{"code":"SASDWN5","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/A","project":{"title":"Dissecting the molecular basis underlying mycobacterial cell-wall hydrolysis by the catalytic domains of D29LysA and DS6ALysA phage endolysins.","publication":{"title":"Dissecting the molecular basis underlying mycobacterial cell-wall hydrolysis by the catalytic domains of D29LysA and DS6ALysA phage endolysins.","author_list":"Ceballos-Zúñiga F, Galvez-Larrosa L, Muñoz IG, Infantes L, Fernández-Carrillo J, Pérez-Dorado I","journal":"Int J Biol Macromol","doi":"10.1016/j.ijbiomac.2025.148896","pmid":"41207583","published_date":"2025 Nov 7"},"status":"released","submitted_date":"2025-01-21","released_date":"2025-11-10"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDWN5.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDWN5.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWN5_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWN5_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDWN5_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWN5_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDWN5.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Eiger 4M","resolution":75.0},"name":"Diamond Light Source","city":"Didcot","country":"UK","beamline_name":"B21","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":"N-acetylmuramoyl-L-alanine amidase","short_name":"DS6A","sequence":">DS6A\r\n\r\nGPMMLTVESFAAAMGNSLSVDRYRQLFPAAVESMVACGCTTVNRAAMWLAQVGHESGGLRWM\r\nEELASGAAYEWRSDLGNTQAGDGVRFKGRGPIQITGRYNYRKVSEWAHAQGIVPTPTYFV\r\nDNPTQLASDQYGFIGVSWYWQHGGPRPGQINGFADAGDILSGSRCVNGWVTTPNGMPDRT\r\nERWNRCRAMGDQILPAGAGTDNGGDGMAWTGDPVWLEDVLRPVLGDRLRVLPSWQMYGHG\r\nDFKDIRGVMVHHTGNARETAESIRKGRPDLRGPLSNIHIAPDGTVTLVAAGVCWHAGAGS\r\nYPWLPTNNANWHMIGIECAWPTIRPNGTYDEREPWPDAQIIAMRDTCAALTKRLGWDASR\r\nVIGHKEYAGASQGKWDPGNLDMGWFRGEVAKAMRG","organism":"Mycobacterium phage 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DTT","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":8.0,"deuteration":null},"purity_method":null,"name":"N-acetylmuramoyl-L-alanine amidase (without His-Tag)","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":"Spanish National Cancer Research Centre (CNIO)","webpage":null}],"contributor_name":"INÉS","contributor_surname":"MUÑOZ","orcid":"https://orcid.org/0000-0001-6732-4059"}],"concentration_method":null,"concentration_unit":null,"date":"2024-09-30","storage_temperature":4.0,"cell_temperature":18.0,"exposure_time":3.0,"number_of_frames":600,"wavelength":1.0,"sample_detector_distance":3.7,"concentration_min":null,"concentration_max":5.9,"sample_volume":null,"flow_rate":null,"s_min":0.045,"s_max":3.399,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDWN5_fit1_model1_img.png","software":"Coot","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDWN5_fit1_model1.pdb","model_mw":43.28,"bead_radius":null,"log":null,"symmetry":"P1","comment":null,"user":973}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWN5_fit1_fixed_fit_img.png","software":"FoXS","chi_square_value":1.628254,"p_value":0.0,"fit_residual_plot":"SASDWN5_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDWN5_fit1.fit","fit_log":null,"software_version":null,"description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDWN5_fit2_model1_img.png","software":"DAMMIN","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDWN5_fit2_model1.pdb","model_mw":34.27,"bead_radius":2.25,"log":"https://www.sasbdb.org/media/log_files/1_GYqQf5w.log","symmetry":"P1","comment":null,"user":973}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWN5_fit2_fixed_fit_img.png","software":"DAMMIN","chi_square_value":0.85,"p_value":0.0594,"fit_residual_plot":"SASDWN5_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDWN5_fit2.fir","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":"SAXS experiments were performed at the beamline B21 of the Diamond Light Source (Harwell Campus, UK) (Cowieson et al, 2020). Samples of 45 µl of 6His-tagged and untagged DS6AGH19-Ami2B protein at 5.6 and 5.9 mg/ml were loaded into a Sodex KW-403 column and a SRT-C SEC-300 (Sepax) column, respectively, equilibrated in buffer (20 mM Tris pH 8.0, 150 mM NaCl and 1 mM DTT) and connected to an Agilent 1200 HPLC system at 18 °C. Continuously eluting samples were exposed for 3 s in 10 s acquisition blocks using an X-ray wavelength of 1 Å, and a sample to detector (Eiger 4M) distance of 3.7 m. The data covered a momentum transfer range of 0.0032 < q < 0.34 Å−1. The frames recorded immediately before elution of the sample were subtracted from the protein scattering profiles. The Scåtter software package (www.bioisis.net) was used to analyse data, buffer-subtraction, scaling, merging and checking possible radiation damage of the samples. The Rg value was calculated with the Guinier approximation assuming that at very small angles q < 1.3/Rg. The particle distance distribution, Dmax, was calculated from the scattering pattern with GNOM, and shape estimation was carried out with DAMMIF/DAMMIN, all these programs included in the ATSAS package. The proteins molecular mass was estimated with GNOM. Interactively generated PDB-based homology models were made using the program COOT by manually adjusting the X-ray structures obtained in this work, into the envelope given by SAXS until a good correlation between the real-space scattering profile calculated for the homology model matched the experimental scattering data. This was computed with the program FoXS.","experiment_description":null,"tags":[],"intensity_unit":"arbitrary","experimental_mw":39.21,"experimental_mw_error":null,"guinier_i0_mw":37.75,"guinier_i0_mw_error":null,"porod_mw":39.8,"porod_mw_error":null,"pddf_i0":0.03921,"pddf_i0_error":null,"guinier_i0":0.0390946,"guinier_i0_error":null,"pddf_rg":2.85,"pddf_rg_error":0.04,"guinier_rg":2.789,"guinier_rg_error":0.052,"pddf_dmax":9.5,"pddf_dmax_error":null,"porod_volume":50.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":80,"guinier_point_last":323,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDWN5_datloglog_img.png","symmetry":null,"last_modified":"2025-11-10T15:23:43.804079+01:00","bragg_peak":[]}