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{
"code": "SASDVX3",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Structural characterization of pH-modulated closed and open states in a pentameric ligand-gated ion channel",
"publication": null,
"status": "released",
"submitted_date": "2024-06-28",
"released_date": "2025-02-25"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVX3.dat",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVX3.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVX3_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVX3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVX3_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVX3_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVX3.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "128 linear sensitive multidetector",
"name": "Reuter-Stokes 3He",
"resolution": 0.8
},
"name": "Institut Laue-Langevin (ILL)",
"city": "Grenoble",
"country": "France",
"beamline_name": "D22",
"beam_geometry": null,
"type_of_source": "neutron source",
"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": "Neurotransmitter-gated ion-channel ligand-binding domain-containing protein",
"short_name": "DeCLIC",
"sequence": "RGSAAATEGRVQHFTGYIEDGRGIFYSLPDMKQGDIIYASMQNTGGNLDPLVGIMAEEIDPAVSLGQVLEKALASENDLISELTAVADRIFLGWDDDGGKGYSASLEFTIPRDGTYHIFAGSTITNQRLDKFQPTYTTGSFQLILGLNAPQVISGEGEPEGEVFASLASLEIKPEAHVQELEIRLDKDTRYLTQHTRNLQPGDTFHALVEPIGEAPLPRLRLTDSGGKPLAFGLIDQPGESVELNYTCDQDICELVVHVDGTDGQKDSGEAVYRLLVGINAPNLRESGQTPVGSSVFLESDLVTVGLAVDQIVGVDQRSENFSVVGTLKLSWHDPKLGFSPDQCGCTVKSFEDASIRAVAGEINLPLPSFSFYNQQGNRWSQNQVIFVTPDGRASYFERFTVTLQAPDFDFLAYPFDRQKFSIKVDLAVPTNMFIFNEIERFQQVVGDQLGEEEWVVTSYSQEITEVPFERGSTNSRFTTTLLVKRNLEYYILRIFVPLFLIISVSWVIFFLKDYGRQLEVASGNLLVFVAFNFTISGDLPRLGYLTVLDRFMIVSFCLTAIVVLISVCQKRLGAVGKQAVAAQIDTWVLVIYPLVYSLYIIWVYLRFFTDHIGW",
"organism": "Desulfofustis sp. PB-SRB1",
"uniprot_code": "V4JF97",
"uniprot_range_first": 34,
"uniprot_range_last": 642,
"oligomerization": "pentamer",
"molecular_type": "protein",
"uniprot_sequence": "MHNLQQLLPTRSLIWIFSFLTSISIWCTVAHAETEGRVQHFTGYIEDGRGIFYSLPDMKQ\nGDIIYASMQNTGGNLDPLVGIMAEEIDPAVSLGQVLEKALASENDLISELTAVADRIFLG\nWDDDGGKGYSASLEFTIPRDGTYHIFAGSTITNQRLDKFQPTYTTGSFQLILGLNAPQVI\nSGEGEPEGEVFASLASLEIKPEAHVQELEIRLDKDTRYLTQHTRNLQPGDTFHALVEPIG\nEAPLPRLRLTDSGGKPLAFGLIDQPGESVELNYTCDQDICELVVHVDGTDGQKDSGEAVY\nRLLVGINAPNLRESGQTPVGSSVFLESDLVTVGLAVDQIVGVDQRSENFSVVGTLKLSWH\nDPKLGFSPDQCGCTVKSFEDASIRAVAGEINLPLPSFSFYNQQGNRWSQNQVIFVTPDGR\nASYFERFTVTLQAPDFDFLAYPFDRQKFSIKVDLAVPTNMFIFNEIERFQQVVGDQLGEE\nEWVVTSYSQEITEVPFERGSTNSRFTTTLLVKRNLEYYILRIFVPLFLIISVSWVIFFLK\nDYGRQLEVASGNLLVFVAFNFTISGDLPRLGYLTVLDRFMIVSFCLTAIVVLISVCQKRL\nGAVGKQAVAAQIDTWVLVIYPLVYSLYIIWVYLRFFTDHIGW",
"mw": 68.352,
"total_mw": 341.76,
"number_molecules": 5,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "The protein construct used for SANS contains an additional non-native RGSAAA N-terminal extension."
