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{
"code": "SASDEX3",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair.",
"publication": {
"title": "M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair.",
"author_list": "Khanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R",
"journal": "Nucleic Acids Res",
"doi": "10.1093/nar/gkaa188",
"pmid": "32232338",
"published_date": "2020 Mar 30"
},
"status": "released",
"submitted_date": "2018-09-06",
"released_date": "2019-05-28"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEX3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEX3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEX3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEX3.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": "DNA ligase A",
"short_name": "MtbLigA",
"sequence": "VSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAGSTVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPECGSPLAPEKEGDADIRCPNARGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIADEGELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPTAARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRMVDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPGSKYDKAVELGVPILDEDGFRRLLADGPASRT 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": 76.079,
"total_mw": 76.079,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Probable exodeoxyribonuclease III protein XthA",
"short_name": "MtbXthA",
"sequence": "MPDGTIDGGHPQRPASPRLRSPLLRLATWNVNSIRTRLDRVLDWLGRADVDVLAMQETKCPDGQFPALPLFELGYDVAHVGFDQWNGVAIASRVGLDDVRVGFDGQPSWSGKPEVAATTEARALGATCGGIRVWSLYVPNGRALDDPHYTYKLDWLAALRDTAEGWLRDDPAAPIALMGDWNIAPTDDDVWSTEFFAGCTHVSEPERKAFNAIVDAQFTDVVRPFTPGPGVYTYWDYTQLRFPKKQGMRIDFILGSPALAARVMDAQIVREERKGKAPSDHAPVLVDLHAG HHHHHH",
"organism": "Mycobacterium tuberculosis",
"uniprot_code": "A0A0T9L251",
"uniprot_range_first": 1,
"uniprot_range_last": 291,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 32.931,
"total_mw": 32.931,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Nicked DNA",
"short_name": null,
"sequence": "GGTAGATCAGTGTCTATGTATGTCAG",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 8.136,
"total_mw": 8.136,
"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": "DNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III protein (MtbXthA) in presence of nicked ds DNA",
"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": "2017-05-13",
"storage_temperature": 4.0,
"cell_temperature": 10.0,
"exposure_time": 1.0,
"number_of_frames": 10,
"wavelength": 0.081,
"sample_detector_distance": 1.1,
"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/SASDEX3_fit1_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "DAMFILT",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEX3_fit1_model1.pdb",
"model_mw": null,
"bead_radius": 3.75,
"log": "https://www.sasbdb.org/media/log_files/sub_001-2.log",
"symmetry": "P1",
"comment": null,
"user": 328
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEX3_fit1_model2_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "dammif",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEX3_fit1_model2.pdb",
"model_mw": null,
"bead_radius": 6.1,
"log": "https://www.sasbdb.org/media/log_files/sub_001-2_aRM4xYd.log",
"symmetry": "P1",
"comment": null,
"user": 328
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEX3_fit1_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.811,
"p_value": 0.13775,
"fit_residual_plot": "SASDEX3_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEX3_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/sub_001-2.log",
"software_version": null,
"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 DNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III protein (MtbXthA) in presence of nicked ds DNA in 50 mM Tris-HCl 200 mM NaCl 2mM β-mercaptoethanol (BME), pH 8 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Dectris Pilatus 1M detector at a sample-detector distance of 1.1 m and at a wavelength of λ = 0.081 nm (l(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": 136.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 8.318,
"pddf_i0_error": null,
"guinier_i0": 8.15,
"guinier_i0_error": 0.073,
"pddf_rg": 4.788,
"pddf_rg_error": null,
"guinier_rg": 4.52,
"guinier_rg_error": 0.45,
"pddf_dmax": 17.06,
"pddf_dmax_error": null,
"porod_volume": 117.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 25,
"guinier_point_last": 55,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEX3_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-13T15:35:02.586842+02:00",
"bragg_peak": []
}
