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{
"code": "SASDGC4",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes.",
"publication": {
"title": "Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes.",
"author_list": "Das S, Malaby AW, Nawrotek A, Zhang W, Zeghouf M, Maslen S, Skehel M, Chakravarthy S, Irving TC, Bilsel O, Cherfils J, Lambright DG",
"journal": "Structure",
"doi": "10.1016/j.str.2019.09.007",
"pmid": "31601460",
"published_date": "2019 Oct 5"
},
"status": "released",
"submitted_date": "2019-08-17",
"released_date": "2019-09-16"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDGC4.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDGC4.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGC4_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGC4_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDGC4_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGC4_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDGC4.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "MAR 165 CCD",
"resolution": null
},
"name": "Advanced Photon Source (APS), Argonne National Laboratory",
"city": "Lemont, IL",
"country": "USA",
"beamline_name": "BioCAT 18ID",
"beam_geometry": null,
"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": "Cytohesin-3",
"short_name": "Cyth3, Grp1",
"sequence": "MGHHHHHHGSEDLSLEEREELLDIRRRKKELIDDIERLKYEIAEVMTEIDNLTSVEESKTTQRNKQI\r\nAMGRKKFNMDPKKGIQFLIENDLLQSSPEDVAQFLYKGEGLNKTVIGDYLGERDDFNIKVLQAFVELHEF\r\nADLNLVQALRQFLWSFRLPGEAQKIDRMMEAFASRYCLCNPGVFQSTDTCYVLSFAIIMLNTSLHNHNVR\r\nDKPTAERFITMNRGINEGGDLPEELLRNLYESIKNEPFKIPEDDGNDLTHTFFNPDREGWLLKLGGRVKT\r\nWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSHKGQVIKACKTEADGRV\r\nVEGNHVVYRISAPSPEEKEEWMKSIKASISRDPFYDMLAT",
"organism": "Mus musculus",
"uniprot_code": "O08967",
"uniprot_range_first": 14,
"uniprot_range_last": 390,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MDEGGGGEGGSVPEDLSLEEREELLDIRRRKKELIDDIERLKYEIAEVMTEIDNLTSVEE\nSKTTQRNKQIAMGRKKFNMDPKKGIQFLIENDLLQSSPEDVAQFLYKGEGLNKTVIGDYL\nGERDDFNIKVLQAFVELHEFADLNLVQALRQFLWSFRLPGEAQKIDRMMEAFASRYCLCN\nPGVFQSTDTCYVLSFAIIMLNTSLHNHNVRDKPTAERFITMNRGINEGGDLPEELLRNLY\nESIKNEPFKIPEDDGNDLTHTFFNPDREGWLLKLGGRVKTWKRRWFILTDNCLYYFEYTT\nDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSHKGQVIKACKTEADGRVVEGNHVVYRI\nSAPSPEEKEEWMKSIKASISRDPFYDMLATRKRRIANKK",
"mw": 45.153,
"total_mw": 90.306,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, 5% glycerol, 0.001 mM insitol 1,3,4,5-tetrakis phosphate",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Active dimer of truncated 6xHis Cytohesin-3 (Grp1, amino acids 14-390) with Inositol 1,3,4,5-tetrakis phosphate (parallel CORAL and MultiFoXS models)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "UMASS",
"address": "Worcester, MA, USA",
"full_name": "UMASS Medical School",
"webpage": "https://www.umassmed.edu/"
}
],
"contributor_name": "David",
"contributor_surname": "Lambright",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2013-11-15",
"storage_temperature": null,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 126,
"wavelength": 0.10332,
"sample_detector_distance": 2.5,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": 100.0,
"flow_rate": 0.25,
"s_min": 0.069,
"s_max": 3.162,
"total_exposure_time": null,
"seccolumn": 14
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGC4_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "2r09",
"ext_code": "2R09",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDGC4_fit1_model1.pdb",
"model_mw": 93.27,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/coral_3pitWPF.log",
"symmetry": "P1",
"comment": "Derived from Grp1 63-399 (2R09) and a canonical parallel coiled coil",
"user": 241
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDGC4_fit1_fixed_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.44,
"p_value": 0.015784,
"fit_residual_plot": "SASDGC4_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDGC4_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/coral_0yjy3Yd.log",
"software_version": "CORAL05",
"description": "Fit for CORAL model derived from Grp1 63-399 (2R09) and a canonical parallel coiled coil"
