{
"code": "SASDEC6",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis\n NAD +\n -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity",
"publication": {
"title": "Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis\n NAD +\n -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity",
"author_list": "Afsar M, Shukla A, Kumar N, Ramachandran R",
"journal": "Acta Crystallographica Section D Structural Biology",
"doi": "10.1107/S2059798321003107",
"pmid": null,
"published_date": "2021 May 14"
},
"status": "released",
"submitted_date": "2019-09-05",
"released_date": "2021-05-18"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEC6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEC6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEC6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEC6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEC6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEC6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEC6.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": "DNA ligase A",
"short_name": null,
"sequence": "VSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPELRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLCELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLEVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGHVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVKVDEVALQRRLGSTSRAPRWAIAYKYPPEHHHHHH",
"organism": "Mycobacterium tuberculosis",
"uniprot_code": "P9WNV1",
"uniprot_range_first": 2,
"uniprot_range_last": 328,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MSSPDADQTAPEVLRQWQALAEEVREHQFRYYVRDAPIISDAEFDELLRRLEALEEQHPE\nLRTPDSPTQLVGGAGFATDFEPVDHLERMLSLDNAFTADELAAWAGRIHAEVGDAAHYLC\nELKIDGVALSLVYREGRLTRASTRGDGRTGEDVTLNARTIADVPERLTPGDDYPVPEVLE\nVRGEVFFRLDDFQALNASLVEEGKAPFANPRNSAAGSLRQKDPAVTARRRLRMICHGLGH\nVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRHEVDHEIDGVVVK\nVDEVALQRRLGSTSRAPRWAIAYKYPPEEAQTKLLDIRVNVGRTGRITPFAFMTPVKVAG\nSTVGQATLHNASEIKRKGVLIGDTVVIRKAGDVIPEVLGPVVELRDGSEREFIMPTTCPE\nCGSPLAPEKEGDADIRCPNARGCPGQLRERVFHVASRNGLDIEVLGYEAGVALLQAKVIA\nDEGELFALTERDLLRTDLFRTKAGELSANGKRLLVNLDKAKAAPLWRVLVALSIRHVGPT\nAARALATEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRM\nVDERDESVPRTLAGLTIVVTGSLTGFSRDDAKEAIVARGGKAAGSVSKKTNYVVAGDSPG\nSKYDKAVELGVPILDEDGFRRLLADGPASRT",
"mw": 37.519,
"total_mw": 37.519,
"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": "Adenylation Domain of DNA ligase A with NAD+",
"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": "2018-10-06",
"storage_temperature": 4.0,
"cell_temperature": 10.0,
"exposure_time": 1800.0,
"number_of_frames": 3,
"wavelength": 0.154,
"sample_detector_distance": 0.3,
"concentration_min": null,
"concentration_max": 10.8,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.104,
"s_max": 6.0,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEC6_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEC6_fit1_model1.pdb",
"model_mw": 46.8,
"bead_radius": 2.2,
"log": null,
"symmetry": "P1",
"comment": null,
"user": 328
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEC6_fit1_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 0.328,
"p_value": 0.001009,
"fit_residual_plot": "SASDEC6_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEC6_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/R4withNAD_001FramesAveraged_000_Process_Q_Transformation_Process_1-10.log",
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEC6_fit2_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/SASDEC6_fit2_model1.pdb",
"model_mw": null,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/R4withNA_2.log",
"symmetry": null,
"comment": null,
"user": 328
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEC6_fit2_fixed_fit_img.png",
"software": "GASBOR",
"chi_square_value": 0.29,
"p_value": 6.2e-05,
"fit_residual_plot": "SASDEC6_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEC6_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/R4withNA_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": "SAXS data from solutions of the adenylation Domain of DNA ligase A with NAD+, in 50 mM Tris-HCl, 200 mM NaCl, 2mM β-mercaptoethanol, pH 8 were collected on the Anton Paar SAXSpace instrument at the CSIR-Central Drug Research Institute storage ring (Lucknow, India) using a Hybrid Photon Counting (HPC) Mythen2 R 1K 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 10.80 mg/ml was measured at 10°C. Three 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": 38.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 59.0,
"porod_mw_error": null,
"pddf_i0": 595300.0,
"pddf_i0_error": null,
"guinier_i0": 599573.0,
"guinier_i0_error": 22300.0,
"pddf_rg": 2.345,
"pddf_rg_error": null,
"guinier_rg": 2.37,
"guinier_rg_error": 0.13,
"pddf_dmax": 6.17,
"pddf_dmax_error": null,
"porod_volume": 94.26,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 26,
"guinier_point_last": 70,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEC6_datloglog_img.png",
"symmetry": null,
"last_modified": "2021-05-18T08:48:35.422747+02:00",
"bragg_peak": []
}