{ "code": "SASDEP4", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2.", "publication": { "title": "Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2.", "author_list": "Pádua RAP, Sun Y, Marko I, Pitsawong W, Stiller JB, Otten R, Kern D", "journal": "Nat Commun", "doi": "10.1038/s41467-018-06814-w", "pmid": "30375376", "published_date": "2018 Oct 30" }, "status": "released", "submitted_date": "2018-09-14", "released_date": "2018-11-05" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEP4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEP4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEP4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEP4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEP4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEP4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEP4.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Rayonix MX225-HE", "resolution": null }, "name": "Stanford Synchrotron Radiation Lightsource (SSRL)", "city": "Menlo Park, CA", "country": "USA", "beamline_name": "BL4-2", "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": "Tyrosine-protein phosphatase non-receptor type 11 E76K", "short_name": "SHP2 E76K", "sequence": "GSGMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTG\r\nDYYDLYGGEKFATLAKLVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGK\r\nEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYD\r\nVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETT\r\nDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEP\r\nVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEV\r\nERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHF\r\nRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIR\r\nEKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRI", "organism": "Homo sapiens", "uniprot_code": "Q06124", "uniprot_range_first": 1, "uniprot_range_last": 529, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTG\nDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGK\nEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYD\nVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETT\nDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEP\nVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEV\nERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHF\nRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIR\nEKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGH\nEYTNIKYSLADQTSGDQSPLPPCTPTPPCAEMREDSARVYENVGLMQQQKSFR", "mw": 60.911, "total_mw": 60.911, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM ADA, 2 mM TCEP", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 6.5, "deuteration": null }, "purity_method": null, "name": "Protein tyrosine phosphatase SHP2 with E76K activating mutation", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Chevy Chase, USA", "full_name": "Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University", "webpage": "https://www.hhmi.org/" } ], "contributor_name": "RIcardo", "contributor_surname": "Padua", "orcid": "https://orcid.org/0000-0001-9719-3440" } ], "concentration_method": null, "concentration_unit": null, "date": "2016-03-28", "storage_temperature": 4.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 10, "wavelength": 0.1127, "sample_detector_distance": 1.65, "concentration_min": 0.76, "concentration_max": 12.2, "sample_volume": null, "flow_rate": null, "s_min": 0.141, "s_max": 3.5, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEP4_fit1_model1_img.png", "software": "AllosMod", "pdb_link": [ { "pdb_code": "6cmq", "ext_code": "6CMQ", "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/SASDEP4_fit1_model1.pdb", "model_mw": 60.91, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 367 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/multi_state_model_88pdb_fitfoxs_img.png", "software": "MultiFoXS", "chi_square_value": 2.535761, "p_value": 0.0, "fit_residual_plot": "multi_state_model_88pdb_fitfoxsresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEP4_fit1.dat", "fit_log": null, "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Protein tyrosine phosphatase SHP2 with E76K activating mutation in 50 mM ADA, 2 mM TCEP, pH 6.5 were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL; Stanford, CA, USA) using a Rayonix MX225-HE detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.1127 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.8 and 12.2 mg/ml were measured at 20°C. 10 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 53.15, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 143.3, "pddf_i0_error": null, "guinier_i0": 142.7, "guinier_i0_error": 0.44, "pddf_rg": 2.95, "pddf_rg_error": null, "guinier_rg": 2.91, "guinier_rg_error": 0.062, "pddf_dmax": 9.53, "pddf_dmax_error": null, "porod_volume": null, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 2, "guinier_point_last": 34, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEP4_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }