{ "code": "SASDDR9", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Human MICAL1: activation by the small GTPase Rab8 and small-angle X-ray scattering studies on the oligomerization state of MICAL1 and its complex with Rab8.", "publication": { "title": "Human MICAL1: activation by the small GTPase Rab8 and small-angle X-ray scattering studies on the oligomerization state of MICAL1 and its complex with Rab8.", "author_list": "Esposito A, Ventura V, Petoukhov MV, Rai A, Svergun DI, Vanoni MA", "journal": "Protein Sci", "doi": "10.1002/pro.3512", "pmid": "30242933", "published_date": "2018 Sep 22" }, "status": "released", "submitted_date": "2018-07-17", "released_date": "2018-09-25" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDR9.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDR9.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDR9_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDR9_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDR9_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDR9_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDR9.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": "[F-actin]-monooxygenase MICAL1 (monomer)", "short_name": "Mical1", "sequence": "MASPTSTNPAHAHFESFLQAQLCQDVLSSFQELCGALGLEPGGGLPQYHKIKDQLNYWSAKSLW\r\nTKLDKRAGQPVYQQGRACTSTKCLVVGAGPCGLRVAVELALLGARVVLVEKRTKFSRHNVLHLW\r\nPFTIHDLRALGAKKFYGRFCTGTLDHISIRQLQLLLLKVALLLGVEIHWGVTFTGLQPPPRKGS\r\nGWRAQLQPNPPAQLANYEFDVLISAAGGKFVPEGFKVREMRGKLAIGITANFVNGRTVEETQVP\r\nEISGVARIYNQSFFQSLLKATGIDLENIVYYKDDTHYFVMTAKKQCLLRLGVLRQDWPDTNRLL\r\nGSANVVPEALQRFTRAAADFATHGKLGKLEFAQDAHGQPDVSAFDFTSMMRAESSARVQEKHGA\r\nRLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMVKRWAEGAESLEVLAERESLYQLLSQTSP\r\nENMHRNVAQYGLDPATRYPNLNLRAVTPNQVRDLYDVLAKEPVQRNNDKTDTGMPATGSAGTQE\r\nELLRWCQEQTAGYPGVHVSDLSSSWADGLALCALVYRLQPGLLEPSELQGLGALEATAWALKVA\r\nENELGITPVVSAQAVVAGSDPLGLIAYLSHFHSAFKSMAHSPGPVSQASPGTSSAVLFLSKLQR\r\nTLQRSRAKENAEDAGGKKLRLEMEAETPSTEVPPDPEPGVPLTPPSQHQEAGAGDLCALCGEHL\r\nYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDHKKEGSDRGPESP\r\nELPTPSENSMPPGLSTPTASQEGAGPVPDPSQPTRRQIRLSSPERQRLSSLNLTPDPEMEPPPK\r\nPPRSCSALARHALESSFVGWGLPVQSPQALVAMEKEEKESPFSSEEEEEDVPLDSDVEQALQTF\r\nAKTSGTMNNYPTWRRTLLRRAKEEEMKRFCKAQTIQRRLNEIEAALRELEAEGVKLELALRRQS\r\nSSPEQQKKLWVGQLLQLVDKKNSLVAEEAELMITVQELNLEEKQWQLDQELRGYMNREENLKTA\r\nADRQAEDQVLRKLVDLVNQRDALIRFQEERRLSELALGTGAQG", "organism": "Homo sapiens", "uniprot_code": "Q8TDZ2", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MASPTSTNPAHAHFESFLQAQLCQDVLSSFQELCGALGLEPGGGLPQYHKIKDQLNYWSA\nKSLWTKLDKRAGQPVYQQGRACTSTKCLVVGAGPCGLRVAVELALLGARVVLVEKRTKFS\nRHNVLHLWPFTIHDLRALGAKKFYGRFCTGTLDHISIRQLQLLLLKVALLLGVEIHWGVT\nFTGLQPPPRKGSGWRAQLQPNPPAQLANYEFDVLISAAGGKFVPEGFKVREMRGKLAIGI\nTANFVNGRTVEETQVPEISGVARIYNQSFFQSLLKATGIDLENIVYYKDDTHYFVMTAKK\nQCLLRLGVLRQDWPDTNRLLGSANVVPEALQRFTRAAADFATHGKLGKLEFAQDAHGQPD\nVSAFDFTSMMRAESSARVQEKHGARLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMV\nKRWAEGAESLEVLAERESLYQLLSQTSPENMHRNVAQYGLDPATRYPNLNLRAVTPNQVR\nDLYDVLAKEPVQRNNDKTDTGMPATGSAGTQEELLRWCQEQTAGYPGVHVSDLSSSWADG\nLALCALVYRLQPGLLEPSELQGLGALEATAWALKVAENELGITPVVSAQAVVAGSDPLGL\nIAYLSHFHSAFKSMAHSPGPVSQASPGTSSAVLFLSKLQRTLQRSRAKENAEDAGGKKLR\nLEMEAETPSTEVPPDPEPGVPLTPPSQHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRS\nCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDHKAEGSDRGPESPELPTPSENSMPP\nGLSTPTASQEGAGPVPDPSQPTRRQIRLSSPERQRLSSLNLTPDPEMEPPPKPPRSCSAL\nARHALESSFVGWGLPVQSPQALVAMEKEEKESPFSSEEEEEDVPLDSDVEQALQTFAKTS\nGTMNNYPTWRRTLLRRAKEEEMKRFCKAQTIQRRLNEIEAALRELEAEGVKLELALRRQS\nSSPEQQKKLWVGQLLQLVDKKNSLVAEEAELMITVQELNLEEKQWQLDQELRGYMNREEN\nLKTAADRQAEDQVLRKLVDLVNQRDALIRFQEERRLSELALGTGAQG", "mw": 