{ "code": "SASDFA7", "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/SASDFA7.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFA7.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFA7_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFA7_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFA7_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFA7_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFA7.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": "Lysinibacillus Mosquito-larvicidal receptor binding component", "short_name": "BinB", "sequence": "MGSSHHHHHHSSGLVPRGSMCDSKDNSGVSEKCGKKFTNYPLNTTPTSLNYNLPEISKKF\r\nYNLKNKYSRNGYGLSKTEFPSSIENCPSNEYSIMYDNKDPRFLIRFLLDDGRYIIADRDD\r\nGEVFDEAPTYLDNNNHPIISRHYTGEERQKFEQVGSGDYITGEQFFQFYTQNKTRVLSNC\r\nRALDSRTILLSTAKIFPIYPPASETQLTAFVNSSFYAAAIPQLPQTSLLENIPEPTSLDD\r\nSGVLPKDAVRAVKGSALLPCIIVHDPNLNNSDKMKFNTYYLLEYKEYWHQLWSQIIPAHQ\r\nTVKIQERTGISEVVQNSMIEDLNMYIGADFGMLFYFRSSGFKEQITRGLNRPLSQTTTQL\r\nGERVEEMEYYNSNDLDVRYVKYALAREFTLKRVNGEIVKNWVAVDYRLAGIQSYPNAPIT\r\nNPLTLTKHTIIRCENSYDGHIFKTPLIFKNGEVIVKTNEELIPKINQ", "organism": "synthetic construct", "uniprot_code": "B1HQ59", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MCDSKDNSGVSEKCGKKFTNYPLNTTPTSLNYNLPEISKKFYNLKNKYSRNGYGLSKTEF\nPSSIENCPSNEYSIMYDNKDPRFLIRFLLDDGRYIIADRDDGEVFDEAPTYLDNNNHPII\nSRHYTGEERQKFEQVGSGDYITGEQFFQFYTQNKTRVLSNCRALDSRTILLSTAKIFPIY\nPPASETQLTAFVNSSFYAAAIPQLPQTSLLENIPEPTSLDDSGVLPKDAVRAVKGSALLP\nCIIVHDPNLNNSDKMKFNTYYLLEYKEYWHQLWSQIIPAHQTVKIQERTGISEVVQNSMI\nEDLNMYIGADFGMLFYFRSSGFKEQITRGLNRPLSQTTTQLGERVEEMEYYNSNDLDVRY\nVKYALAREFTLKRVNGEIVKNWVAVDYRLAGIQSYPNAPITNPLTLTKHTIIRCENSYDG\nHIFKTPLIFKNGEVIVKTNEELIPKINQ", "mw": 53.457, "total_mw": 53.457, "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": "Protein maintained in 100% D2O", "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Receptor binding BinB protein of mosquito-larvicidal Binary toxin 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": "2019-04-24", "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": 3.3, "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/SASDFA7_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/SASDFA7_fit1_model1.pdb", "model_mw": 16.23, "bead_radius": 2.5, "log": null, "symmetry": "P1", "comment": null, "user": 457 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFA7_fit1_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 0.385, "p_value": 0.086659, "fit_residual_plot": "SASDFA7_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFA7_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/hBinB-DAMMIN.log", "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFA7_fit2_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "5foy", "ext_code": "5FOY", "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/SASDFA7_fit2_model1.pdb", "model_mw": 48.48, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/BinB00-Cryson.log", "symmetry": null, "comment": null, "user": 457 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFA7_fit2_fixed_fit_img.png", "software": "CRYSON", "chi_square_value": 0.523, "p_value": 0.010821, "fit_residual_plot": "fit4columns2358_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFA7_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/BinB00-Cryson.log", "software_version": null, "description": "Coordinates are available for the partial structure (PDB code 5FOY_B) for residues 28 to 448. Coordinates for poly-His tag of 18 residues and N-terminal 27 residues are not available and were not used in the SANS modeling." } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.5a", "i0_calibration_standard": null, "description": "Experimental Molecular weight Value estimated using I(0) values from GNOM analysis. Intensity has been normalized to protein concentration of 1 mg/ml. Actual sample used was 3.3 mg/ml.", "experiment_description": null, "tags": [], "intensity_unit": "1/cm", "experimental_mw": 61.9, "experimental_mw_error": null, "guinier_i0_mw": 62.3, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.04353, "pddf_i0_error": 0.002346, "guinier_i0": 0.045, "guinier_i0_error": 0.002, "pddf_rg": 3.16, "pddf_rg_error": 0.283, "guinier_rg": 3.28, "guinier_rg_error": 0.55, "pddf_dmax": 9.92, "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": 13, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDFA7_datloglog_img.png", "symmetry": null, "last_modified": "2020-02-03T17:29:35.244841+01:00", "bragg_peak": [] }