{ "code": "SASDBL4", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system.", "publication": { "title": "Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system.", "author_list": "Gleditzsch D, Müller-Esparza H, Pausch P, Sharma K, Dwarakanath S, Urlaub H, Bange G, Randau L", "journal": "Nucleic Acids Res", "doi": "10.1093/nar/gkw469", "pmid": "27216815", "published_date": "2016 Jul 8" }, "status": "released", "submitted_date": "2016-03-18", "released_date": "2016-09-01" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBL4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBL4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBL4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBL4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBL4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBL4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBL4.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": "Cas6f: CRISPR/Cas Type I-F Cascade component (CRISPR-associated protein, Csy4 family)", "short_name": "Cas6f", "sequence": "MNSYIDIRLKPDAEMREAELSSKVFTKFHKALVTLNSHKIGISFPQMKLSLGQLFRIHGDASLLHDLQGLDWLGPLAGYCQVTAVSAVPDHVQYRIVSVKRSNLSKAKLKRLIARGSIDKDGEKRYKVKMLGQGFDNPYLDLFSSSTGQVYRKFFEFSDIQAHPLDGEFDSYGLSKTATVPWF", "organism": "Shewanella putrefaciens", "uniprot_code": "A4Y6G3", "uniprot_range_first": 1, "uniprot_range_last": 183, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MNSYIDIRLKPDAEMREAELSSKVFTKFHKALVTLNSHKIGISFPQMKLSLGQLFRIHGD\nASLLHDLQGLDWLGPLAGYCQVTAVSAVPDHVQYRIVSVKRSNLSKAKLKRLIARGSIDK\nDGEKRYKVKMLGQGFDNPYLDLFSSSTGQVYRKFFEFSDIQAHPLDGEFDSYGLSKTATV\nPWF", "mw": 20.674, "total_mw": 20.674, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Cas5fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1822)", "short_name": "Cas5fv", "sequence": "MKIIIEYDSCWRNAFLGGSNNEPVPKKGREFLGSMTSLKKEGNFKVCENTLDTVMGVLNRLIGDQRKLYQARSKMYESAYYFEALEDKVSFIDKPQLTNEISFIRNMNGSTDQNAFTGMIKVSDPVFTSEYSQQFWGVLALDFTQLCDFIIKQSQVVGSIELNPLSIINRLESLNQEKALENSDDLAQVLKVLNEYFPDIEYLNNKGLITPISIYCSALYLQLARLETSFNMTTAKTKAGGISGISKRGFTKKDFMDRYTTGPKKTIWGNPFIKKEKIKGQGEVTSMMTKASGQLEISIDVDRDKAQEIKILIENAGVSSFYLGKKGLAYVSNIKL", "organism": "Shewanella putrefaciens", "uniprot_code": "A4Y6G2", "uniprot_range_first": 1, "uniprot_range_last": 336, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MKIIIEYDSCWRNAFLGGSNNEPVPKKGREFLGSMTSLKKEGNFKVCENTLDTVMGVLNR\nLIGDQRKLYQARSKMYESAYYFEALEDKVSFIDKPQLTNEISFIRNMNGSTDQNAFTGMI\nKVSDPVFTSEYSQQFWGVLALDFTQLCDFIIKQSQVVGSIELNPLSIINRLESLNQEKAL\nENSDDLAQVLKVLNEYFPDIEYLNNKGLITPISIYCSALYLQLARLETSFNMTTAKTKAG\nGISGISKRGFTKKDFMDRYTTGPKKTIWGNPFIKKEKIKGQGEVTSMMTKASGQLEISID\nVDRDKAQEIKILIENAGVSSFYLGKKGLAYVSNIKL", "mw": 37.861, "total_mw": 37.861, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Hexameric Cas7fv: CRISPR/Cas Type I-F Cascade component (Uncharacterized protein, Sputcn32_1821)", "short_name": "Cas7fv-hexamer", "sequence": "MGSSHHHHHHSQNPMQKVTGIKSVDFKIKALGHGVVNWNGPTTLTGDDGKTVDNHTLPKLRGYTNLTGKVKDETGYKYKKQATDINFKETPLYISQNCIRHHLFREQAFDLHYASDKNLKNVLASITGLIRGYVVPSSQCKRTSPLLLEDFVDQLGNGNFEQYGQAGARDSTSFFSKTTFGDTEYISYGSISIEQLQFISLDKKFDRAAMVIKEGEGEVIAAELQNYIQSLNPSLNPQAIFHSNYVRRGTIFEEGECGILLNDDAVKALVAETLERLANLSIRQAKGYMYVDDITVDYNDSHKMMRIKRDESEIINEQHAPFAQYFYAK\r\n", "organism": "Shewanella putrefaciens", "uniprot_code": "A4Y6G1", "uniprot_range_first": 1, "uniprot_range_last": 315, "oligomerization": "hexamer", "molecular_type": "protein", "uniprot_sequence": "MQKVTGIKSVDFKIKALGHGVVNWNGPTTLTGDDGKTVDNHTLPKLRGYTNLTGKVKDET\nGYKYKKQATDINFKETPLYISQNCIRHHLFREQAFDLHYASDKNLKNVLASITGLIRGYV\nVPSSQCKRTSPLLLEDFVDQLGNGNFEQYGQAGARDSTSFFSKTTFGDTEYISYGSISIE\nQLQFISLDKKFDRAAMVIKEGEGEVIAAELQNYIQSLNPSLNPQAIFHSNYVRRGTIFEE\nGECGILLNDDAVKALVAETLERLANLSIRQAKGYMYVDDITVDYNDSHKMMRIKRDESEI\nINEQHAPFAQYFYAK", "mw": 