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{
"code": "SASDDT9",
"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/SASDDT9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDT9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDT9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDT9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDT9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDT9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDT9.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
},
{
"long_name": "Ras-related protein 8",
"short_name": "Rab8",
"sequence": "GHMAKKTYDLLFKLLLIGDSGVGKTCVLFRFSDDAFNTTFISTIGIDFKIKTVELQGKKIKLQIWDTAGQERFHTITTSYYRGAMGIMLVYDITNGKSFENISKWLRNIDEHANEDVERMLLGNKCDMDDKRVVPKGKGEQIAREHGIRFFETSAKANINIEKAFLTLAEDILRKTP",
"organism": null,
"uniprot_code": "P61026",
"uniprot_range_first": 1,
"uniprot_range_last": 175,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MAKKTYDLLFKLLLIGDSGVGKTCVLFRFSDDAFNTTFISTIGIDFKIKTVELQGKKIKL\nQIWDTAGQERFHTITTSYYRGAMGIMLVYDITNGKSFENISKWLRNIDEHANEDVERMLL\nGNKCDMDDKRVVPKGKGEQIAREHGIRFFETSAKANINIEKAFLTLAEDILRKTPVKEPN\nSENVDISSGGGVTGWKSKCC",
"mw": 20.171,
"total_mw": 20.171,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Hepes/NaOH, pH 7.5, 50 mM NaCl, 2 mM MgCl2, 2 mM DTT",
"concentration_unit": null,
"comment": "Mical1:Rab8",
"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) in complex with Ras-related protein Rab 8 (MICAL1-Rab8 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": "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": 0.108,
"s_max": 5.035,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDT9_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/SASDDT9_fit1_model1.pdb",
"model_mw": 136.5,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/cor22.log",
"symmetry": null,
"comment": null,
"user": 102
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDT9_fit1_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.28,
"p_value": 0.006548,
"fit_residual_plot": "SASDDT9_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDT9_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/cor22_YM8qp0q.log",
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDT9_fit2_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/SASDDT9_fit2_model1.pdb",
"model_mw": 135.5,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/cor23.log",
"symmetry": null,
"comment": null,
"user": 102
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDT9_fit2_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.39,
"p_value": 0.000409,
"fit_residual_plot": "SASDDT9_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDT9_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/cor23_7l78BXN.log",
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDT9_fit3_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/SASDDT9_fit3_model1.pdb",
"model_mw": 154.8,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 102
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDT9_fit3_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.5,
"p_value": 0.0,
"fit_residual_plot": "SASDDT9_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDT9_fit3.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/cor24_1V5jUEf.log",
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "1:1 Complex between Mical1 and Rab8. Note: The protein in the SAXS experiments is Rab8, however the protein used for modelling is Rab10.",
"experiment_description": "Synchrotron SAXS data, I(s) vs s (where s = 4πsinθ/λ, and 2θ is the scattering angle), were measured from the MICAL1:Rab8 complex 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 20 mM Hepes/NaOH, pH 7.5, 50 mM NaCl, 2 mM MgCl2, 2 mM DTT, pH 7.5 (23°C). The sample load concentration onto the SEC column was 10 mg/ml (75 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": 142.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 142.0,
"porod_mw_error": null,
"pddf_i0": 8764.0,
"pddf_i0_error": null,
"guinier_i0": 8788.0,
"guinier_i0_error": null,
"pddf_rg": 3.637,
"pddf_rg_error": null,
"guinier_rg": 3.7,
"guinier_rg_error": 0.1,
"pddf_dmax": 11.81,
"pddf_dmax_error": null,
"porod_volume": 234.0,
"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": "SASDDT9_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
