{
"code": "SASDCH9",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "The GDP-switched GAF domain of DcpA modulates the concerted synthesis/hydrolysis of c-di-GMP in Mycobacterium smegmatis.",
"publication": {
"title": "The GDP-switched GAF domain of DcpA modulates the concerted synthesis/hydrolysis of c-di-GMP in Mycobacterium smegmatis.",
"author_list": "Chen HJ, Li N, Luo Y, Jiang YL, Zhou CZ, Chen Y, Li Q",
"journal": "Biochem J",
"doi": "10.1042/BCJ20180079",
"pmid": "29555845",
"published_date": "2018 Apr 9"
},
"status": "released",
"submitted_date": "2017-11-23",
"released_date": "2018-09-05"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCH9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCH9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCH9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCH9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCH9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCH9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCH9.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "Shanghai Synchrotron Radiation Facility (SSRF)",
"city": "Shanghai",
"country": "China",
"beamline_name": "BL19U2",
"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": "Sensory box/response regulator",
"short_name": null,
"sequence": "MGHHHHHHM\r\nMSESLDVLVTSVATQLMAVEAATSVSVSQQVLAELVSFFDVDVSFLRHNDHRAHATRLVAEWPPRPVDAATDPIAVVHFADADPVFAMAEHLKEPAVFRPEPLYDDYQRTIEAGRHIPATSMACVPLLSGDVTTGVLGFVKFGDREWLPAELNALKAIASLFAQVQARIEAEERLRYLADHDHLTGLYNRRALMAHLEARLAPGQPGPVAVMFFDLDRLKAINDYLGHTAGDAFISILAQRLQRGDDAPKLIARLGGDEFVVVPDDPMSLDEATALAYRLQSVLRERVTVDGEMLTRTVSIGIAQGIPGKDSTSDVLNRADHAVLTAKGSGGNRVAVFSDAMAMEIDFRNDIELHLQSVIEGGALVLHYLPEIDMRTGEVLAAEALVRWEHPTRGLLSPDSFIGVAESINLAGELGRWVLRTACAEFSRWRANGVGRNIVLRINVSPVQLVTDGFVESVAGIMKEFGLPRGSVCLEITESVVVQDIETTRTTLTGLHNVGVQVAIDDFGTGYSVLSLLKSLPVDTLKIDRSFVAELGSNPGDLPIVRAVIALAGAFGLQLVAEGVETERAALTLLRHGCYRAQGFLLSKPILGSEMQTLLAKGRVPVHFSAAPRM",
"organism": "Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)",
"uniprot_code": "A0QUG3",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MSESLDVLVTSVATQLMAVEAATSVSVSQQVLAELVSFFDVDVSFLRHNDHRAHATRLVA\nEWPPRPVDAATDPIAVVHFADADPVFAMAEHLKEPAVFRPEPLYDDYQRTIEAGRHIPAT\nSMACVPLLSGDVTTGVLGFVKFGDREWLPAELNALKAIASLFAQVQARIEAEERLRYLAD\nHDHLTGLYNRRALMAHLEARLAPGQPGPVAVMFFDLDRLKAINDYLGHTAGDAFISILAQ\nRLQRGDDAPKLIARLGGDEFVVVPDDPMSLDEATALAYRLQSVLRERVTVDGEMLTRTVS\nIGIAQGIPGKDSTSDVLNRADHAVLTAKGSGGNRVAVFSDAMAMEIDFRNDIELHLQSVI\nEGGALVLHYLPEIDMRTGEVLAAEALVRWEHPTRGLLSPDSFIGVAESINLAGELGRWVL\nRTACAEFSRWRANGVGRNIVLRINVSPVQLVTDGFVESVAGIMKEFGLPRGSVCLEITES\nVVVQDIETTRTTLTGLHNVGVQVAIDDFGTGYSVLSLLKSLPVDTLKIDRSFVAELGSNP\nGDLPIVRAVIALAGAFGLQLVAEGVETERAALTLLRHGCYRAQGFLLSKPILGSEMQTLL\nAKGRVPVHFSAAPRM",
"mw": 67.758,
"total_mw": 135.516,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM HEPES, 100 mM NaCl, 5% glycerol, 2 mM MgCl2",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Bifunctional enzyme responsible for the synthesis and hydrolysis of c-di-GMP (DcpA) with GDP",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Shanghai, China",
"full_name": "National Center for Protein Science Shanghai",
"webpage": "http://www.sibcb-ncpss.org"
}
],
"contributor_name": "Na",
"contributor_surname": "LI",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-06-26",
"storage_temperature": 4.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 20,
"wavelength": 0.103,
"sample_detector_distance": 2.25,
"concentration_min": null,
"concentration_max": 5.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.082,
"s_max": 2.971,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCH9_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "4rnh",
"ext_code": "4RNH",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCH9_fit1_model1.pdb",
"model_mw": 129.3,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": null,
"user": 254
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCH9_fit1_fit_img.png",
"software": "CORAL",
"chi_square_value": 2.54,
"p_value": 1.7e-05,
"fit_residual_plot": "SASDCH9_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCH9_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/4RNH7.log",
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCH9_fit2_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/SASDCH9_fit2_model1.pdb",
"model_mw": 455.207,
"bead_radius": 4.5,
"log": null,
"symmetry": "P1",
"comment": null,
"user": 254
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCH9_fit2_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 4.837,
"p_value": 0.0,
"fit_residual_plot": "SASDCH9_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCH9_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/10.log",
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of bifunctional enzyme responsible for the synthesis and hydrolysis of c-di-GMP (DcpA) with GDP in 20 mM HEPES, 100 mM NaCl, 5% glycerol, 2 mM MgCl2, pH 7.5, were collected on the BL19U2 beam line at the Shanghai Synchrotron Radiation Facility (SSRF; Shanghai, China) using a Pilatus 1M detector at a sample-detector distance of 2.3 m and at a wavelength of λ = 0.103 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). One solute concentration of 5.00 mg/ml was measured at 20°C. 20 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 and the different curves were scaled for protein concentration.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 156.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 157.0,
"porod_mw_error": null,
"pddf_i0": 336.4,
"pddf_i0_error": 0.4,
"guinier_i0": 337.3,
"guinier_i0_error": 7.23,
"pddf_rg": 5.16,
"pddf_rg_error": 0.01,
"guinier_rg": 5.01,
"guinier_rg_error": 0.01,
"pddf_dmax": 20.0,
"pddf_dmax_error": null,
"porod_volume": 298.9,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 16,
"guinier_point_last": 30,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCH9_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}