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{
"code": "SASDF97",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/A",
"project": {
"title": "Small-angle neutron scattering studies suggest the mechanism of BinAB protein internalization",
"publication": {
"title": "Small-angle neutron scattering studies suggest the mechanism of BinAB protein internalization",
"author_list": "Sharma M, Aswal V, Kumar V, Chidambaram R",
"journal": "IUCrJ",
"doi": "10.1107/S2052252519017159",
"pmid": null,
"published_date": "2020 Jan 25"
},
"status": "released",
"submitted_date": "2019-06-09",
"released_date": "2020-02-03"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDF97.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF97.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF97_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF97_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF97_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF97_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF97.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Custom-built",
"name": "1 m long He3 position sensitive detector",
"resolution": 12.0
},
"name": "Dhruva Reactor, Bhabha Atomic Research Centre",
"city": "Mumbai",
"country": "India",
"beamline_name": "SANS-I facility",
"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": "Binary toxin receptor Cqm1 protein",
"short_name": "Cqm1",
"sequence": "MHHHHHHSSGVDLGTENLYFQSMREPDSKDWYQHATFYQIYPRSFLDSNGDGIGDLAGITSKMKYLADIGIDA\r\nTWLSPPFKSPLKDFGYDVSDFYAIQPEYGNLTDFDKLVEESHKNGIKLMLDFIPNHSSDQHEWFVKSVVRDPE\r\nYSDFYVWRPPATGGGPPNNWISVFGGSAWTYNQARGEYYLHQFTPQQPDLNYRNPKVLAEMTKMLFFWLDRGV\r\nDGFRLDAINHMFEDEQFRDEPLSGWGQPGEYDSLDHIYTKDIPDVYDVVYNWRDQMDKYSAEKGRTIILMTEA\r\nYSSIEGTMLYYESADRKRQGAHMPFNFQLIYDFKKEQNAVGLKSSIDWWMNNMPARHTPSWVAGSHDHSRVAS\r\nRVGLDRVDQVMTLLHTLPGTSITYYGEEVAMQDFKEAQQFDNRDPNRTPMQWDSSTSAGFSTNTNTWLRVHPD\r\nYARYNVDVMQKNPQSTFHHFQHLTKLRRHRTMQSGEYVHKTVGTKVYALLRELRGEDSFLTVLNMAGAEDTVD\r\nLGDFVNLPQKMRVEVAQPNSKSKAGNEVDISKLTLGPYDSVVLRATVSSA",
"organism": "synthetic construct",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 64.665,
"total_mw": 64.665,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Deuterated BinB component of mosquito-larvicidal Binary toxin",
"short_name": "dBinB",
"sequence": "MGSSHHHHHHSSGLVPRGSMCDSKDNSGVSEKCGKKFTNYPLNTTPTSLNYNLPEISKKF\r\nYNLKNKYSRNGYGLSKTEFPSSIENCPSNEYSIMYDNKDPRFLIRFLLDDGRYIIADRDD\r\nGEVFDEAPTYLDNNNHPIISRHYTGEERQKFEQVGSGDYITGEQFFQFYTQNKTRVLSNC\r\nRALDSRTILLSTAKIFPIYPPASETQLTAFVNSSFYAAAIPQLPQTSLLENIPEPTSLDD\r\nSGVLPKDAVRAVKGSALLPCIIVHDPNLNNSDKMKFNTYYLLEYKEYWHQLWSQIIPAHQ\r\nTVKIQERTGISEVVQNSMIEDLNMYIGADFGMLFYFRSSGFKEQITRGLNRPLSQTTTQL\r\nGERVEEMEYYNSNDLDVRYVKYALAREFTLKRVNGEIVKNWVAVDYRLAGIQSYPNAPIT\r\nNPLTLTKHTIIRCENSYDGHIFKTPLIFKNGEVIVKTNEELIPKINQ",
"organism": "synthetic construct",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 56.4,
"total_mw": 56.4,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "25 mM HEPES, pH 7.5, 25 mM NaCl, in 100% D2O",
"concentration_unit": null,
"comment": "SANS experiment were carried out in 100% D2O",
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Complex of Binary toxin receptor (Cqm1) with deuterated BinB component protein in 100% D2O",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Mumbai 400085, INDIA",
"full_name": "Bhabha Atomic Research Centre",
"webpage": null
}
],
"contributor_name": "Vinay",
"contributor_surname": "Kumar",
"orcid": "https://orcid.org/0000-0002-7619-6236"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2019-04-23",
"storage_temperature": 25.0,
"cell_temperature": 25.0,
"exposure_time": 43200.0,
"number_of_frames": 1,
"wavelength": 0.52,
"sample_detector_distance": 2.0,
"concentration_min": null,
"concentration_max": 1.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.162,
"s_max": 1.99,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF97_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDF97_fit1_model1.pdb",
"model_mw": 14.773,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "dBinB component is fully 'contrast matched' with 100% D2O,",
"user": 457
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF97_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 0.318,
"p_value": 0.086659,
"fit_residual_plot": "SASDF97_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF97_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Cqm1dBinB-Dammin.log",
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF97_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "6k5p",
"ext_code": "6K5P",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDF97_fit2_model1.pdb",
"model_mw": 60.95,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/Cqm1A00-Cryson.log",
"symmetry": null,
"comment": null,
"user": 457
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF97_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 0.348,
"p_value": 0.00032,
"fit_residual_plot": "fit4columns2362_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF97_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Cqm1A00-Cryson.log",
"software_version": null,
"description": "Fit against DAMMIN dummy model suggested presence of only Cqm1 monomer. This is in agreement with \"Contrast matched\" SANS experiment, as scattering length density of deuterated BinB (dBinB) nearly matches that of solvent D2O (100%) and dBinB contribution to the scattering is expected to be eliminated."
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "4.5a",
"i0_calibration_standard": null,
"description": "This data is for a stable complex of receptor Cqm1 protein and deuterated BinB component of mosquito-larvicidal Binary (BinAB) toxin. Deuterated BinB (dBinB) protein was synthesized using E. coli based protein expression system grown in M9+ medium in D2O after three step adaption. The extent of deuteration for dBinB was estimated from contrast (p − s)2 values to be ~77%. Theoretical molecular weight of the dBinB protein includes 77% of D atoms.\r\nSANS analysis (DAMMIN and CRYSON fit) suggest that deuterated BinB (dBinB), expectedly, is fully matched out against the used solvent (100% D2O) and only monomer of Cqm1 is modelled from SANS experiments",
"experiment_description": null,
"tags": [],
"intensity_unit": "1/cm",
"experimental_mw": 70.6,
"experimental_mw_error": null,
"guinier_i0_mw": 66.5,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.04963,
"pddf_i0_error": 0.0022,
"guinier_i0": 0.048,
"guinier_i0_error": 0.0013,
"pddf_rg": 2.18,
"pddf_rg_error": 0.121,
"guinier_rg": 1.87,
"guinier_rg_error": 0.43,
"pddf_dmax": 7.29,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 29,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDF97_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-02-03T17:29:13.561891+01:00",
"bragg_peak": []
}