37.168, "total_mw": 223.01, "number_molecules": 6, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "wildtype-crRNA: CRISPR/Cas Type I-F Cascade component", "short_name": "wildtype-crRNA", "sequence": "CUUAGAAAUAUCGCCCAGCAAGACGCGCAAACCUAUAACCGUUCACCGCCGCACAGGCGG", "organism": null, "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "RNA", "uniprot_sequence": null, "mw": 19.29, "total_mw": 19.29, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM HEPES 150 mM NaCl 1mM DTT 1mM EDTA", "concentration_unit": "mM", "comment": null, "additive": "150 mM NaCl, 1mM DTT, 1mM EDTA", "concentration": 50.0, "pka": null, "ph": 7.0, "deuteration": null }, "purity_method": null, "name": "The 1:1:6:1 crRNA:Cas6f:Cas7fv:Cas5fv CRISPR/Cas Type I-F wild-type Cascade complex", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Marburg, Germany", "full_name": "University of Marburg", "webpage": "http://www.uni-marburg.de/" } ], "contributor_name": "Patrick", "contributor_surname": "Pausch", "orcid": null } ], "concentration_method": null, "concentration_unit": "mg/ml", "date": "2015-06-27", "storage_temperature": 4.0, "cell_temperature": 4.0, "exposure_time": 1.0, "number_of_frames": 10, "wavelength": 0.93, "sample_detector_distance": 2.43, "concentration_min": null, "concentration_max": 20.0, "sample_volume": null, "flow_rate": null, "s_min": 0.033, "s_max": 4.934, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBL4_fit1_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBL4_fit1_model1.pdb", "model_mw": null, "bead_radius": 3.8, "log": null, "symmetry": "", "comment": "", "user": 118 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBL4_fit1_fit_img.png", "software": null, "chi_square_value": 2.37, "p_value": 0.0003, "fit_residual_plot": "SASDBL4_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBL4_fit1.fir", "fit_log": null, "software_version": null, "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBL4_fit2_model1_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBL4_fit2_model1.pdb", "model_mw": null, "bead_radius": 4.75, "log": null, "symmetry": "", "comment": "", "user": 118 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBL4_fit2_fit_img.png", "software": null, "chi_square_value": 2.18, "p_value": 0.0003, "fit_residual_plot": "SASDBL4_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBL4_fit2.fir", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": null, "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of the 1:1:6:1 crRNA:Cas6f:Cas7fv:Cas5fv CRISPR/Cas Type I-F Cascade complex in 50 mM HEPES 150 mM NaCl, 1mM DTT, 1mM EDTA, pH 7 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 2M detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.124 nm). The data displayed in this entry were measured from one sample at a solute concentration of 20 mg/ml using an exposure time of 10 s (collected as 10 x 1 s frames). The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering from the matched solvent-blank was subtracted. The data were normalized to protein concentration. ", "tags": [], "intensity_unit": null, "experimental_mw": 225.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 160.4, "pddf_i0_error": 0.06, "guinier_i0": 160.6, "guinier_i0_error": 0.1, "pddf_rg": 5.44, "pddf_rg_error": 0.03, "guinier_rg": 5.43, "guinier_rg_error": 0.06, "pddf_dmax": 18.4, "pddf_dmax_error": null, "porod_volume": null, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 11, "guinier_point_last": 34, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDBL4_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }