{
"code": "SASDBC9",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/A",
"project": {
"title": "Structural and biochemical analysis of Escherichia coli ObgE, a central regulator of bacterial persistence.",
"publication": {
"title": "Structural and biochemical analysis of Escherichia coli ObgE, a central regulator of bacterial persistence.",
"author_list": "Gkekas S, Singh RK, Shkumatov AV, Messens J, Fauvart M, Verstraeten N, Michiels J, Versées W",
"journal": "J Biol Chem",
"doi": "10.1074/jbc.M116.761809",
"pmid": "28223358",
"published_date": "2017 Apr 7"
},
"status": "released",
"submitted_date": "2016-09-28",
"released_date": "2017-02-23"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBC9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBC9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBC9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBC9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBC9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBC9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBC9.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 100K",
"resolution": 172.0
},
"name": null,
"city": "Brussels",
"country": "Belgium",
"beamline_name": "Rigaku BioSAXS-2000",
"beam_geometry": "",
"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": "GTPase ObgE/CgtA",
"short_name": "ObgE_340",
"sequence": "MGSSHHHHHHSSGLVPRGSHMKFVDEASILVVAGDGGNGCVSFRREKYIPKGGPDGGDGGDGGDVWMEADENLNTLIDYR\r\nFEKSFRAERGQNGASRDCTGKRGKDVTIKVPVGTRVIDQGTGETMGDMTKHGQRLLVAKGGWHGLGNTRFKSSVNRTPRQ\r\nKTNGTPGDKRELLLELMLLADVGMLGMPNAGKSTFIRAVSAAKPKVADYPFTTLVPSLGVVRMDNEKSFVVADIPGLIEG\r\nAAEGAGLGIRFLKHLERCRVLLHLIDIDPIDGTDPVENARIIISELELYSQDLATKPRWLVFNKIDLLDKVEAEEKAKAI\r\nAEALGWEDKYYLISAASGLGVKDLCWDVMTFIIENPVA",
"organism": "Escherichia coli",
"uniprot_code": "P42641",
"uniprot_range_first": 1,
"uniprot_range_last": 340,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MKFVDEASILVVAGDGGNGCVSFRREKYIPKGGPDGGDGGDGGDVWMEADENLNTLIDYR\nFEKSFRAERGQNGASRDCTGKRGKDVTIKVPVGTRVIDQGTGETMGDMTKHGQRLLVAKG\nGWHGLGNTRFKSSVNRTPRQKTNGTPGDKRELLLELMLLADVGMLGMPNAGKSTFIRAVS\nAAKPKVADYPFTTLVPSLGVVRMDNEKSFVVADIPGLIEGAAEGAGLGIRFLKHLERCRV\nLLHLIDIDPIDGTDPVENARIIISELEKYSQDLATKPRWLVFNKIDLLDKVEAEEKAKAI\nAEALGWEDKYYLISAASGLGVKDLCWDVMTFIIENPVVQAEEAKQPEKVEFMWDDYHRQQ\nLEEIAEEDDEDWDDDWDEDDEEGVEFIYKR",
"mw": 38.899,
"total_mw": 38.899,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Hepes, 300 mM NaCl, 250 mM imidazole, 5 mM MgCl2, 2 mM DTT, 400 uM GDP",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "GDP bound form of C-terminal deletion mutant of ObgE from E.coli (ObgE_340 with GDP)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "VUB",
"address": "Pleinlaan 2 1050 Brussel ",
"full_name": "Vrije Universiteit Brussel",
"webpage": "http://www.vub.ac.be/"
}
],
"contributor_name": "Alexander",
"contributor_surname": "Shkumatov",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2015-02-01",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 1800.0,
"number_of_frames": 3,
"wavelength": 1.54,
"sample_detector_distance": 1.0,
"concentration_min": 1.0,
"concentration_max": 8.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.08,
"s_max": 6.829,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBC9_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "v2.7.2",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBC9_fit1_model1.pdb",
"model_mw": 37.72,
"bead_radius": 2.5,
"log": "https://www.sasbdb.org/media/log_files/refine-1.pdb",
"symmetry": "P1",
"comment": "Average model generated by DAMAVER and used as a starting model for refinement with DAMMIN (r7897M)",
"user": 104
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBC9_fit1_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 0.606,
"p_value": 0.531,
"fit_residual_plot": "SASDBC9_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBC9_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/refine_xwNoevO.log",
"software_version": "v2.7.2",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM v4.6",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "SAXS data collected from solutions of the GDP bound form of the C-terminal deletion mutant of ObgE from E.coli (ObgE_340 with GDP) in 20 mM HEPES, 300 mM NaCl, 250 mM imidazole, 5 mM MgCl2, 2 mM DTT, 400 µM GDP, pH 7.5, were collected at the Rigaku BioSAXS-2000 instrument\r\nusing a CCD detector at a sample-detector distance of 1.0 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Data collection was performed at at 10°C at four different concentrations of 1, 2, 4 and 8 mg/ml with 30 min exposure each intermittent by reference buffer. Rigaku SAXSLab was used for data reduction. \r\nThe sample protein includes an N-terminal poly-histidine tag. Data was merged using PRIMUS from ATSAS package.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 39.1,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 41.5,
"porod_mw_error": null,
"pddf_i0": 1.04,
"pddf_i0_error": 0.01,
"guinier_i0": 1.01,
"guinier_i0_error": 0.01,
"pddf_rg": 3.17,
"pddf_rg_error": 0.4,
"guinier_rg": 2.95,
"guinier_rg_error": 0.04,
"pddf_dmax": 11.0,
"pddf_dmax_error": 1.0,
"porod_volume": 70673.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 14,
"guinier_point_last": 26,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBC9_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}