{"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":[]}