117.93, "total_mw": 117.93, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM sodium phosphate buffer, pH 7.5, 5 % glycerol, 100 mM NaCl, 1 mM EDTA, 1 mM DTT", "concentration_unit": null, "comment": "Mical1", "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "NADPH oxidase (H2O2 producing and [F-actin] oxidizing) MICAL1 (monomer)", "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": "Maxim", "contributor_surname": "Petoukhov", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2017-06-20", "storage_temperature": 23.0, "cell_temperature": 10.0, "exposure_time": 1.0, "number_of_frames": 3600, "wavelength": 0.124, "sample_detector_distance": 3.0, "concentration_min": null, "concentration_max": 10.0, "sample_volume": null, "flow_rate": null, "s_min": 0.061, "s_max": 5.035, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDR9_fit1_model1_img.png", "software": "CORAL", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDR9_fit1_model1.pdb", "model_mw": 117.5, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/cor04.log", "symmetry": null, "comment": null, "user": 102 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDR9_fit1_fit_img.png", "software": "CORAL", "chi_square_value": 1.86, "p_value": 0.0, "fit_residual_plot": "SASDDR9_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDR9_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/cor04.log", "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data, I(s) vs s (where s = 4πsinθ/λ, and 2θ is the scattering angle), were measured from MICAL1 (monomer) using continuous-flow size-exclusion chromatography SAXS (SEC-SAXS) on the EMBL-P12 beam line at the PETRA III storage ring (Hamburg, Germany). Data were collected a using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm. The SEC mobile phase (0.5 ml/min) consisted of 50 mM sodium phosphate buffer, pH 7.5, 5 % glycerol, 100 mM NaCl, 1 mM EDTA, 1 mM DTT, pH 7.5 (23°C). The sample load concentration onto the SEC column was 10 mg/ml (90 µl injection volume). The SAXS data measured from the SEC-elution (sample peak and buffer; 3600 successive 1 s frames) were normalized to the intensity of the transmitted beam and radially averaged. The scattering of an appropriate solvent-blank was subtracted from the sample frames to produce the scaled and averaged data displayed in this entry.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 128.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 128.0, "porod_mw_error": null, "pddf_i0": 17040.0, "pddf_i0_error": null, "guinier_i0": 17075.0, "guinier_i0_error": 12.0, "pddf_rg": 3.659, "pddf_rg_error": null, "guinier_rg": 3.7, "guinier_rg_error": 0.1, "pddf_dmax": 12.13, "pddf_dmax_error": null, "porod_volume": 212.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": null, "guinier_point_last": null, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDDR9_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:56:39.492710+02:00", "bragg_peak": [] }