{ "code": "SASDB65", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Global Disordering in Stereo-Specific Protein Association", "publication": { "title": "Global Disordering in Stereo-Specific Protein Association", "author_list": "Gupta A, Reinartz I, Spilotros A, Jonna V, Hofer A, Svergun D, Schug A, Wolf-Watz M", "journal": "Biophysical Journal", "doi": "10.1016/j.bpj.2016.11.211", "pmid": null, "published_date": "2017 Feb" }, "status": "released", "submitted_date": "2016-08-12", "released_date": "2017-04-21" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDB65.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDB65.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB65_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB65_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDB65_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB65_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDB65.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "PETRA III", "city": "DESY; Hamburg", "country": "Germany", "beamline_name": "EMBL P12", "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": "SycH putative yopH targeting protein", "short_name": "SycH", "sequence": "MRTYSSLLEEFATELGLEEIETNELGHGAVTIDKIWVVHLAPINEKELVAFMRAGILTGQSQLYDILRKNLFSPLSGVIRCALDKDDHWLLWSQLNINDTSGTQLASVLTSLVDKAVTLSCEPTMKKEEDDHRPSSSHLLV", "organism": "Yersinia pseudotuberculosis", "uniprot_code": "I3NIC8", "uniprot_range_first": 1, "uniprot_range_last": 141, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MRTYSSLLEEFATELGLEEIETNELGHGAVTIDKIWVVHLAPINEKELVAFMRAGILTGQ\nSQLYDILRKNLFSPLSGVIRCALDKDDHWLLWSQLNINDTSGTQLASVLTSLVDKAVTLS\nCEPTMKKEEDDHRPSSSHLLV", "mw": 15.763, "total_mw": 31.526, "number_molecules": 2, "complex_state": null, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Tyrosine-protein phosphatase YopH", "short_name": "YopH", "sequence": "MNLSLSDLHRQVSRLVQQESGDCTGKLRGNVAANKETTFQGLTIASGARESEKVFAQTVLSHVANVVLTQEDTAKLLQST\r\nVKHNLNNYDLRSVGNGNSVLVSLRSDQMTLQDAKVLLEAALRQESGARG", "organism": "Yersinia pseudotuberculosis", "uniprot_code": "P08538", "uniprot_range_first": 1, "uniprot_range_last": 129, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MNLSLSDLHRQVSRLVQQESGDCTGKLRGNVAANKETTFQGLTIASGARESEKVFAQTVL\nSHVANVVLTQEDTAKLLQSTVKHNLNNYDLRSVGNGNSVLVSLRSDQMTLQDAKVLLEAA\nLRQESGARGHVSSHSHSALHAPGTPVREGLRSHLDPRTPPLPPRERPHTSGHHGAGEARA\nTAPSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCCRQTAV\nRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPD\nYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAV\nSSEVTKALASLVDQTAETKRNMYESKGSSAVGDDSKLRPVIHCRAGVGRTAQLIGAMCMN\nDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS", "mw": 13.95, "total_mw": 13.95, "number_molecules": 1, "complex_state": null, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM HEPES 2mM TCEP", "concentration_unit": "mM", "comment": null, "additive": "2mM TCEP", "concentration": 50.0, "pka": null, "ph": 6.8, "deuteration": null }, "purity_method": null, "name": "Tyrosine-protein phosphatase (YopH)/putative yopH targeting protein (SycH) heterotrimeric complex", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "EMBL-Hamburg", "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany", "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation", "webpage": "http://www.embl-hamburg.de/index.php" } ], "contributor_name": "Alessandro", "contributor_surname": "Spilotros", "orcid": null } ], "concentration_method": null, "concentration_unit": "mg/ml", "date": "2016-08-01", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 0.05, "number_of_frames": 20, "wavelength": 0.12, "sample_detector_distance": 3.1, "concentration_min": null, "concentration_max": 1.0, "sample_volume": null, "flow_rate": null, "s_min": 0.066, "s_max": 4.808, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB65_fit1_model1_img.png", "software": "CRYSOL", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDB65_fit1_model1.pdb", "model_mw": 45.45, "bead_radius": 1.9, "log": null, "symmetry": "", "comment": "", "user": 109 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB65_fit1_fit_img.png", "software": null, "chi_square_value": 1.27, "p_value": 0.0, "fit_residual_plot": "fit4columns464_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDB65_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": null, "experiment_description": "X-ray synchrotron radiation scattering data from a solution of dimeric YopH protein in complex with the tyrosine-protein phosphatase, SycH, in 50 mM HEPES, 2 mM TCEP, pH 6.8 were collected on the P12 beam line of Petra-III (Hamburg, Germany) using a Pilatus 2M detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.12 nm). One solute concentration of 1.00 mg/ml was measured using an exposure time of 1 s (recorded as 20 x 0.050 s frames). The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering from the matched solvent-blank was subtracted. The data were scaled to protein concentration. The results presented here were obtained from a single concentration scattering curve.", "tags": [], "intensity_unit": null, "experimental_mw": 52.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 55.8, "porod_mw_error": null, "pddf_i0": 74550.0, "pddf_i0_error": 130.0, "guinier_i0": 74475.0, "guinier_i0_error": 117.0, "pddf_rg": 3.01, "pddf_rg_error": 0.013, "guinier_rg": 2.96, "guinier_rg_error": 0.13, "pddf_dmax": 12.5, "pddf_dmax_error": null, "porod_volume": 89.2, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 22, "guinier_point_last": 115, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDB65_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:56:39.492710+02:00", "bragg_peak": [] }