The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
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{
"code": "SASDDB5",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Conformational States of ABC Transporter MsbA in a Lipid Environment Investigated by Small-Angle Scattering Using Stealth Carrier Nanodiscs.",
"publication": {
"title": "Conformational States of ABC Transporter MsbA in a Lipid Environment Investigated by Small-Angle Scattering Using Stealth Carrier Nanodiscs.",
"author_list": "Josts I, Nitsche J, Maric S, Mertens HD, Moulin M, Haertlein M, Prevost S, Svergun DI, Busch S, Forsyth VT, Tidow H",
"journal": "Structure",
"doi": "10.1016/j.str.2018.05.007",
"pmid": "29937358",
"published_date": "2018 Aug 7"
},
"status": "released",
"submitted_date": null,
"released_date": "2018-06-27"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDB5.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDB5.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDB5_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDB5_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDB5_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDB5_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDB5.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "3-He gas detector",
"name": "CERCA",
"resolution": 7.5
},
"name": "ILL",
"city": "Grenoble",
"country": "France",
"beamline_name": "D11",
"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": "Lipid A export ATP-binding/permease protein MsbA",
"short_name": "MsbA",
"sequence": "MHHHHHHGENLYFQGSHNDKDLSTWQTFRRLWPTIAPFKAGLIVAGVALILNAASDTFMLSLLKPLLDDGFGKTD\r\nRSVLVWMPLVVIGLMILRGITSYVSSYCISWVSGKVVMTMRRRLFGHMMGMPVSFFDKQS\r\nTGTLLSRITYDSEQVASSSSGALITVVREGASIIGLFIMMFYYSWQLSIILIVLAPIVSI\r\nAIRVVSKRFRNISKNMQNTMGQVTTSAEQMLKGHKEVLIFGGQEVETKRFDKVSNRMRLQ\r\nGMKMVSASSISDPIIQLIASLALAFVLYAASFPSVMDSLTAGTITVVFSSMIALMRPLKS\r\nLTNVNAQFQRGMAACQTLFTILDSEQEKDEGKRVIERATGDVEFRNVTFTYPGRDVPALR\r\nNINLKIPAGKTVALVGRSGSGKSTIASLITRFYDIDEGEILMDGHDLREYTLASLRNQVA\r\nLVSQNVHLFNDTVANNIAYARTEQYSREQIEEAARMAYAMDFINKMDNGLDTVIGENGVL\r\nLSGGQRQRIAIARALLRDSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRLS\r\nTIEKADEIVVVEDGVIVERGTHNDLLEHRGVYAQLHKMQFGQ",
"organism": "Escherichia coli",
"uniprot_code": "P60752",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MHNDKDLSTWQTFRRLWPTIAPFKAGLIVAGVALILNAASDTFMLSLLKPLLDDGFGKTD\nRSVLVWMPLVVIGLMILRGITSYVSSYCISWVSGKVVMTMRRRLFGHMMGMPVSFFDKQS\nTGTLLSRITYDSEQVASSSSGALITVVREGASIIGLFIMMFYYSWQLSIILIVLAPIVSI\nAIRVVSKRFRNISKNMQNTMGQVTTSAEQMLKGHKEVLIFGGQEVETKRFDKVSNRMRLQ\nGMKMVSASSISDPIIQLIASLALAFVLYAASFPSVMDSLTAGTITVVFSSMIALMRPLKS\nLTNVNAQFQRGMAACQTLFTILDSEQEKDEGKRVIERATGDVEFRNVTFTYPGRDVPALR\nNINLKIPAGKTVALVGRSGSGKSTIASLITRFYDIDEGEILMDGHDLREYTLASLRNQVA\nLVSQNVHLFNDTVANNIAYARTEQYSREQIEEAARMAYAMDFINKMDNGLDTVIGENGVL\nLSGGQRQRIAIARALLRDSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRLS\nTIEKADEIVVVEDGVIVERGTHNDLLEHRGVYAQLHKMQFGQ",
"mw": 66.279,
"total_mw": 132.558,
"number_molecules": 2,
"complex_state": false,
"deuteration": 0.0,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Membrane scaffold protein 1D1 (deuterated, 75%)",
"short_name": "d75-msp1d1",
"sequence": "GHHHHHHHDYDIPTTENLYFQGSTFSKLREQLGPVTQEFWDNLEKETEGLRQEM\r\nSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVEPLRAELQEGARQKLHELQE\r\nKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAARLEALKENGGARLAEY\r\nHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKLNTQ",
"organism": null,
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 24.661,
"total_mw": 49.322,
"number_molecules": 0,
"complex_state": false,
"deuteration": 75.0,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "1-palmitoyl-2-palmitoleoyl-sn-glycero-3-phosphocholine (deuteration: 78% head, 92% acyl)",
"short_name": "d(78,92)-POPC",
"sequence": "C42H82NO8P",
"organism": "Escherichia coli",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "unknown",
"molecular_type": "other",
"uniprot_sequence": null,
"mw": 0.76,
"total_mw": 0.76,
"number_molecules": 124,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "30 mM Tris, 150 mM NaCl",
"concentration_unit": null,
"comment": "nanodisc buffer",
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "MsbA in stealth nanodisc (SANS, 100% D2O)",
"ext_coefficient": null,
"contrast": -3.313,
"specific_vol": 0.745,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Haydyn",
"contributor_surname": "Mertens",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-03-09",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 4200.0,
"number_of_frames": 2,
"wavelength": 0.46,
"sample_detector_distance": null,
"concentration_min": 1.0,
"concentration_max": 6.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.097,
"s_max": 3.091,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDB5_fit1_model1_img.png",
"software": "SASREF CV",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "2.8.3",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDB5_fit1_model1.pdb",
"model_mw": 121.5,
"bead_radius": null,
"log": null,
"symmetry": "P2",
"comment": "Dimer model of MsbA using ambiguous distance constraints between monomers (PDB ID: 3B5X)",
"user": 12
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDB5_fit1_fit_img.png",
"software": "SASREF",
"chi_square_value": 1.407,
"p_value": 2e-06,
"fit_residual_plot": "SASDDB5_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDB5_fit1.fit",
"fit_log": null,
"software_version": "2.8.3",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "2.8.3",
"i0_calibration_standard": null,
"description": "MsbA ABC transporter protein encapsulated in a partially deuterated \"stealth-nanodisc\": (sND). Disc components (MSP1D1 scaffold protein - 75% deuterated, and POPC lipid - heads/tails 78% and 92% deuterated) are effectively matched out at 100% D2O. Thus the expected molecular weight should correspond to that of the MsbA protein (~132 kDa). Data measured in two configurations: 1.5 m / 1.5 m and 8 m / 8 m (collimation length / sample-detector distances) with a fixed neutron wavelength (λ) of 5 Å. Data is merged from these two configurations.",
"experiment_description": null,
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 145.0,
"experimental_mw_error": null,
"guinier_i0_mw": 145.0,
"guinier_i0_mw_error": 15.0,
"porod_mw": 118.0,
"porod_mw_error": null,
"pddf_i0": 0.8931,
"pddf_i0_error": 0.003,
"guinier_i0": 0.89,
"guinier_i0_error": 0.003,
"pddf_rg": 4.01,
"pddf_rg_error": 0.1,
"guinier_rg": 4.0,
"guinier_rg_error": 0.1,
"pddf_dmax": 13.0,
"pddf_dmax_error": 0.5,
"porod_volume": 189.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 8,
"guinier_point_last": 22,
"pddf_point_first": 9,
"pddf_point_last": 100,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDB5_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-11-27T06:49:40.800927+01:00",
"bragg_peak": []
}
