{ "code": "SASDG84", "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/SASDG84.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDG84.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG84_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG84_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDG84_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG84_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDG84.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-2", "short_name": "Cyth2, ARNO", "sequence": "MGHHHHHHGSEDGVYEPPDLTPEERMELENIRRRKQELLVEIQRLREELSEAMSEVEGLEANEGSKTLQRNRKMA\r\nMGRKKFNMDPKKGIQFLVEHELLQNTPEEIARFLYKGEGLNKTAIGDYLGEREELNLSVLHAFVDLHEFTDLNLVQA\r\nLRQFLWSFRLPGEAQKIDRMMEAFAQRYCLCNPGVFQSTDTCYVLSFAVIMLNTSLHNPNVRDKPGL\r\nERFVAMNRGINEGGDLPEDLLRNLYDSIRNEPFKIPEDDGNDLTHTFFNPDREGWLLKLGGGRVKTWKRR\r\nWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVDDPRKPNCFELYIPNNKGQLIKACKTEADGRVVEGN\r\nHMVYRISAPTQEEKDEWIKSIQAAVSVDPFYEMLAARKKRISVKKKQEQP", "organism": "Mus musculus", "uniprot_code": "P63034", "uniprot_range_first": 2, "uniprot_range_last": 400, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MEDGVYEPPDLTPEERMELENIRRRKQELLVEIQRLREELSEAMSEVEGLEANEGSKTLQ\nRNRKMAMGRKKFNMDPKKGIQFLVEHELLQNTPEEIARFLYKGEGLNKTAIGDYLGEREE\nLNLSVLHAFVDLHEFTDLNLVQALRQFLWSFRLPGEAQKIDRMMEAFAQRYCLCNPGVFQ\nSTDTCYVLSFAVIMLNTSLHNPNVRDKPGLERFVAMNRGINEGGDLPEDLLRNLYDSIRN\nEPFKIPEDDGNDLTHTFFNPDREGWLLKLAGGRVKTWKRRWFILTDNCLYYFEYTTDKEP\nRGIIPLENLSIREVDDPRKPNCFELYIPNNKGQLIKACKTEADGRVVEGNHMVYRISAPT\nQEEKDEWIKSIQAAVSVDPFYEMLAARKKRISVKKKQEQP", "mw": 47.595, "total_mw": 95.19, "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": "Autoinhibited dimer of truncated 6xHis Cytohesin-2 (ARNO, amino acids 2-400) with Inositol 1,3,4,5-tetrakis phosphate (DAMMIF, GASBOR and antiparallel CORAL 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": 121, "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/SASDG84_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "dammif (r9988)", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDG84_fit1_model1.pdb", "model_mw": 63.7, "bead_radius": 3.0, "log": "https://www.sasbdb.org/media/log_files/dammif-15_8Xedsc6.log", "symmetry": "P1", "comment": "Most representative of 100 DAMMIF models", "user": 241 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG84_fit1_model2_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "DAMFILT 5.0 (r9988)", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDG84_fit1_model2.pdb", "model_mw": 116.672, "bead_radius": 4.25, "log": null, "symmetry": "P1", "comment": "Filtered average of 10 filtered averages of 10 DAMMIF models", "user": 241 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG84_fit1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.219, "p_value": 0.127961, "fit_residual_plot": "SASDG84_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG84_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/dammif-15_mGKquP2.log", "software_version": "r9988", "description": "Fit for most representative of 100 DAMMIF models" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG84_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/SASDG84_fit2_model1.pdb", "model_mw": null, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/gasbor30.log", "symmetry": "P1", "comment": "Most representative of 100 GASBOR models", "user": 241 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG84_fit2_model2_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "DAMFILT 5.0 (r9988)", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDG84_fit2_model2.pdb", "model_mw": 96.566, "bead_radius": 3.75, "log": null, "symmetry": "P1", "comment": "Filtered average of 10 filtered averages of 10 GASBOR models", "user": 241 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG84_fit2_fixed_fit_img.png", "software": "GASBOR", "chi_square_value": 1.3, "p_value": 0.001891, "fit_residual_plot": "SASDG84_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG84_fit2.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/gasbor30.log", "software_version": "2.3i", "description": "Fit for most representative of 100 GASBOR models" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG84_fit3_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/SASDG84_fit3_model1.pdb", "model_mw": 96.05, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/coral_ThUF6NM.log", "symmetry": "P1", "comment": "Derived from Grp1 63-399 (2R09) and a canonical antiparallel coiled coil", "user": 241 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG84_fit3_fixed_fit_img.png", "software": "CORAL", "chi_square_value": 1.29, "p_value": 0.003841, "fit_residual_plot": "SASDG84_fit3_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG84_fit3.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/coral_tQqVMgw.log", "software_version": "CORAL05", "description": "Fit for CORAL model derived from Grp1 63-399 (2R09) and canonical antiparallel 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 autoinhibited dimer Cytohesin-2 (ARNO, amino acids 2-400) 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": 95.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 1.037, "pddf_i0_error": 0.004, "guinier_i0": 1.03, "guinier_i0_error": 0.002, "pddf_rg": 5.6, "pddf_rg_error": 0.13, "guinier_rg": 5.3, "guinier_rg_error": 0.04, "pddf_dmax": 27.0, "pddf_dmax_error": 0.1, "porod_volume": 180.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 19, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDG84_datloglog_img.png", "symmetry": null, "last_modified": "2024-10-17T15:36:29.094582+02:00", "bragg_peak": [] }