}
],
"buffer": {
"name": "20 mM citrate, 150 mM NaCl, 10 mM CaCl2, 0.5 mM deuterated n-Dodecyl-B-D-Maltoside, in D2O",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 5.0,
"deuteration": null
},
"purity_method": null,
"name": "Desulfofustis sp. PB-SRB1 ligand-gated ion channel DeCLIC with calcium at pH 5 by paused SEC-SANS",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": null,
"full_name": "Stockholm University",
"webpage": null
}
],
"contributor_name": "Marie",
"contributor_surname": "Lycksell",
"orcid": "https://orcid.org/0000-0003-3271-7973"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2021-06-17",
"storage_temperature": 0.0,
"cell_temperature": 10.0,
"exposure_time": 30.0,
"number_of_frames": 161,
"wavelength": 0.6,
"sample_detector_distance": 8.0,
"concentration_min": null,
"concentration_max": 5.5,
"sample_volume": 250.0,
"flow_rate": 0.0,
"s_min": 0.065,
"s_max": 7.279,
"total_exposure_time": null,
"seccolumn": 1
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVX3_fit1_model1_img.png",
"software": "GROMACS",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "2021.3",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVX3_fit1_model1.pdb",
"model_mw": 334.1,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 665
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVX3_fit1_fixed_fit_img.png",
"software": "Pepsi-SANS",
"chi_square_value": 5.4728,
"p_value": 0.0,
"fit_residual_plot": "SASDVX3_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVX3_fit1.txt",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/pH5cacl2_md1_fit99.log",
"software_version": "3.0",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVX3_fit2_model1_img.png",
"software": "GROMACS",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "2021.3",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVX3_fit2_model1.pdb",
"model_mw": 335.0,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 665
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVX3_fit2_model2_img.png",
"software": "GROMACS",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "2021.3",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVX3_fit2_model2.pdb",
"model_mw": 341.6,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 665
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVX3_fit2_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 3.25,
"p_value": 0.0,
"fit_residual_plot": "SASDVX3_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVX3_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_011_1_r8V6TCD.log",
"software_version": "2.1",
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "BayesApp",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "Paused SEC-SANS.",
"experiment_description": "SANS data from solutions of Desulfofustis sp. PB-SRB1 ligand-gated ion channel DeCLIC in 20 mM citrate, 150 mM NaCl, 10 mM CaCl2, 0.5 mM deuterated n-Dodecyl-B-D-Maltoside, in D2O, pH 5 were collected on the D22 instrument at the ILL (Grenoble, France) using a Reuter-Stokes 3He detector at a sample-detector distances of 1.4 m and 8 m (measured simultaneously with the D22 dual detector banks) and at a wavelength of λ = 0.6 nm; Δλ/λ = 10% (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 250.00 μl sample at 5.5 mg/ml was injected onto a GE Superdex 200 Increase 10/300 column at 10°C. Data collection was done as a paused-flow SEC-SANS measurement: an initial flow rate of 0.2 ml/min was used, slowed to 0.01 ml/min when the protein peak entered the measuring cell, and paused to 0 ml/min at the peak maximum for the data collection, after which the flow was turned on to pass the remainder of the column volume. 161 successive 30 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": "1/cm",
"experimental_mw": 347.62,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 38993.93,
"pddf_i0_error": null,
"guinier_i0": 3112.79,
"guinier_i0_error": null,
"pddf_rg": 5.02,
"pddf_rg_error": null,
"guinier_rg": 5.067,
"guinier_rg_error": 0.072,
"pddf_dmax": 17.09,
"pddf_dmax_error": null,
"porod_volume": 580.8,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 5,
"guinier_point_last": 29,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDVX3_datloglog_img.png",
"symmetry": null,
"last_modified": "2025-02-25T16:12:25.584068+01:00",
"bragg_peak": []
}
