{ "code": "SASDC82", "status": "Published", "type_of_curve": "Other", "angular_unit": "1/nm", "project": { "title": "A homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover.", "publication": { "title": "A homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover.", "author_list": "Deyaert E, Wauters L, Guaitoli G, Konijnenberg A, Leemans M, Terheyden S, Petrovic A, Gallardo R, Nederveen-Schippers LM, Athanasopoulos PS, Pots H, Van Haastert PJM, Sobott F, Gloeckner CJ, Efremov R, Kortholt A, Versées W", "journal": "Nat Commun", "doi": "10.1038/s41467-017-01103-4", "pmid": "29044096", "published_date": "2017 Oct 18" }, "status": "released", "submitted_date": "2017-03-21", "released_date": "2017-10-20" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDC82.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDC82.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC82_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC82_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC82_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC82_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC82.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "beam_geometry": "", "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": "Rab family protein", "short_name": "CtRoco", "sequence": "MSYYHHHHHHDYDIPTTENLYFQGAMGSMSDLDVIRQIEQELGMQLEPVDKLKWYSKGYKLDKDQRVTAIGLYDCGSDTLDRIIQPLESLKSLSELSLSSNQITDISPLASLNSLSMLWLDRNQITDIAPLASLNSLSMLWLFGNKISDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELSLSGNNISDIAPLESLKSLTELSLSSNQITDIAPLASLKSLTELSLSSNQISDIAPLESLKSLTELQLSRNQISDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELQLSRNQISDIAPLESLNSLSKLWLNGNQITDIAPLASLNSLTELELSSNQITDIAPLASLKSLSTLWLSSNQISDIAPLASLESLSELSLSSNQISDISPLASLNSLTGFDVRRNPIKRLPETITGFDMEILWNDFSSSGFITFFDNPLESPPPEIVKQGKEAVRQYFQSIEEARSKGEALVHLQEIKVHLIGDGMAGKTSLLKQLIGETFDPKESQTHGLNVVTKQAPNIKGLENDDELKECLFHFWDFGGQEIMHASHQFFMTRSSVYMLLLDSRTDSNKHYWLRHIEKYGGKSPVIVVMNKIDENPSYNIEQKKINERFPAIENRFHRISCKNGDGVESIAKSLKSAVLHPDSIYGTPLAPSWIKVKEKLVEATTAQRYLNRTEVEKICNDSGITDPGERKTLLGYLNNLGIVLYFEALDLSEIYVLDPHWVTIGVYRIINSSKTKNGHLNTSALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNLPTQIDNEPEITEGEPLRFIMKYDYLPSTIIPRLMIAMQHQILDRMQWRYGMVLKSQDHEGALAKVVAETKDSTITIAIQGEPRCKREYLSIIWYEIKKINANFTNLDVKEFIPLPGHPDELVEYKELLGLEKMGRDEYVSGKLEKVFSVSKMLDSVISKEERNKERLMGDINIKLENIGNPTIPIHQQVEVNVSQETVQHVENLQGFFENLKADILREAELEIDDPKERKRLANELELAENAITKMDAAVKSGKNKLKPDVKDRLGEFIDNLANENSRLRKGIALVMNGAEKVQKLARYYNNVAPFFDLPSVPPVLLGKEKT", "organism": "Chlorobaculum tepidum", "uniprot_code": "Q8KC98", "uniprot_range_first": 1, "uniprot_range_last": 1102, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MSDLDVIRQIEQELGMQLEPVDKLKWYSKGYKLDKDQRVTAIGLYDCGSDTLDRIIQPLE\nSLKSLSELSLSSNQITDISPLASLNSLSMLWLDRNQITDIAPLASLNSLSMLWLFGNKIS\nDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELSLSGNNISDIAPLESLKSLTELSL\nSSNQITDIAPLASLKSLTELSLSSNQISDIAPLESLKSLTELQLSRNQISDIAPLESLKS\nLTELQLSSNQITDIAPLASLKSLTELQLSRNQISDIAPLESLNSLSKLWLNGNQITDIAP\nLASLNSLTELELSSNQITDIAPLASLKSLSTLWLSSNQISDIAPLASLESLSELSLSSNQ\nISDISPLASLNSLTGFDVRRNPIKRLPETITGFDMEILWNDFSSSGFITFFDNPLESPPP\nEIVKQGKEAVRQYFQSIEEARSKGEALVHLQEIKVHLIGDGMAGKTSLLKQLIGETFDPK\nESQTHGLNVVTKQAPNIKGLENDDELKECLFHFWDFGGQEIMHASHQFFMTRSSVYMLLL\nDSRTDSNKHYWLRHIEKYGGKSPVIVVMNKIDENPSYNIEQKKINERFPAIENRFHRISC\nKNGDGVESIAKSLKSAVLHPDSIYGTPLAPSWIKVKEKLVEATTAQRYLNRTEVEKICND\nSGITDPGERKTLLGYLNNLGIVLYFEALDLSEIYVLDPHWVTIGVYRIINSSKTKNGHLN\nTSALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNL\nPTQIDNEPEITEGEPLRFIMKYDYLPSTIIPRLMIAMQHQILDRMQWRYGMVLKSQDHEG\nALAKVVAETKDSTITIAIQGEPRCKREYLSIIWYEIKKINANFTNLDVKEFIPLPGHPDE\nLVEYKELLGLEKMGRDEYVSGKLEKVFSVSKMLDSVISKEERNKERLMGDINIKLENIGN\nPTIPIHQQVEVNVSQETVQHVENLQGFFENLKADILREAELEIDDPKERKRLANELELAE\nNAITKMDAAVKSGKNKLKPDVKDRLGEFIDNLANENSRLRKGIALVMNGAEKVQKLARYY\nNNVAPFFDLPSVPPVLLGKEKT", "mw": 