{ "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 DS6A", "uniprot_code": "G8I4E0", "uniprot_range_first": 1, "uniprot_range_last": 395, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MMLTVESFAAAMGNSLSVDRYRQLFPAAVESMVACGCTTVNRAAMWLAQVGHESGGLRWM\nEELASGAAYEWRSDLGNTQAGDGVRFKGRGPIQITGRYNYRKVSEWAHAQGIVPTPTYFV\nDNPTQLASDQYGFIGVSWYWQHGGPRPGQINGFADAGDILSGSRCVNGWVTTPNGMPDRT\nERWNRCRAMGDQILPAGAGTDNGGDGMAWTGDPVWLEDVLRPVLGDRLRVLPSWQMYGHG\nDFKDIRGVMVHHTGNARETAESIRKGRPDLRGPLSNIHIAPDGTVTLVAAGVCWHAGAGS\nYPWLPTNNANWHMIGIECAWPTIRPNGTYDEREPWPDAQIIAMRDTCAALTKRLGWDASR\nVIGHKEYAGASQGKWDPGNLDMGWFRGEVAKAMRGEFDPKAPAPAPNPPADNDNGGFLMA\nLNDKQQHDLYNAVMTIAAVAADIQTQLRGPGLRGWPQLGRNANGEALTLVDAVGVIKAIA\nDREAGR", "mw": 43.458, "total_mw": 43.458, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "The molecule beahves as a monomer in solution" } ], "buffer": { "name": "20 mM Tris, 150 mM NaCl and 1 mM 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": [] }