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGC4_fit2_model1_img.png",
"software": "MultiFoXS",
"pdb_link": [
{
"pdb_code": "2r09",
"ext_code": "2R09",
"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/SASDGC4_fit2_model1.pdb",
"model_mw": 91.5,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/ensembles_size_4.txt",
"symmetry": "P1",
"comment": "Derived from Grp1 63-399 (2R09) and a canonical parallel coiled coil",
"user": 241
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGC4_fit2_model2_img.png",
"software": "MultiFoXS",
"pdb_link": [
{
"pdb_code": "2r09",
"ext_code": "2R09",
"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/SASDGC4_fit2_model2.pdb",
"model_mw": 91.5,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/ensembles_size_4_VZjOKFq.txt",
"symmetry": "P1",
"comment": "Derived from Grp1 63-399 (2R09) and a canonical parallel coiled coil",
"user": 241
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGC4_fit2_model3_img.png",
"software": "MultiFoXS",
"pdb_link": [
{
"pdb_code": "2r09",
"ext_code": "2R09",
"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/SASDGC4_fit2_model3.pdb",
"model_mw": 91.5,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/ensembles_size_4_lI0K7MU.txt",
"symmetry": "P1",
"comment": "Derived from Grp1 63-399 (2R09) and a canonical parallel coiled coil",
"user": 241
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGC4_fit2_model4_img.png",
"software": "MultiFoXS",
"pdb_link": [
{
"pdb_code": "2r09",
"ext_code": "2R09",
"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/SASDGC4_fit2_model4.pdb",
"model_mw": 91.5,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/ensembles_size_4_fsHShcZ.txt",
"symmetry": "P1",
"comment": "Derived from Grp1 63-399 (2R09) and a canonical parallel coiled coil",
"user": 241
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDGC4_fit2_fitfoxs_img.png",
"software": "MultiFoXS",
"chi_square_value": 1.157454,
"p_value": 0.064794,
"fit_residual_plot": "SASDGC4_fit2_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDGC4_fit2.dat",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/ensembles_size_4.txt",
"software_version": null,
"description": "Fit for MultiFoXS ensemble with 4 models derived from Grp1 63-399 (2R09) and a canonical parallel coiled coil"
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The protein was equilibrated with a 1.2 molar excess of inositol 1,3,4,5-tetrakis phosphate (IP4) and concentrated to 10 mg/ml prior to injection.",
"experiment_description": "Synchrotron SAXS data from solutions of the active dimer of Cytohesin-3 (Grp1, amino acids 14-390) in 20 mM Tris, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, 5% glycerol, 0.001 mM insitol 1,3,4,5-tetrakis phosphate, pH 8 were collected on the BioCAT 18ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA) using a MAR 165 CCD detector at a sample-detector distance of 2.5 m and at a wavelength of λ = 0.10332 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 100.00 μl sample at 10 mg/ml was injected at a 0.25 ml/min flow rate onto a GE Superdex 200 Increase 3.2/300 column at 20°C. SAXS data sets were acquired with 1 s exposures at 5 s intervals during the elution. Raw SAXS images were radially averaged on a log scale over the s range 0.0621-3.33 nm-1 and normalized by the incident beam intensity. The protein scattering profile was reconstructed by singular value decomposition and linear combination (SVD-LC) as described in Malaby et al. (2015) Methods for analysis of size-exclusion chromatography-small angle X-ray scattering and reconstruction of protein scattering. J Appl Crystallogr 48: 1102-1113.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 86.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 1.03,
"pddf_i0_error": 0.005,
"guinier_i0": 1.02,
"guinier_i0_error": 0.002,
"pddf_rg": 5.43,
"pddf_rg_error": 0.14,
"guinier_rg": 5.06,
"guinier_rg_error": 0.04,
"pddf_dmax": 25.7,
"pddf_dmax_error": 0.1,
"porod_volume": 168.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 20,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDGC4_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-10-17T15:36:28.837973+02:00",
"bragg_peak": []
}
