The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
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{
"code": "SASDVF8",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Structural and Functional Investigation of Putative Peptidase from <i>Mycolicibacterium phlei</i>\n : An Exclusive Endopeptidase among S9C Subfamily",
"publication": {
"title": "Structural and Functional Investigation of Putative Peptidase from <i>Mycolicibacterium phlei</i>\n : An Exclusive Endopeptidase among S9C Subfamily",
"author_list": "Chandravanshi K, Jamdar S, Singh R, Kumar A, Mahato A, Agrawal R, Kumar S, Kumar A, Makde R",
"journal": "Biochemistry",
"doi": "10.1021/acs.biochem.5c00047",
"pmid": null,
"published_date": "2025 May 28"
},
"status": "released",
"submitted_date": "2024-10-14",
"released_date": "2025-05-28"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVF8.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVF8.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVF8_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVF8_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVF8_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVF8_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVF8.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "MAR 345 Image Plate",
"resolution": null
},
"name": "INDUS-2",
"city": "Indore",
"country": "India",
"beamline_name": "BL-18",
"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": "Peptidase S9",
"short_name": "S9mp",
"sequence": "MASWSHPQFEKGSSHHHHHHSSGSGGGGGENLYFQGSTPFHDLDDYLALPRVSGLALSPDGTRLLTTIAELNDKRTEYVSAVWEIDPAGERPARRLTRGAKGESAPAFTADGDILFVAVRPTEDDDKPPAALWRLPAAGGEAYEALTLPGGVEAVRTAREADVAVVRASLLPSARDIDDDRRLRKIRKDNKISAILHTGYPIRYWDADLGPAEPHLLGLDLGDGDVRDLTAAPGGTLRESDFDVSADGRFLVTTWQRPAPGASRHSVLVRIDLDSGERTVLVEEPEADVWRPVIAPDGSGVVYIRETFSTPHAAPRMTLGYLRFGEEPVILAGDWDRWPASVTWLRDGSAVLVTADQDGRAPVFRVDVPGGSVTQLTFDDYAYTDVVTGPDGAAYALRSSYAAPPHPVRLDADGGVTELPCVALPELPGTLTELETTAADGTRVRSWLVLPAGDGKAPLLLWIHGGPLSSWNAWSWRWNPWLLAARGYAVLLPDPGLSTGYGQDFIQRGWGAWGGAPYEDLMAATDAACEHPRIDPDHTAAMGGSFGGYMANWVAGHTDRFDAIVTHASLWALDQFGATTDSSYYWLREMTREMAQANSPHNHVHNIRTPMLVIHGDKDYRVPIGEALRLWYELLTHSALPADDDGCSPHRFLYFPSENHWVLAPQHAKVWYQVVTAFLARHVLDEDVELPETLG",
"organism": "Mycolicibacterium phlei DSM 43239 = CCUG 21000",
"uniprot_code": "A0A5N5URA7",
"uniprot_range_first": 4,
"uniprot_range_last": 661,
"oligomerization": "tetramer",
"molecular_type": "protein",
"uniprot_sequence": "MSPTPFHDLDDYLALPRVSGLALSPDGTRLLTTIAELNDKRTEYVSAVWEIDPAGERPAR\nRLTRGAKGESAPAFTADGDILFVAVRPTEDDDKPPAALWRLPAAGGEAYEALTLPGGVEA\nVRTAREADVAVVRASLLPSARDIDDDRRLRKIRKDNKISAILHTGYPIRYWDADLGPAEP\nHLLGLDLGDGDVRDLTAAPGGTLRESDFDVSADGRFLVTTWQRPAPGASRHSVLVRIDLD\nSGERTVLVEEPEADVWRPVIAPDGSGVVYIRETFSTPHAAPRMTLGYLRFGEEPVILAGD\nWDRWPASVTWLRDGSAVLVTADQDGRAPVFRVDVPGGSVTQLTFDDYAYTDVVTGPDGAA\nYALRSSYAAPPHPVRLDADGGVTELPCVALPELPGTLTELETTAADGTRVRSWLVLPAGD\nGKAPLLLWIHGGPLSSWNAWSWRWNPWLLAARGYAVLLPDPGLSTGYGQDFIQRGWGAWG\nGAPYEDLMAATDAACEHPRIDPDHTAAMGGSFGGYMANWVAGHTDRFDAIVTHASLWALD\nQFGATTDSSYYWLREMTREMAQANSPHNHVHNIRTPMLVIHGDKDYRVPIGEALRLWYEL\nLTHSALPADDDGCSPHRFLYFPSENHWVLAPQHAKVWYQVVTAFLARHVLDEDVELPETL\nG",
"mw": 75.917,
"total_mw": 303.668,
"number_molecules": 4,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "The S9 peptidase of M. Phlei (S9mp) was cloned and recombinantly expressed in E. coli. The recombinant S9mp protein was purified to homogeneity using Ni-IMAC followed by size exclusion chromatography (SEC). Both SEC and dynamic light scattering confirmed the oligomeric state of S9mp as tetramer. The protein construct used for SAXS contains additional N-terminal non native amino acids, including a polyhistidine tag (MASWSHPQFEKGSSHHHHHHSSGSGGGGGENLYFQGS)."
