279, "pddf_rg_error": null, "guinier_rg": 2.28, "guinier_rg_error": 0.014, "pddf_dmax": 7.5, "pddf_dmax_error": null, "porod_volume": 48.4, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 23, "guinier_point_last": 124, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDX82_datloglog_img.png", "symmetry": null, "last_modified": "2026-04-14T12:48:12.254122+02:00", "bragg_peak": [] }