{ "code": "SASDFH5", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases.", "publication": { "title": "Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases.", "author_list": "Dos Santos Morais R, Santo PE, Ley M, Schelcher C, Abel Y, Plassart L, Deslignière E, Chagot ME, Quinternet M, Paiva ACF, Hessmann S, Morellet N, M F Sousa P, Vandermoere F, Bertrand E, Charpentier B, Bandeiras TM, Plisson-Chastang C, Verheggen C, Cianférani S, Manival X", "journal": "J Mol Biol", "doi": "10.1016/j.jmb.2022.167760", "pmid": "35901867", "published_date": "2022 Jul 25" }, "status": "released", "submitted_date": "2019-04-15", "released_date": "2022-08-08" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFH5.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFH5.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFH5_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFH5_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFH5_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFH5_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFH5.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Eiger 4M", "resolution": 75.0 }, "name": "SOLEIL", "city": "Saint-Aubin", "country": "France", "beamline_name": "SWING", "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": "Protein DPCD", "short_name": null, "sequence": "GPHMAVTGWLESLRTAQKTALLQDGRRKVHYLFPDGKEMAEEYDEKTSELLVRKWRVKSALGAMGQWQLEVGDPAPLGAGNLGPELIKESNANPIFMRKDTKMSFQWRIRNLPYPKDVYSVSVDQKERCIIVRTTNKKYYKKFSIPDLDRHQLPLDDASLSFAHANCTLIISYQKPKEVVVAESELQKELKKVKTAHSNDGDCKTQ", "organism": "Homo sapiens", "uniprot_code": "Q9BVM2", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "trimer", "molecular_type": "protein", "uniprot_sequence": "MAVTGWLESLRTAQKTALLQDGRRKVHYLFPDGKEMAEEYDEKTSELLVRKWRVKSALGA\nMGQWQLEVGDPAPLGAGNLGPELIKESNANPIFMRKDTKMSFQWRIRNLPYPKDVYSVSV\nDQKERCIIVRTTNKKYYKKFSIPDLDRHQLPLDDALLSFAHANCTLIISYQKPKEVVVAE\nSELQKELKKVKTAHSNDGDCKTQ", "mw": 23.505, "total_mw": 70.515, "number_molecules": 3, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "RuvB-like 1", "short_name": null, "sequence": "MVHHHHHHLVPRGSKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK", "organism": "Homo sapiens", "uniprot_code": "Q9Y265", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "trimer", "molecular_type": "protein", "uniprot_sequence": "MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKK\nMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAI\nGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESL\nQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTL\nHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLF\nVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMI\nIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKIN\nGKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK", "mw": 51.759, "total_mw": 155.277, "number_molecules": 3, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "RuvB-like 2", "short_name": null, "sequence": "MATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEGEVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAMGSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNELKGETMDTSLEVLFQ", "organism": "Homo sapiens", "uniprot_code": "Q9Y230", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "trimer", "molecular_type": "protein", "uniprot_sequence": "MATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVL\nEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALT\nQAFRRSIGVRIKEETEIIEGEVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIE\nSLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAMGSQTKFVQCPDGELQKRKEVVH\nTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDE\nVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTT\nPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTE\nVQVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNELKGETMDTS", "mw": 51.886, "total_mw": 155.658, "number_molecules": 3, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM HEPES, 150 mM NaCl, 1% glycerol, 5 mM TCEP", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "DPCD His-RuvBl1/RuvBl2 hexamer complex", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "France", "full_name": "University of Lorraine", "webpage": "http://welcome.univ-lorraine.fr/" } ], "contributor_name": "Raphael", "contributor_surname": "Dos Santos Morais", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2019-03-21", "storage_temperature": null, "cell_temperature": 15.0, "exposure_time": 1.0, "number_of_frames": 41, "wavelength": 0.1033, "sample_detector_distance": 2.0, "concentration_min": null, "concentration_max": 4.0, "sample_volume": null, "flow_rate": null, "s_min": 0.041, "s_max": 5.782, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFH5_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFH5_fit1_model1.pdb", "model_mw": 479.0, "bead_radius": 2.9, "log": null, "symmetry": null, "comment": null, "user": 427 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFH5_fit1_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.507, "p_value": 0.347397, "fit_residual_plot": "SASDFH5_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFH5_fit1.fir", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFH5_fit2_model1_img.png", "software": "GASBOR", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDFH5_fit2_model1.pdb", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": "P6", "comment": null, "user": 427 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFH5_fit2_fixed_fit_img.png", "software": "GASBOR", "chi_square_value": 1.6, "p_value": 0.1001, "fit_residual_plot": "SASDFH5_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFH5_fit2.fir", "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": "The experimental molecular weight was determined from SEC-RALS/LALS experiment (370 kDa).", "experiment_description": "Synchrotron SAXS data from solutions of the DPCD His-RuvBl1/RuvBl2 hexamer complex in 20 mM HEPES, 150 mM NaCl, 1% glycerol, 5 mM TCEP, pH 7.5 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the SWING beam line at SOLEIL (Saint-Aubin, France) using a Eiger 4M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.1033 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 15°C using the following parameters: Column: BioSEC5-500A (4.6 mm id * 300 mm); Flow rate: 0.3 mL/min; Sample injection concentration: 4 mg/mL; Injection volume: 50 μL. The data were collected through the SEC peak of the protein as a series of 41 x 1 second exposures. Each unsubtracted data frame was normalised to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted. The resulting subtracted frames were scaled and averaged to generate the final SAXS profile displayed in this entry.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 370.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.09084, "pddf_i0_error": null, "guinier_i0": 0.09066, "guinier_i0_error": 5e-05, "pddf_rg": 5.33, "pddf_rg_error": null, "guinier_rg": 5.39, "guinier_rg_error": 0.04, "pddf_dmax": 15.9, "pddf_dmax_error": null, "porod_volume": 856.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 5, "guinier_point_last": 44, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFH5_datloglog_img.png", "symmetry": null, "last_modified": "2022-08-08T12:03:29.471419+02:00", "bragg_peak": [] }