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{
"code": "SASDGE5",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "The dual PDZ domain from Postsynaptic density protein 95 forms a scaffold with peptide ligand",
"publication": {
"title": "The dual PDZ domain from Postsynaptic density protein 95 forms a scaffold with peptide ligand",
"author_list": "Rodzli N, Lockhart-Cairns M, Levy C, Chipperfield J, Bird L, Baldock C, Prince S",
"journal": "Biophysical Journal",
"doi": "10.1016/j.bpj.2020.06.018",
"pmid": null,
"published_date": "2020 Jun"
},
"status": "released",
"submitted_date": "2019-09-16",
"released_date": "2019-09-20"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDGE5.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDGE5.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGE5_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGE5_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDGE5_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGE5_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDGE5.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"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": "PDZ1-2 fragment of PSD-95/Disks large homolog 4",
"short_name": "PDZ1-2",
"sequence": "GPGTEGEMEYEEITLERGNSGLGFSIAGGTDNPHIGDDPSIFITKIIPGGAAAQDGRLRV\r\nNDSILFVNEVDVREVTHSAAVEALKEAGSIVRLYVMRRKPPAEKVMEIKLIKGPKGLGFS\r\nIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALK\r\nNTYDVVYLKVAKPSNA",
"organism": "Homo sapiens",
"uniprot_code": "P78352",
"uniprot_range_first": 55,
"uniprot_range_last": 249,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MDCLCIVTTKKYRYQDEDTPPLEHSPAHLPNQANSPPVIVNTDTLEAPGYELQVNGTEGE\nMEYEEITLERGNSGLGFSIAGGTDNPHIGDDPSIFITKIIPGGAAAQDGRLRVNDSILFV\nNEVDVREVTHSAAVEALKEAGSIVRLYVMRRKPPAEKVMEIKLIKGPKGLGFSIAGGVGN\nQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKNTYDVVY\nLKVAKPSNAYLSDSYAPPDITTSYSQHLDNEISHSSYLGTDYPTAMTPTSPRRYSPVAKD\nLLGEEDIPREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDQIL\nSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRFEAKIHDLREQLMNSSLGSGT\nASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDASDEEWWQARRVHSDS\nETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYETVTQMEVHYARPIIIL\nGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIE\nAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLE\nINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPA\nRERL",
"mw": 20.8,
"total_mw": 20.8,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM TRIS/HCl, 150 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.5,
"deuteration": null
},
"purity_method": null,
"name": "The PDZ1-2 domain of postsynaptic density protein 95 (PSD-95)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Manchester, UK",
"full_name": "University of Manchester",
"webpage": "http://www.manchester.ac.uk/"
}
],
"contributor_name": "Stephen",
"contributor_surname": "Prince",
"orcid": "https://orcid.org/0000-0003-0929-0254"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2015-06-11",
"storage_temperature": 15.0,
"cell_temperature": 15.0,
"exposure_time": 0.05,
"number_of_frames": 13,
"wavelength": 0.123987,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 15.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.085,
"s_max": 4.799,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGE5_fit1_model1_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDGE5_fit1_model1.pdb",
"model_mw": 20.12,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 486
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGE5_fit1_model2_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDGE5_fit1_model2.pdb",
"model_mw": 19.54,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 486
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGE5_fit1_model3_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDGE5_fit1_model3.pdb",
"model_mw": 19.54,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 486
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGE5_fit1_model4_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDGE5_fit1_model4.pdb",
"model_mw": 39.87,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 486
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDGE5_fit1_model5_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDGE5_fit1_model5.pdb",
"model_mw": 79.74,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 486
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/CON-APO-Jun15-clo_fixed_fit_img.png",
"software": "OLIGOMER",
"chi_square_value": 6.31,
"p_value": 0.0,
"fit_residual_plot": "CON-APO-Jun15-clo_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDGE5_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/oligo_CON-APO-Jun15-clo.log",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "Scattering data are fitted using the ATSAS OLIGOMER program using a suite of models. The ATSAS program FFMAKER was used to generate form factors for each model in the suite. Each model is assigned a volume fraction to fit the observed scattering profile. 3 monomer models are included, the first is a compact conformation of PDZ1-2 similar to PDB entries 6spv/6spz; the other two are domain models obtained from a representative run of the ATSAS EOM program with data projected to infinite dilution. Multimeric models are drawn from a \"clustering Spacegroup\", unit cell 14.8nm symmetry I2(1)3, and consist of identical copies of an extended conformation of PDZ1-2 (similar to PDB entry 3zrt) assembled by symmetry operations. \r\n\r\nIn the order of deposition:\r\n Model number; Stoichiometry; MW (kDa); source; Volume fraction. \r\n 1; 1; 21; Crystal Structure; 0.691.\r\n 2; 1; 21; EOM; 0.237.\r\n 3; 1; 21; EOM; 0.000.\r\n 4; 2; 42; clustering Spacegroup; 0.043.\r\n 5; 4; 84; clustering Spacegroup; 0.030.",
"experiment_description": "Synchrotron SAXS data from solutions of the PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) in 20 mM TRIS/HCl, 150 mM NaCl, pH 8.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123987 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 15.00 mg/ml was measured at 15°C. 13 successive 0.050 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.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 20.8,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 20.0,
"porod_mw_error": null,
"pddf_i0": 19630.0,
"pddf_i0_error": null,
"guinier_i0": 19485.0,
"guinier_i0_error": 17.78,
"pddf_rg": 2.46,
"pddf_rg_error": null,
"guinier_rg": 2.374,
"guinier_rg_error": 0.005,
"pddf_dmax": 9.23,
"pddf_dmax_error": null,
"porod_volume": 32.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 4,
"guinier_point_last": 173,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDGE5_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