}
],
"buffer": {
"name": "10 mM Tris-HCl, 135 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "S9 peptidase form Mycobacterium phlei (8 mg/ml)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Mumbai 400085, INDIA",
"full_name": "Bhabha Atomic Research Centre",
"webpage": null
}
],
"contributor_name": "Dr. Rahul",
"contributor_surname": "Singh",
"orcid": "https://orcid.org/0000-0003-4871-3600"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2024-03-21",
"storage_temperature": 25.0,
"cell_temperature": 25.0,
"exposure_time": null,
"number_of_frames": null,
"wavelength": 0.1033,
"sample_detector_distance": 2.2,
"concentration_min": null,
"concentration_max": 8.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.087,
"s_max": 3.69,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVF8_fit1_model1_img.png",
"software": "GASBOR",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "GASBOR 2.3i (r14885)",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVF8_fit1_model1.cif",
"model_mw": null,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/S9mp-8-S.log",
"symmetry": "P4",
"comment": null,
"user": 649
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVF8_fit1_fixed_fit_img.png",
"software": "GASBOR",
"chi_square_value": 1.45,
"p_value": 0.0,
"fit_residual_plot": "SASDVF8_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVF8_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/S9mp-8-S.log",
"software_version": "GASBOR 2.3i (r14885)",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVF8_fit2_model1_img.png",
"software": "GASBOR",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "GASBOR 2.3i (r14885)",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVF8_fit2_model1.cif",
"model_mw": null,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/S9mp-8-N.log",
"symmetry": null,
"comment": null,
"user": 649
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVF8_fit2_fixed_fit_img.png",
"software": "GASBOR",
"chi_square_value": 1.59,
"p_value": 0.0,
"fit_residual_plot": "SASDVF8_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVF8_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/S9mp-8-N.log",
"software_version": "GASBOR 2.3i (r14885)",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVF8_fit3_model1_img.png",
"software": "AlphaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "AlphaFold 3",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVF8_fit3_model1.pdb",
"model_mw": 303.5,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/S9MP_8mg-Ang_fold_s9mp_model_1.log",
"symmetry": "P4",
"comment": null,
"user": 649
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVF8_fit3_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 93.515,
"p_value": 0.0,
"fit_residual_plot": "SASDVF8_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVF8_fit3.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/S9MP_8mg-Ang_fold_s9mp_model_1.log",
"software_version": "ATSAS 3.3.0 (r14945)",
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "Likely aggregated. X-ray Exposure time = UNKNOWN. Number of frames = UNKNOWN",
"experiment_description": "Synchrotron SAXS data from solutions of S9 peptidase form Mycobacterium phlei in 10 mM Tris-HCl, 135 mM NaCl, pH 8 were collected on the BL-18 beam line at INDUS-2 (Indore, India) using a MAR 345 Image Plate detector at a sample-detector distance of 2.2 m and at a wavelength of λ = 0.1033 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 8.00 mg/ml was measured at 25°C. 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": 318.4,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 350.0,
"porod_mw_error": null,
"pddf_i0": 14.16,
"pddf_i0_error": null,
"guinier_i0": 14.9421,
"guinier_i0_error": null,
"pddf_rg": 5.02,
"pddf_rg_error": null,
"guinier_rg": 5.206,
"guinier_rg_error": 0.1,
"pddf_dmax": 15.8,
"pddf_dmax_error": null,
"porod_volume": 559.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 39,
"guinier_point_last": 69,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDVF8_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-05-28T14:09:06.734998+02:00",
"bragg_peak": []
}