127.147, "total_mw": 254.294, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM HEPES 150 mM NaCl 5 mM MgCl2 5% Glycerol 1 mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Rab family protein CtRoco nucleotide free", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "VUB", "address": "Pleinlaan 2 1050 Brussel ", "full_name": "Vrije Universiteit Brussel", "webpage": "http://www.vub.ac.be/" } ], "contributor_name": "Egon", "contributor_surname": "Deyaert", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2015-02-16", "storage_temperature": null, "cell_temperature": 25.0, "exposure_time": null, "number_of_frames": 55, "wavelength": 0.099, "sample_detector_distance": null, "concentration_min": 1.0, "concentration_max": 2.0, "sample_volume": null, "flow_rate": null, "s_min": 0.032, "s_max": 4.975, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC82_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5.3", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDC82_fit1_model1.pdb", "model_mw": 283.95, "bead_radius": 5.5, "log": "https://www.sasbdb.org/media/log_files/refine_kEg200J.log", "symmetry": "P2", "comment": "", "user": 98 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC82_fit1_fit_img.png", "software": "DAMMIN", "chi_square_value": 9.3, "p_value": 0.078515, "fit_residual_plot": "SASDC82_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC82_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/refine_eK7rGlo.log", "software_version": "5.3", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "GNOM 4.6", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Rab family protein CtRoco (nucleotide free) in 20 mM HEPES 150 mM NaCl 5 mM MgCl2 5% Glycerol 1 mM DTT, pH 7.5 were collected on the BM29 camera on the storage ring ESRF (Grenoble, France) using a Pilatus 1M detector at a wavelength of λ = 0.099 nm (I(s) vs s, where s = 4πsin θ/λ and 2θ is the scattering angle). Inline SEC-SAXS was employed at 25°C (50 µl injection volume of an 8 mg/ml protein solution on a Bio SEC-3 HPLC column (Agilent, 3 µm 300 Å)). 55 successive frames were collected through the elution peak. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled and averaged to produce the final SAXS data displayed in this entry.", "tags": [], "intensity_unit": null, "experimental_mw": 246.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 259.0, "porod_mw_error": null, "pddf_i0": 125.4, "pddf_i0_error": 0.06, "guinier_i0": 125.13, "guinier_i0_error": 0.0625, "pddf_rg": 5.04, "pddf_rg_error": 0.004, "guinier_rg": 4.98, "guinier_rg_error": 0.004, "pddf_dmax": 18.39, "pddf_dmax_error": null, "porod_volume": 440.41, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 7, "guinier_point_last": 49, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDC82_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }