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{
"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": []
}
