{ "code": "SASDV88", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "The UvrA2B2 pre-initiation complex from the Nucleotide Excision Repair pathway of Mycobacterium tuberculosis.", "publication": null, "status": "released", "submitted_date": "2024-10-15", "released_date": "2025-10-15" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDV88.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDV88.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV88_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV88_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDV88_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV88_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDV88.sascif", "experiment": { "instrument": { "detector": { "type": "Hybrid Photon Counting (HPC)", "name": "Mythen2 R 1K", "resolution": null }, "name": "CSIR-Central Drug Research Institute", "city": "Lucknow", "country": "India", "beamline_name": "Anton Paar SAXSpace", "beam_geometry": null, "type_of_source": "X-ray in house", "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": "UvrABC system protein A", "short_name": "UvrA", "sequence": "MADRLIVKGAREHNLRSVDLDLPRDALIVFTGLSGSGKSSLAFDTIFAEGQRRYVESLSAYARQFLGQMDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEVYDYLRLLYARAGTPHCPTCGERVARQTPQQIVDQVLAMPEGTRFLVLAPVVRTRKGEFADLFDKLNAQGYSRVRVDGVVHPLTDPPKLKKQEKHDIEVVVDRLTVKAAAKRRLTDSVETALNLADGIVVLEFVDHELGAPHREQRFSEKLACPNGHALAVDDLEPRSFSFNSPYGACPECSGLGIRKEVDPELVVPDPDRTLAQGAVAPWSNGHTAEYFTRMMAGLGEALGFDVDTPWRKLPAKARKAILEGADEQVHVRYRNRYGRTRSYYADFEGVLAFLQRKMSQTESEQMKERYEGFMRDVPCPVCAGTRLKPEILAVTLAGESKGEHGAKSIAEVCELSIADCADFLNALTLGPREQAIAGQVLKEIRSRLGFLLDVGLEYLSLSRAAATLSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLTRLRDLGNTLIVVEHDEDTIEHADWIVDIGPGAGEHGGRIVHSGPYDELLRNKDSITGAYLSGRESIEIPAIRRSVDPRRQLTVVGAREHNLRGIDVSFPLGVLTSVTGVSGSGKSTLVNDILAAVLANRLNGARQVPGRHTRVTGLDYLDKLVRVDQSPIGRTPRSNPATYTGVFDKIRTLFAATTEAKVRGYQPGRFSFNVKGGRCEACTGDGTIKIEMNFLPDVYVPCEVCQGARYNRETLEVHYKGKTVSEVLDMSIEEAAEFFEPIAGVHRYLRTLVDVGLGYVRLGQPAPTLSGGEAQRVKLASELQKRSTGRTVYILDEPTTGLHFDDIRKLLNVINGLVDKGNTVIVIEHNLDVIKTSDWIIDLGPEGGAGGGTVVAQGTPEDVAAVPASYTGKFLAEVVGGGASAATSRSNRRRNVSA", "organism": "Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)", "uniprot_code": "P9WQK7", "uniprot_range_first": 1, "uniprot_range_last": 972, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MADRLIVKGAREHNLRSVDLDLPRDALIVFTGLSGSGKSSLAFDTIFAEGQRRYVESLSA\nYARQFLGQMDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEVYDYLRLLYARAGTPH\nCPTCGERVARQTPQQIVDQVLAMPEGTRFLVLAPVVRTRKGEFADLFDKLNAQGYSRVRV\nDGVVHPLTDPPKLKKQEKHDIEVVVDRLTVKAAAKRRLTDSVETALNLADGIVVLEFVDH\nELGAPHREQRFSEKLACPNGHALAVDDLEPRSFSFNSPYGACPECSGLGIRKEVDPELVV\nPDPDRTLAQGAVAPWSNGHTAEYFTRMMAGLGEALGFDVDTPWRKLPAKARKAILEGADE\nQVHVRYRNRYGRTRSYYADFEGVLAFLQRKMSQTESEQMKERYEGFMRDVPCPVCAGTRL\nKPEILAVTLAGESKGEHGAKSIAEVCELSIADCADFLNALTLGPREQAIAGQVLKEIRSR\nLGFLLDVGLEYLSLSRAAATLSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRR\nLIETLTRLRDLGNTLIVVEHDEDTIEHADWIVDIGPGAGEHGGRIVHSGPYDELLRNKDS\nITGAYLSGRESIEIPAIRRSVDPRRQLTVVGAREHNLRGIDVSFPLGVLTSVTGVSGSGK\nSTLVNDILAAVLANRLNGARQVPGRHTRVTGLDYLDKLVRVDQSPIGRTPRSNPATYTGV\nFDKIRTLFAATTEAKVRGYQPGRFSFNVKGGRCEACTGDGTIKIEMNFLPDVYVPCEVCQ\nGARYNRETLEVHYKGKTVSEVLDMSIEEAAEFFEPIAGVHRYLRTLVDVGLGYVRLGQPA\nPTLSGGEAQRVKLASELQKRSTGRTVYILDEPTTGLHFDDIRKLLNVINGLVDKGNTVIV\nIEHNLDVIKTSDWIIDLGPEGGAGGGTVVAQGTPEDVAAVPASYTGKFLAEVVGGGASAA\nTSRSNRRRNVSA", "mw": 106.13, "total_mw": 212.26, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" }, { "long_name": "UvrABC system protein B", "short_name": "UvrB", "sequence": "MAFATEHPVVAHSEYRAVEEIVRAGGHFEVVSPHAPAGDQPAAIDELERRINAGERDVVLLGATGTGKSATTAWLIERLQRPTLVMAPNKTLAAQLANELREMLPHNAVEYFVSYYDYYQPEAYIAQTDTYIEKDSSINDDVERLRHSATSALLSRRDVVVVASVSCIYGLGTPQSYLDRSVELKVGEEVPRDGLLRLLVDVQYTRNDMSFTRGSFRVRGDTVEIIPSYEELAVRIEFFGDEIEALYYLHPLTGEVIRQVDSLRIFPATHYVAGPERMAHAVSAIEEELAERLAELESQGKLLEAQRLRMRTNYDIEMMRQVGFCSGIENYSRHIDGRGPGTPPATLLDYFPEDFLLVIDESHVTVPQIGGMYEGDISRKRNLVEYGFRLPSACDNRPLTWEEFADRIGQTVYLSATPGPYELSQTGGEFVEQVIRPTGLVDPKVVVKPTKGQIDDLIGEIRTRADADQRVLVTTLTKKMAEDLTDYLLEMGIRVRYLHSEVDTLRRVELLRQLRLGDYDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSSRSLIQTIGRAARNVSGEVHMYADKITDSMREAIDETERRRAKQIAYNEANGIDPQPLRKKIADILDQVYREADDTAVVEVGGSGRNASRGRRAQGEPGRAVSAGVFEGRDTSAMPRAELADLIKDLTAQMMAAARDLQFELAARFRDEIADLKRELRGMDAAGLK", "organism": "Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)", "uniprot_code": "P9WFC7", "uniprot_range_first": 1, "uniprot_range_last": 719, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MAFATEHPVVAHSEYRAVEEIVRAGGHFEVVSPHAPAGDQPAAIDELERRINAGERDVVL\nLGATGTGKSATTAWLIERLQRPTLVMAPNKTLAAQLANELREMLPHNAVEYFVSYYDYYQ\nPEAYIAQTDTYIEKDSSINDDVERLRHSATSALLSRRDVVVVASVSCIYGLGTPQSYLDR\nSVELKVGEEVPRDGLLRLLVDVQYTRNDMSFTRGSFRVRGDTVEIIPSYEELAVRIEFFG\nDEIEALYYLHPLTGEVIRQVDSLRIFPATHYVAGPERMAHAVSAIEEELAERLAELESQG\nKLLEAQRLRMRTNYDIEMMRQVGFCSGIENYSRHIDGRGPGTPPATLLDYFPEDFLLVID\nESHVTVPQIGGMYEGDISRKRNLVEYGFRLPSACDNRPLTWEEFADRIGQTVYLSATPGP\nYELSQTGGEFVEQVIRPTGLVDPKVVVKPTKGQIDDLIGEIRTRADADQRVLVTTLTKKM\nAEDLTDYLLEMGIRVRYLHSEVDTLRRVELLRQLRLGDYDVLVGINLLREGLDLPEVSLV\nAILDADKEGFLRSSRSLIQTIGRAARNVSGEVHMYADKITDSMREAIDETERRRAKQIAY\nNEANGIDPQPLRKKIADILDQVYREADDTAVVEVGGSGRNASRGRRAQGEPGRAVSAGVF\nEGRDTSAMPRAELADLIKDLTAQMMAAARDLQFELAARFRDEIADLKRELRGMDAAGLK", "mw": 80.406, "total_mw": 160.812, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "50 mM Tris pH 8, 200 mM NaCl, 2% glycerol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": null, "deuteration": null }, "purity_method": null, "name": "Mycobacterium tuberculosis UvrA2.UvrB2 complex", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "India", "full_name": "CSIR - Central Drug Research