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{
"code": "SASDD88",
"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/SASDD88.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD88.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD88_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD88_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD88_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD88_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDD88.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": "M.tb. LigA BRCT domain (DNA ligase A)",
"short_name": "BRCT",
"sequence": "VDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPGSKYDKAVELGVPILDEDGFRRLLADGPASRT",
"organism": "Mycobacterium tuberculosis",
"uniprot_code": "P9WNV1",
"uniprot_range_first": 601,
"uniprot_range_last": 691,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPE\nLRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLC\nELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLE\nVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGH\nVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVK\nVDEVALQRRLGSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAG\nSTVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPE\nCGSPLAPEKEGDADIRCPNARGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIA\nDEGELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPT\nAARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRM\nVDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPG\nSKYDKAVELGVPILDEDGFRRLLADGPASRT",
"mw": 9.449,
"total_mw": 13.4,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM Tris-HCl 500 mM NaCl 5mM β-mercaptoethanol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "The BRCT domain from Mycobacterium tuberculosis DNA ligase",
"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": "2018-06-02",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 1800.0,
"number_of_frames": 2,
"wavelength": 0.154,
"sample_detector_distance": 0.3171,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.091,
"s_max": 7.368,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD88_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDD88_fit1_model1.pdb",
"model_mw": 9.46,
"bead_radius": 1.3,
"log": null,
"symmetry": "P1",
"comment": null,
"user": 328
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD88_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.43,
"p_value": 0.000494,
"fit_residual_plot": "SASDD88_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD88_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/BRCT_10mg-7.log",
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD88_fit2_model1_img.png",
"software": "Phyre2",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDD88_fit2_model1.pdb",
"model_mw": 9.447,
"bead_radius": null,
"log": null,
"symmetry": "P1",
"comment": null,
"user": 328
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD88_fit2_fixed_fit_img.png",
"software": "FoXS",
"chi_square_value": 4.498358,
"p_value": 0.0,
"fit_residual_plot": "SASDD88_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD88_fit2.fit",
"fit_log": null,
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD88_fit3_model1_img.png",
"software": "elNémo",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDD88_fit3_model1.pdb",
"model_mw": 9.447,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 328
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/2_BRCT_10mg_fixed_fit_img.png",
"software": "FoXS",
"chi_square_value": 2.790025,
"p_value": 0.0,
"fit_residual_plot": "2_BRCT_10mg_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD88_fit3.fit",
"fit_log": null,
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The experimental molecular weight quoted for this entry was evaluated using calibrated size-exclusion chromatography (GE Healthcare Superdex75 10/30 column). The atomistic models displayed in this entry (ribbon format) are a parent Phyre2 protein homology model (top) and one of ten structures obtained from the parent after elNémo normal mode calculations (bottom). Refer to: Kelley et al. (2015) Nature Protocols 10, 845-858; Suhre & Sanejouand (2004) Nucleic Acids Res. 32(Web Server issue): W610–W614.",
"experiment_description": "In house laboratory SAXS data from a solution of the BRCT domain from M. tuberculosis DNA ligase in 50 mM Tris-HCl 500 mM NaCl 5mM β-mercaptoethanol, pH 8 were collected using an Anton Paar SAXSpace instrument at the CSIR-Central Drug Research Institute (Lucknow, India) using a Dectris Mythen 2R1K detector at a sample-detector distance of 0.3 m and at a wavelength of λ = 0.154 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 10.00 mg/ml was measured at 10°C. Two successive 1800 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": 15.3,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 24290.0,
"pddf_i0_error": null,
"guinier_i0": 25148.2,
"guinier_i0_error": 58.86,
"pddf_rg": 1.441,
"pddf_rg_error": null,
"guinier_rg": 1.58,
"guinier_rg_error": 0.02,
"pddf_dmax": 3.73,
"pddf_dmax_error": null,
"porod_volume": 22.59,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 115,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDD88_datloglog_img.png",
"symmetry": null,
"last_modified": "2021-08-18T17:34:34.477729+02:00",
"bragg_peak": []
}
