{"code":"SASDVH8","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/SASDVH8.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDVH8.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVH8_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVH8_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVH8_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVH8_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDVH8.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 tetrameric quaternary state and monodispersed. 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 (4 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":4.0,"sample_volume":null,"flow_rate":null,"s_min":0.087,"s_max":3.686,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVH8_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/SASDVH8_fit1_model1.cif","model_mw":null,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/S9mp-4-S.log","symmetry":"P4","comment":null,"user":649}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVH8_fit1_fixed_fit_img.png","software":"GASBOR","chi_square_value":1.04,"p_value":0.0,"fit_residual_plot":"SASDVH8_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVH8_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/S9mp-4-S.log","software_version":"GASBOR 2.3i (r14885)","description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVH8_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/SASDVH8_fit2_model1.cif","model_mw":null,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/S9mp-4-N.log","symmetry":null,"comment":null,"user":649}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVH8_fit2_fixed_fit_img.png","software":"GASBOR","chi_square_value":0.86,"p_value":0.0,"fit_residual_plot":"SASDVH8_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVH8_fit2.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/S9mp-4-N.log","software_version":"GASBOR 2.3i (r14885)","description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDVH8_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/SASDVH8_fit3_model1.pdb","model_mw":303.5,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/S9MP_4mg-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/SASDVH8_fit3_fixed_fit_img.png","software":"CRYSOL","chi_square_value":3.735,"p_value":0.0,"fit_residual_plot":"SASDVH8_fit3_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDVH8_fit3.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/S9MP_4mg-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":null,"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 4.00 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":351.0,"porod_mw_error":null,"pddf_i0":7.514,"pddf_i0_error":null,"guinier_i0":7.6482,"guinier_i0_error":null,"pddf_rg":5.06,"pddf_rg_error":null,"guinier_rg":5.112,"guinier_rg_error":0.375,"pddf_dmax":16.2,"pddf_dmax_error":null,"porod_volume":563.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":18,"guinier_point_last":41,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDVH8_datloglog_img.png","symmetry":null,"last_modified":"2025-05-28T14:09:07.404782+02:00","bragg_peak":[]}