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{
"code": "SASDEN8",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "Structural Insights into the Intracellular Region of the Human Magnesium Transport Mediator CNNM4.",
"publication": {
"title": "Structural Insights into the Intracellular Region of the Human Magnesium Transport Mediator CNNM4.",
"author_list": "Giménez-Mascarell P, Oyenarte I, González-Recio I, Fernández-Rodríguez C, Corral-Rodríguez MÁ, Campos-Zarraga I, Simón J, Kostantin E, Hardy S, Díaz Quintana A, Zubillaga Lizeaga M, Merino N, Diercks T, Blanco FJ, Díaz Moreno I, Martínez-Chantar ML, Tremblay ML, Müller D, Siliqi D, Martínez-Cruz LA",
"journal": "Int J Mol Sci",
"doi": "10.3390/ijms20246279",
"pmid": "31842432",
"published_date": "2019 Dec 12"
},
"status": "released",
"submitted_date": "2018-12-06",
"released_date": "2020-01-09"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEN8.dat",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEN8.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEN8_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEN8_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEN8_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEN8_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEN8.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 2M",
"resolution": null
},
"name": "Diamond Light Source",
"city": "Didcot",
"country": "UK",
"beamline_name": "B21",
"beam_geometry": "1 x 5 mm",
"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": "CNNM4_BAT-cNMP-Ctail",
"short_name": "CNNM4_intra",
"sequence": "KEELNMIQGALELRTKTVEDIMTQLQDCFMIRSDAILDFNTMSEIMESGYTRIPVFEDEQSNIVD\r\nILYVKDLAFVDPDDCTPLKTITRFYNHPVHFVFHDTKLDAMLEEFKKGKSHLAIVQKVNN\r\nEGEGDPFYEVLGLVTLEDVIEEIIKSEILDESDMYTDNRSRKRVSEKNKRDFSAFKDADN\r\nELKVKISPQLLLAAHRFLATEVSQFSPSLISEKILLRLLKYPDVIQELKFDEHNKYYARH\r\nYLYTRNKPADYFILILQGKVEVEAGKENMKFETGAFSYYGTMALTSVPSDRSPAHPTPLS\r\nRSASLSYPDRTDVSTAATLAGSSNQFGSSVLGQYISDFSVRALVDLQYIKITRQQYQNGL\r\nLASRMENSPQFPIDGCTTHMENLAEKSELPVVDETTTLLNERNSLLHKASHENAI",
"organism": "Homo sapiens",
"uniprot_code": "Q6P4Q7",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MAPVGGGGRPVGGPARGRLLLAAPVLLVLLWALGARGQGSPQQGTIVGMRLASCNKSCGT\nNPDGIIFVSEGSTVNLRLYGYSLGNISSNLISFTEVDDAETLHKSTSCLELTKDLVVQQL\nVNVSRGNTSGVLVVLTKFLRRSESMKLYALCTRAQPDGPWLKWTDKDSLLFMVEEPGRFL\nPLWLHILLITVLLVLSGIFSGLNLGLMALDPMELRIVQNCGTEKERRYARKIEPIRRKGN\nYLLCSLLLGNVLVNTSLTILLDNLIGSGLMAVASSTIGIVIFGEILPQALCSRHGLAVGA\nNTILLTKFFMLLTFPLSFPISKLLDFFLGQEIRTVYNREKLMEMLKVTEPYNDLVKEELN\nMIQGALELRTKTVEDIMTQLQDCFMIRSDAILDFNTMSEIMESGYTRIPVFEDEQSNIVD\nILYVKDLAFVDPDDCTPLKTITRFYNHPVHFVFHDTKLDAMLEEFKKGKSHLAIVQKVNN\nEGEGDPFYEVLGLVTLEDVIEEIIKSEILDESDMYTDNRSRKRVSEKNKRDFSAFKDADN\nELKVKISPQLLLAAHRFLATEVSQFSPSLISEKILLRLLKYPDVIQELKFDEHNKYYARH\nYLYTRNKPADYFILILQGKVEVEAGKENMKFETGAFSYYGTMALTSVPSDRSPAHPTPLS\nRSASLSYPDRTDVSTAATLAGSSNQFGSSVLGQYISDFSVRALVDLQYIKITRQQYQNGL\nLASRMENSPQFPIDGCTTHMENLAEKSELPVVDETTTLLNERNSLLHKASHENAI",
"mw": 47.861,
"total_mw": 95.722,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Protein tyrosine phosphatase type IVA 1",
"short_name": null,
"sequence": "MARMNRPAPVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEK\r\nEGIHVLDWPFDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALI\r\nEGGMKYEDAVQFIRQKRRGAFNSKQLLYLEKYRPKMRLRFKDSNGHRNNCCIQ",
"organism": "Mus musculus",
"uniprot_code": "Q63739",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MARMNRPAPVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEK\nEGIHVLDWPFDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALI\nEGGMKYEDAVQFIRQKRRGAFNSKQLLYLEKYRPKMRLRFKDSNGHRNNCCIQ",
"mw": 19.815,