Institute", "webpage": "https://cdri.res.in/" } ], "contributor_name": "farheen", "contributor_surname": "jahan", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2022-06-06", "storage_temperature": 4.0, "cell_temperature": 10.0, "exposure_time": 30.0, "number_of_frames": 2, "wavelength": 0.154, "sample_detector_distance": 320.0, "concentration_min": null, "concentration_max": 0.9, "sample_volume": null, "flow_rate": null, "s_min": 0.095, "s_max": 7.584, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDV88_fit1_model1_img.png", "software": "GASBOR", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDV88_fit1_model1.cif", "model_mw": null, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/UvrA2B2_1.log", "symmetry": null, "comment": null, "user": 883 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDV88_fit1_fixed_fit_img.png", "software": "GASBOR", "chi_square_value": 0.55, "p_value": 0.0, "fit_residual_plot": "SASDV88_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDV88_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/UvrA2B2_1.log", "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": "Note: Data are of very-low quality. The experimental molecular weight cannot be obtained/confirmed from the SAXS data data. Due to the low concentration, the data contains noise in the sample—the complex of Mtb. UvrA dimer and UvrB dimer were purified by co-expressing His-tagged Mtb. UvrA and untagged Mtb.UvrB protein in BL-21 cells. The untagged UvrB forms a complex with UvrA (pre-initiation complex) and is purified. Further purification was performed by size exclusion chromatography using a superose 6 10/300 GL column, which shows the protein's equimolar and homogenous solution—the calculated molecular weight of the Mtb. UvrA2B2 complex using SEC is 343kDa.", "experiment_description": "SAXS data from solutions of Mycobacterium tuberculosis UvrA2.UvrB2 complex in 50 mM Tris pH 8, 200 mM NaCl, 2% glycerol were collected using an Anton Paar SAXSpace instrument at the CSIR-Central Drug Research Institute (Lucknow India) equipped with a Mythen2 R 1K detector at a sample-detector distance of 0.320 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 0.90 mg/ml was measured at 10°C. Two successive 30 second frames were collected. 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": 343.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 658.0, "porod_mw_error": null, "pddf_i0": 69930.0, "pddf_i0_error": null, "guinier_i0": 63683.7, "guinier_i0_error": null, "pddf_rg": 5.666, "pddf_rg_error": null, "guinier_rg": 5.282, "guinier_rg_error": 0.563, "pddf_dmax": 15.84, "pddf_dmax_error": null, "porod_volume": 1053.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 4, "guinier_point_last": 27, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDV88_datloglog_img.png", "symmetry": null, "last_modified": "2025-10-21T13:34:29.483230+02:00", "bragg_peak": [] }