{"code":"SASDX92","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/SASDX92.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDX92.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX92_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX92_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDX92_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX92_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDX92.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":"dimer","molecular_type":"protein","uniprot_sequence":"MDSPGVVLVSKYVSGKSTKFSKYVNYINRDEAVRTEKFQTYNVNKLDGYNQYMGNPEKSS\nGIFTQHKDSLSPVEKNQLKEIFRQAQKNDSVMWQDVISFDNKWLEERGIYNSQTGWVNEG\nAIQNSIRKGMEVLLREEQLEQSGVWSAAIHYNTDNIHVHIALVEPNPTKEYGVFTNKKTG\nEVYQARRGNRKLKTLDKMKSKVANTLMDRDKELSKISQLIHDRIAPKGLKFQPRLDTYMT\nKMYNHIYENLPEDMRLWKYNNNALNNIRPEIDSVITMYIQKYHPEDYKELDQSLKEEMEF\nRKSVYGDGPKQVERYKEYRKNKHKELYTKLGNSMLKEMAEIRRRESQSKQMNRSGTYAPS\nSVSNRQWDTKGRRIKRSDINKIKHALDKDYQSMKNMRKYQQMQYEMEQSR","mw":28.502,"total_mw":57.004,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"Relaxase dimer. The protein construct used for SAXS contains an additional non-native 15 amino acid C-terminal extension including a polyhistidine tag (VDKLAAALEHHHHHH)."},{"long_name":"core region, single stranded","short_name":"ssnic","sequence":"AGTTTCCCCTTATGCTCTT","organism":"Bacillus subtilis","uniprot_code":null,"uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"dimer","molecular_type":"DNA","uniprot_sequence":"","mw":5.776,"total_mw":11.552,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":""}],"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 in complex with the core region","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":0.144,"s_max":5.82,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDX92_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/SASDX92_fit1_model1.pdb","model_mw":25.03,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":1088}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDX92_fit1_fixed_fit_img.png","software":"CRYSOL","chi_square_value":7.029,"p_value":0.0,"fit_residual_plot":"SASDX92_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDX92_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/Ratio1AverageSubs38-1964_p58_Monomer.log","software_version":"ATSAS 3.3.0","description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDX92_fit2_model1_img.png","software":"PyMOL","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDX92_fit2_model1.pdb","model_mw":48.48,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":1088}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDX92_fit2_fixed_fit_img.png","software":"CRYSOL","chi_square_value":2.047,"p_value":0.0,"fit_residual_plot":"SASDX92_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDX92_fit2.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/Ratio1AverageSubs38-1964_p58DimerDNA.log","software_version":"ATSAS 3.3.0","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 complex with nic sequence DNA 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":49.11,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":3.29,"pddf_i0_error":null,"guinier_i0":3.42864,"guinier_i0_error":null,"pddf_rg":2.445,"pddf_rg_error":null,"guinier_rg":2.52,"guinier_rg_error":0.01,"pddf_dmax":8.21,"pddf_dmax_error":null,"porod_volume":50.26,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":47,"guinier_point_last":128,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDX92_datloglog_img.png","symmetry":null,"last_modified":"2026-04-14T16:07:36.162012+02:00","bragg_peak":[]}