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": "SASDFG6",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex",
"publication": {
"title": "Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex",
"author_list": "Shukla A, Afsar M, Khanam T, Kumar N, Ali F, Kumar S, Jahan F, Ramachandran R",
"journal": "International Journal of Biological Macromolecules",
"doi": "10.1016/j.ijbiomac.2022.11.094",
"pmid": null,
"published_date": "2022 Nov"
},
"status": "released",
"submitted_date": "2019-05-24",
"released_date": "2021-09-27"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFG6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFG6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFG6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFG6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFG6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFG6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFG6.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "ESRF",
"city": "Grenoble",
"country": "France",
"beamline_name": "BM29",
"beam_geometry": "",
"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": "Beta sliding clamp",
"short_name": null,
"sequence": "MDAATTRVGLTDLTFRLLRESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVDVHVEGNRVALTCGNARFSLPTMPVEDYPTLPTLPEETGLLPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDIEAAVLVPAKTLAEAAKAGIGGSDVRLSLGTGPGVGKDGLLGISGNGKRSTTRLLDAEFPKFRQLLPTEHTAVATMDVAELIEAIKLVALVADRGAQVRMEFADGSVRLSAGADDVGRAEEDLVVDYAGEPLTIAFNPTYLTDGLSSLRSERVSFGFTTAGKPALLRPVSGDDRPVAGLNGNGPFPAVSTDYVYLLMPVRLPGHHHHHH",
"organism": "Mycobacterium tuberculosis",
"uniprot_code": "P9WNU1",
"uniprot_range_first": 1,
"uniprot_range_last": 402,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MDAATTRVGLTDLTFRLLRESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGFD\nYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVDVHVEGNRVALTCGNARFSLPT\nMPVEDYPTLPTLPEETGLLPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAA\nTDRFRLAVRELKWSASSPDIEAAVLVPAKTLAEAAKAGIGGSDVRLSLGTGPGVGKDGLL\nGISGNGKRSTTRLLDAEFPKFRQLLPTEHTAVATMDVAELIEAIKLVALVADRGAQVRME\nFADGSVRLSAGADDVGRAEEDLVVDYAGEPLTIAFNPTYLTDGLSSLRSERVSFGFTTAG\nKPALLRPVSGDDRPVAGLNGNGPFPAVSTDYVYLLMPVRLPG",
"mw": 42.935,
"total_mw": 85.87,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Probable exodeoxyribonuclease III protein XthA",
"short_name": "MtbXthA",
"sequence": "MRLATWNVNSVKARLPRLLAWLDETKPDVVCLQETKSAADGFPSGDVAELGYTTAAYGEGRWNGVAILSRVGIEDVSKSFPGEPVYQGEAPAGPGVQTQLTEPVLLAPQARAIGATCGGIRVWSLYAPNGRTPESAHYLYKLEWFAALRDALAAELSAGTPLVATGDYNVAPTDDDVWDPSVFVGSTHVTPAERQALAELRDLGLHDIVPTPMKGPHPYTYWDYRAGSFHKDLGMRIDLVYGNGAFAERVRSAYVDREARKGRGPSDHAPVVVDLDHHHHHH",
"organism": "Mycobacterium tuberculosis",
"uniprot_code": "A0A0T9L251",
"uniprot_range_first": 1,
"uniprot_range_last": 289,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 30.699,
"total_mw": 30.699,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "DNA ligase A",
"short_name": null,
"sequence": "MSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAGSTVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPECGSPLAPEKEGDADIRCPNARGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIADEGELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPTAARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRMVDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPGSKYDKAVELGVPILDEDGFRRLLADGPASRTHHHHHH",
"organism": "Mycobacterium tuberculosis",
"uniprot_code": "P9WNV1",
"uniprot_range_first": 1,
"uniprot_range_last": 691,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPE\nLRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLC\nELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLE\nVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGH\nVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVK\nVDEVALQRRLGSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAG\nSTVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPE\nCGSPLAPEKEGDADIRCPNARGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIA\nDEGELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPT\nAARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRM\nVDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPG\nSKYDKAVELGVPILDEDGFRRLLADGPASRT",
"mw": 76.111,
"total_mw": 76.111,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Probable exodeoxyribonuclease III protein XthA, sliding beta clamp, DNA ligase-A tricomplex",
"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": "Ravishankar",
"contributor_surname": "Ramachandran",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-05-17",
"storage_temperature": 4.0,
"cell_temperature": 10.0,
"exposure_time": 1.0,
"number_of_frames": 10,
"wavelength": 0.0992,
"sample_detector_distance": 2.9,
"concentration_min": null,
"concentration_max": 2.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.031,
"s_max": 4.944,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFG6_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "DAMAVER",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFG6_fit1_model1.pdb",
"model_mw": 346.167,
"bead_radius": 5.75,
"log": null,
"symmetry": null,
"comment": null,
"user": 328
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFG6_fit1_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.119,
"p_value": 0.0,
"fit_residual_plot": "SASDFG6_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFG6_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/2.0_r_mgml_complex_420_sub-1.log",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The presented model shows the spatial alignment of several individually calculated models and does not fit the SAXS data. A corresponding individual model fit (individual model not provided for this entry) is shown. The sample shows signs of severe aggregation.",
"experiment_description": "Synchrotron SAXS data from solutions of the probable XthA, sliding beta clamp, DNA ligase-A tricomplex in 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH 8 were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.0992 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.00 mg/ml was measured at 10°C. 10 successive 1 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": 205.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 313.0,
"porod_mw_error": null,
"pddf_i0": 62.81,
"pddf_i0_error": null,
"guinier_i0": 60.38,
"guinier_i0_error": 0.23,
"pddf_rg": 6.391,
"pddf_rg_error": null,
"guinier_rg": 5.76,
"guinier_rg_error": 0.069,
"pddf_dmax": 25.33,
"pddf_dmax_error": null,
"porod_volume": 501.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 24,
"guinier_point_last": 41,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFG6_datloglog_img.png",
"symmetry": null,
"last_modified": "2022-11-17T09:57:12.570420+01:00",
"bragg_peak": []
}