"total_mw": 39.63,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "HEPES buffer pH 7.4, 200 mM NaCl , 1mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Intracellular region of the human Cyclin and CBS domain divalent metal cation transport mediator-4 in complex with Phosphatase of Regenerating Liver-1 and MgATP",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Bari, Italy",
"full_name": "CNR - Institute of Crystallography, Bari, Italy",
"webpage": "http://www.ba.ic.cnr.it"
}
],
"contributor_name": "Dritan",
"contributor_surname": "Siliqi",
"orcid": "https://orcid.org/0000-0003-1415-8725"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-09-17",
"storage_temperature": null,
"cell_temperature": 20.0,
"exposure_time": 3.0,
"number_of_frames": 620,
"wavelength": 0.1,
"sample_detector_distance": 4.014,
"concentration_min": null,
"concentration_max": 5.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.075,
"s_max": 2.56,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEN8_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEN8_fit1_model1.pdb",
"model_mw": 114.2,
"bead_radius": 1.9,
"log": null,
"symmetry": "P2",
"comment": null,
"user": 396
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEN8_fit1_fixed_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.51,
"p_value": 0.0,
"fit_residual_plot": "SASDEN8_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEN8_fit1.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEN8_fit2_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "DAMFILT 5.",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEN8_fit2_model1.pdb",
"model_mw": 136.031,
"bead_radius": 3.5,
"log": null,
"symmetry": "P2",
"comment": null,
"user": 396
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEN8_fit2_fixed_fit_img.png",
"software": "GASBOR",
"chi_square_value": 1.26,
"p_value": 2.2e-05,
"fit_residual_plot": "SASDEN8_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEN8_fit2.fir",
"fit_log": null,
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ScÅtter",
"pddf_software_version": "3.1v",
"i0_calibration_standard": null,
"description": "SEC-SAXS was performed at 20°C using the following parameters: Column Shodex KW-403 ; Flow rate: 0.08 mL/min; Total acquisition time: 1860s; Sample injection concentration: 5.0 mg/mL; Injection volume: 45μL.",
"experiment_description": "Synchrotron SAXS data from solutions of the intracellular region of the human cyclin and CBS domain divalent metal cation transport mediator-4 in complex with phosphatase of regenerating Liver-1 and MgATP in HEPES buffer pH 7.4, 200 mM NaCl , 1mM DTT, pH 7.4 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the B21 camera at the Diamond Light Source storage ring (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The data obtained through the sample elution peak (collected as 620 successive 3 second frames) were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the individual subtracted data sets were scaled and averaged to generate the scattering profile displayed in this entry.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 125.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 115.0,
"porod_mw_error": null,
"pddf_i0": 0.03633,
"pddf_i0_error": 0.001778,
"guinier_i0": 0.03598,
"guinier_i0_error": 0.0001853,
"pddf_rg": 4.722,
"pddf_rg_error": 0.255,
"guinier_rg": 4.448,
"guinier_rg_error": 0.143,
"pddf_dmax": 18.3,
"pddf_dmax_error": null,
"porod_volume": 216.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 11,
"guinier_point_last": 92,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEN8_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-01-09T14:41:45.042038+01:00",
"bragg_peak": []
}
