{ "code": "SASDB36", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Structural basis of myelin-associated glycoprotein adhesion and signalling.", "publication": { "title": "Structural basis of myelin-associated glycoprotein adhesion and signalling.", "author_list": "Pronker MF, Lemstra S, Snijder J, Heck AJ, Thies-Weesie DM, Pasterkamp RJ, Janssen BJ", "journal": "Nat Commun", "doi": "10.1038/ncomms13584", "pmid": "27922006", "published_date": "2016 Dec 6" }, "status": "released", "submitted_date": "2016-07-24", "released_date": "2016-12-13" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDB36.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDB36.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB36_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB36_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDB36_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDB36_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDB36.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": "Myelin-associated glycoprotein (20-508; N406Q mutant)", "short_name": "MAG", "sequence": "GHWGAWMPSTISAFEGTCVSIPCRFDFPDELRPAVVHGVWY\r\nFNSPYPKNYPPVVFKSRTQVVHESFQGRSRLLGDLGLRNCTLLLSTLSPELGGKYYFRGD\r\nLGGYNQYTFSEHSVLDIVNTPNIVVPPEVVAGTEVEVSCMVPDNCPELRPELSWLGHEGL\r\nGEPTVLGRLREDEGTWVQVSLLHFVPTREANGHRLGCQAAFPNTTLQFEGYASLDVKYPP\r\nVIVEMNSSVEAIEGSHVSLLCGADSNPPPLLTWMRDGMVLREAVAKSLYLDLEEVTPGED\r\nGVYACLAENAYGQDNRTVELSVMYAPWKPTVNGTVVAVEGETVSILCSTQSNPDPILTIF\r\nKEKQILATVIYESQLQLELPAVTPEDDGEYWCVAENQYGQRATAFQ\r\nLSVEFAPIILLESH\r\nCAAARDTVQCLCVVKSNPEPSVAFELPSRNVTVNETEREFVYSERSGLLLTSILTIRGQA\r\nQAPPRVICTSRNLYGTQSLELPFQGAHR", "organism": "Mus musculus", "uniprot_code": "P20917", "uniprot_range_first": 20, "uniprot_range_last": 508, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MIFLATLPLFWIMISASRGGHWGAWMPSTISAFEGTCVSIPCRFDFPDELRPAVVHGVWY\nFNSPYPKNYPPVVFKSRTQVVHESFQGRSRLLGDLGLRNCTLLLSTLSPELGGKYYFRGD\nLGGYNQYTFSEHSVLDIVNTPNIVVPPEVVAGTEVEVSCMVPDNCPELRPELSWLGHEGL\nGEPTVLGRLREDEGTWVQVSLLHFVPTREANGHRLGCQAAFPNTTLQFEGYASLDVKYPP\nVIVEMNSSVEAIEGSHVSLLCGADSNPPPLLTWMRDGMVLREAVAKSLYLDLEEVTPGED\nGVYACLAENAYGQDNRTVELSVMYAPWKPTVNGTVVAVEGETVSILCSTQSNPDPILTIF\nKEKQILATVIYESQLQLELPAVTPEDDGEYWCVAENQYGQRATAFNLSVEFAPIILLESH\nCAAARDTVQCLCVVKSNPEPSVAFELPSRNVTVNETEREFVYSERSGLLLTSILTIRGQA\nQAPPRVICTSRNLYGTQSLELPFQGAHRLMWAKIGPVGAVVAFAILIAIVCYITQTRRKK\nNVTESSSFSGGDNPHVLYSPEFRISGAPDKYESEKQRLGSERRLLGLRGESPELDLSYSH\nSDLGKRPTKDSYTLTEELAEYAEIRVK", "mw": 53.978, "total_mw": 53.978, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM HEPES 150 mM NaCl", "concentration_unit": "mM", "comment": null, "additive": "150 mM NaCl", "concentration": 20.0, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Glycosylated myelin-associated glycoprotein full extracellular domain (Ig1-5) N406Q mutant", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Utrecht, Netherlands", "full_name": "Utrecht University", "webpage": "http://www.uu.nl/" } ], "contributor_name": "Matti", "contributor_surname": "Pronker", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2016-02-05", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 9, "wavelength": 0.0992, "sample_detector_distance": 2.87, "concentration_min": null, "concentration_max": 2.12, "sample_volume": null, "flow_rate": null, "s_min": 0.033, "s_max": 4.945, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDB36_fit1_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "5lfu", "ext_code": "5LFU", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "atomic", "software_version": "2.8.3", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDB36_fit1_model1.pdb", "model_mw": 112.1, "bead_radius": 1.9, "log": null, "symmetry": "", "comment": "", "user": 52 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDB36_fit1_fit_img.png", "software": null, "chi_square_value": 11.89, "p_value": 0.0, "fit_residual_plot": null, "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDB36_fit1.fit", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "Gnom 4.5a", "i0_calibration_standard": null, "description": "Myelin-associated glycoprotein (MAG) full extracellular domain (immunoglobulin domains 1-5) with an N406Q mutation that should, based on the crystal structure, enhance MAG dimerization by removing an N-linked glycan that clashes with its symmetry mate.", "experiment_description": "Synchrotron SAXS data from solutions of glycosylated myelin-associated glycoprotein (full extracellular domain (Ig1-5) N406Q mutant) in HEPES, pH 7.5 were collected on the BM29 camera on the storage ring ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). One solute concentration of 2.12 mg/ml was measured at 20°C. Nine successive 1 second frames were collected. 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 for protein concentration.", "tags": [], "intensity_unit": null, "experimental_mw": 63.7, "experimental_mw_error": null, "guinier_i0_mw": 82.0, "guinier_i0_mw_error": null, "porod_mw": 112.74, "porod_mw_error": null, "pddf_i0": 82.23, "pddf_i0_error": null, "guinier_i0": 82.0, "guinier_i0_error": null, "pddf_rg": 7.6, "pddf_rg_error": null, "guinier_rg": 7.3, "guinier_rg_error": null, "pddf_dmax": 25.6, "pddf_dmax_error": null, "porod_volume": 193.23, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 13, "guinier_point_last": 27, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDB36_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }