{ "code": "SASDA89", "status": "Published", "type_of_curve": "Other", "angular_unit": "1/nm", "project": { "title": "Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.", "publication": { "title": "Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.", "author_list": "Felix J, Kandiah E, De Munck S, Bloch Y, van Zundert GC, Pauwels K, Dansercoer A, Novanska K, Read RJ, Bonvin AM, Vergauwen B, Verstraete K, Gutsche I, Savvides SN", "journal": "Nat Commun", "doi": "10.1038/ncomms13228", "pmid": "27819269", "published_date": "2016 Nov 7" }, "status": "released", "submitted_date": "2015-08-07", "released_date": "2016-12-16" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDA89.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDA89.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA89_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA89_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDA89_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA89_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDA89.sascif", "experiment": { "instrument": { "detector": { "type": "CCD", "name": "AVIEX PCCD170170", "resolution": null }, "name": "SOLEIL", "city": "Saint-Aubin", "country": "France", "beamline_name": "SWING", "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": "GM-CSF/IL-2 inhibition factor", "short_name": null, "sequence": "MACLRVFLAVLALCGSVHSAQWIGERDFCTAHAQDVFARLQVWMRIDRNVTAADNSSACALAIETPPSNFDADVYVAAAGINVSVSAINCGFFNMRQVETTYNTARRQMYVYMDSWDPWVIDDPQPLFSQEYENETLPYLLEVLELARLYIRVGCTVPGEQPFEVIPGIDYPHTGMEFLQHVLRPNRRFAPAKLHMDLEVDHRCVSAVHVKAFLQDACSARKARTPLYFAGHGCNHPDRRPKNPVPRPQHVSSPISRKCSMQTAR", "organism": "Orf virus", "uniprot_code": "Q9J5U5", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "tetramer", "molecular_type": "protein", "uniprot_sequence": "MACLRVFLAVLALCGSVHSAQWIGERDFCTAHAQDVFARLQVWMRIDRNVTAADNSSACA\nLAIETPPSNFDADVYVAAAGINVSVSAINCGFFNMRQVETTYNTARRQMYVYMDSWDPWV\nIDDPQPLFSQEYENETLPYLLEVLELARLYIRVGCTVPGEQPFEVIPGIDYPHTGMEFLQ\nHVLRPNRRFAPAKLHMDLEVDHRCVSAVHVKAFLQDACSARKARTPLYFAGHGCNHPDRR\nPKNPVPRPQHVSSPISRKCSMQTAR", "mw": 29.924, "total_mw": 119.696, "number_molecules": 4, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Granulocyte-macrophage colony-stimulating factor", "short_name": null, "sequence": "APTRQPSPVTRPWQHVDAIKEALSLLNDSTDTAAVMDETVEVVSEMFDSQEPTCLQTRLE\r\nLYKQGLRGSLTSLTGSLTMMASHYKKHCPPTQETSCETQIITFKSFKENLKDFLFIIPFD\r\nCWEPVQK", "organism": "Ovis aries", "uniprot_code": "P28773", "uniprot_range_first": 18, "uniprot_range_last": 144, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MWLQNLLLLGTVVCSFSAPTRQPSPVTRPWQHVDAIKEALSLLNDSTDTAAVMDETVEVV\nSEMFDSQEPTCLQTRLELYKQGLRGSLTSLTGSLTMMASHYKKHCPPTQETSCETQIITF\nKSFKENLKDFLFIIPFDCWEPVQK", "mw": 14.411, "total_mw": 28.823, "number_molecules": 2, "complex_state": true, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM HEPES 150 mM NaCl", "concentration_unit": "mM", "comment": null, "additive": "150 mM NaCl", "concentration": 20.0, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": "SEC-SAXS", "name": "Complex between ovine GM-CSF and GM-CSF/IL-2 inhibition factor", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [], "contributor_name": "Jan", "contributor_surname": "Felix", "orcid": null } ], "concentration_method": null, "concentration_unit": "mg/ml", "date": "2014-09-10", "storage_temperature": null, "cell_temperature": 20.0, "exposure_time": null, "number_of_frames": 16, "wavelength": 0.1, "sample_detector_distance": 1.82, "concentration_min": null, "concentration_max": 9.7, "sample_volume": null, "flow_rate": null, "s_min": 0.076, "s_max": 5.496, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SAXS_MODEL_GIF_GMCSF_img.png", "software": "FoXS", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDA89_fit1_model1.pdb", "model_mw": 102.1, "bead_radius": 1.9, "log": null, "symmetry": "", "comment": "", "user": 29 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDA89_fit1_fit_img.png", "software": null, "chi_square_value": 99.0, "p_value": 0.0, "fit_residual_plot": "SASDA89_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDA89_fit1.fit", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": null, "i0_calibration_standard": null, "description": "Modeling of SAXS data: The crystal structure of the GIF:oGM-CSF complex was used as an input for the Allosmod-FoXS web server to model missing loops, N- and C-termini and N-linked glycosylation. During each Allosmod-FoXS run, data up to a scattering angle of 0.5 Å-1 was used. Fits to the experimental SAXS data were calculated using the FoXS software.", "experiment_description": "X-ray synchrotron radiation scattering data from solutions of the complex between GM-CSF/IL-2 inhibition factor and ovine Granulocyte-macrophage colony-stimulating factor in 20 mM HEPES 150 mM NaCl were collected on the SWING camera on the storage ring SOLEIL (Saint-Aubin, France) using a CCD AVIEX detector (I(s) vs s, where s = 4π sin θ/λ, where 2θ is the scattering angle). One solute concentration of 10 mg/ml was measured. 10 successive 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. The purity of the sample was obtained via SEC-SAXS.", "tags": [], "intensity_unit": null, "experimental_mw": 153.0, "experimental_mw_error": null, "guinier_i0_mw": 153.0, "guinier_i0_mw_error": null, "porod_mw": 144.0, "porod_mw_error": null, "pddf_i0": 0.1494, "pddf_i0_error": null, "guinier_i0": 0.151381, "guinier_i0_error": 0.0001, "pddf_rg": 3.77, "pddf_rg_error": null, "guinier_rg": 3.79, "guinier_rg_error": 0.13, "pddf_dmax": 12.4, "pddf_dmax_error": null, "porod_volume": 231.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 17, "guinier_point_last": 47, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDA89_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }