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{
"code": "SASDFH6",
"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/SASDFH6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFH6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFH6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFH6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFH6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFH6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFH6.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": "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": "MSSPDADQTA PEVLRQWQAL AEEVREHQFR YYVRDAPIIS DAEFDELLRR \r\n \r\nLEALEEQHPE LRTPDSPTQL VGGAGFATDF EPVDHLERML SLDNAFTADE \r\n \r\nLAAWAGRIHA EVGDAAHYLC ELKIDGVALS LVYREGRLTR ASTRGDGRTG \r\n\r\nEDVTLNARTI ADVPERLTPG DDYPVPEVLE VRGEVFFRLD DFQALNASLV \r\n \r\nEEGKAPFANP RNSAAGSLRQ KDPAVTARRR LRMICHGLGH VEGFRPATLH \r\n \r\nQAYLALRAWG LPVSEHTTLA TDLAGVRERI DYWGEHRHEV DHEIDGVVVK \r\n \r\nVDEVALQRRL GSTSRAPRWA IAYKYPPEEA QTKLLDIRVN VGRTGRITPF \r\n \r\nAFMTPVKVAG STVGQATLHN ASEIKRKGVL IGDTVVIRKA GDVIPEVLGP \r\n \r\nVVELRDGSER EFIMPTTCPE CGSPLAPEKE GDADIRCPNA RGCPGQLRER \r\n \r\nVFHVASRNGL DIEVLGYEAG VALLQAKVIA DEGELFALTE RDLLRTDLFR \r\n \r\nTKAGELSANG KRLLVNLDKA KAAPLWRVLV ALSIRHVGPT AARALATEFG \r\n \r\nSLDAIAAAST DQLAAVEGVG PTIAAAVTEW FAVDWHREIV DKWRAAGVRM \r\n \r\nVDERDESVPR TLAGLTIVVT GSLTGFSRDD AKEAIVARGG KAAGSVSKKT \r\n \r\nNYVVAGDSPG SKYDKAVELG VPILDEDGFR RLLADGPASR T HHHHHH",
"organism": "Mycobacterium tuberculosis",
"uniprot_code": "P9WNV1",
"uniprot_range_first": null,
"uniprot_range_last": null,
"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
},
{
"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": "DNA ligase A nicked DNA substrate",
"short_name": null,
"sequence": "GGTAGATCAGTGTCTATGTATGTCAG",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 8.1,
"total_mw": 16.2,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM Tris pH 8.0, 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 in the presence of DNA substrate",
"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": 2.5,
"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/SASDFH6_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/SASDFH6_fit1_model1.pdb",
"model_mw": null,
"bead_radius": 5.25,
"log": null,
"symmetry": null,
"comment": null,
"user": 328
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFH6_fit1_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.761,
"p_value": 0.063504,
"fit_residual_plot": "SASDFH6_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFH6_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/complex_424_sub_XBLDB.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 is severely aggregated.",
"experiment_description": "Synchrotron SAXS data from solutions of the XthA, sliding beta clamp, DNA ligase-A tricomplex with DNA substrate in 50 mM Tris pH 8.0, 200 mM NaCl , 2 mM β-mercaptoethanol, 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 2.50 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": 214.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 133.0,
"pddf_i0_error": null,
"guinier_i0": 136.9,
"guinier_i0_error": 8.0,
"pddf_rg": 5.818,
"pddf_rg_error": null,
"guinier_rg": 5.76,
"guinier_rg_error": 0.33,
"pddf_dmax": 19.13,
"pddf_dmax_error": null,
"porod_volume": 496.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 38,
"guinier_point_last": 43,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFH6_datloglog_img.png",
"symmetry": null,
"last_modified": "2022-11-17T09:57:12.695739+01:00",
"bragg_peak": []
}
