查看完整 summary.json 原文
{
"code": "SASDDH6",
"status": "Published",
"type_of_curve": "Merged",
"angular_unit": "1/A",
"project": {
"title": "Solution Structure and Conformational Dynamics of a Doublet Acyl Carrier Protein from Prodigiosin Biosynthesis.",
"publication": {
"title": "Solution Structure and Conformational Dynamics of a Doublet Acyl Carrier Protein from Prodigiosin Biosynthesis.",
"author_list": "Thongkawphueak T, Winter AJ, Williams C, Maple HJ, Soontaranon S, Kaewhan C, Campopiano DJ, Crump MP, Wattana-Amorn P",
"journal": "Biochemistry",
"doi": "10.1021/acs.biochem.0c00830",
"pmid": "33416314",
"published_date": "2021 Jan 8"
},
"status": "released",
"submitted_date": "2018-05-10",
"released_date": "2020-03-25"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDH6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDH6.dat",
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"experiment": {
"instrument": {
"detector": {
"type": "CCD",
"name": "Rayonix SX165",
"resolution": 15.0
},
"name": "Synchrotron Light Research Institute (SLRI)",
"city": "Nakhon Ratchasima",
"country": "Thailand",
"beamline_name": "BL1.3W",
"beam_geometry": null,
"type_of_source": "X-ray synchrotron",
"point_source": null,
"line_collimation": null,
"sample_path_length": null,
"line_collimation_slitlength": null,
"line_collimation_integrationwidth": null,
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},
"sample": {
"molecule": [
{
"long_name": "Di-domain acyl carrier protein of PigH from prodigiosin biosynthesis",
"short_name": "Di-domain ACP",
"sequence": ">PigHACP1ACP2\r\nGSHMNDVTTETYETLKQSVLHTFAQLTGYNVSELSLTSHLENDLGVDSIALAEIAVSLSRQFQLNTPLLIQDINTIKDALDGILQREFQLSEKVEPAAIALSGDADLWLGNLVRQIFASHSGYDVNALALDAEIESDLGIDSVSVASAQGELFNTLQLNSETIIANCNTLSALKQCLAARLVQEKGQDWFELTRAPPPPPLRSGC",
"organism": "Serratia sp. ATCC 39006",
"uniprot_code": "Q5W264",
"uniprot_range_first": 4,
"uniprot_range_last": 191,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MNDVTTETYETLKQSVLHTFAQLTGYNVSELSLTSHLENDLGVDSIALAEIAVSLSRQFQ\nLNTPLLIQDINTIKDALDGILQREFQLSEKVEPAAIALSGDADLWLGNLVRQIFASHSGY\nDVNALALDAEIESDLGIDSVSVASAQGELFNTLQLNSETIIANCNTLSALKQCLAARLVQ\nEKGQDWFEQRGRGQSDSAIDHDADTTAEVTPPTATPVAINAEIGDPRTMRDFVGIEHPDI\nFHKAREFHLFYQDKKKRQLYFYGMPLETPCKNRAVMFDEATGQHREFLMFGSNSYLGLSN\nHPEIIHAIQDAASLYGATNTGCRIIAGSNVLHLELERKLAKLKGRDDCIVYPSGYSANLG\nCISALTSRHDLVFTDAINHMSIQDGCKLAGAQRKIYNHSLTSLEKSLAKYADHPGGKLIV\nTDGVFSMHGDIVDLPRLMKLAERYGARVLVDDAHSTGVLGKTGAGTSEHFNMKGQVDLEL\nGTMSKALSGLGGYVCGDGDVVEYLRFYSNSYVFAATIPAPVAAGVIASIDVMLREPERLA\nKLWDNIYYFRTRLLNAGFDLENSDSAIIPIVVGDDAKTLFFGRAVRARGMFCQTVVFPGV\nSVGDARLRISITSEHTREDLDEAYAILVASALEVGVPVNASAHQEENASVAEA",
"mw": 22.209,
"total_mw": 22.209,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris supplemented with 5 mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.0,
"deuteration": null
},
"purity_method": null,
"name": "Di-domain acyl carrier protein of the seryltransferase from prodigiosin biosynthesis",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Thailand",
"full_name": "Kasetsart University",
"webpage": "https://www.ku.ac.th"
}
],
"contributor_name": "Pakorn",
"contributor_surname": "Wattana-Amorn",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-01-13",
"storage_temperature": 25.0,
"cell_temperature": 25.0,
"exposure_time": 600.0,
"number_of_frames": 1,
"wavelength": 0.131,
"sample_detector_distance": 0.85,
"concentration_min": 1.7,
"concentration_max": 6.8,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.411,
"s_max": 3.612,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDH6_fit1_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "r6669",
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"model_mw": 22.5,
"bead_radius": 1.8,
"log": null,
"symmetry": "P1",
"comment": null,
"user": 318
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDH6_fit1_model2_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "5",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDH6_fit1_model2.pdb",
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"bead_radius": 2.0,
"log": null,
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"comment": null,
"user": 318
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDH6_fit1_fixed_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 2.864,
"p_value": 0.3102,
"fit_residual_plot": "SASDDH6_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDH6_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/run_1_alDHk3F.log",
"software_version": null,
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "4.5a",
"i0_calibration_standard": null,
"description": "Two DAMMIF-derived dummy atom models are displayed. Top: The best-fit individual DAMMIF model and corresponding fit to the SAXS data. Bottom: The average spatial representation of the protein obtained after the alignment of multiple individual DAMMIF models combined with volume and bead-occupancy corrections (damfilt).",
"experiment_description": "Synchrotron SAXS data from solutions of the di-domain acyl carrier protein of the seryltransferase from prodigiosin biosynthesis in 20 mM Tris, 5 mM DTT, pH 7, were collected on the BL1.3W beam line at the Synchrotron Light Research Institute (Nakhon Ratchasima, Thailand) using a CCD Rayonix SX165 detector at a sample-detector distance of 0.9 m and at a wavelength of λ = 0.131 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.7 and 6.8 mg/ml were measured at 25°C. One 600 second frame was collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 19.107,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 2.343e-05,
"pddf_i0_error": 3.811e-06,
"guinier_i0": 2.2764e-05,
"guinier_i0_error": 1.6e-06,
"pddf_rg": 2.56,
"pddf_rg_error": 0.36,
"guinier_rg": 2.39,
"guinier_rg_error": 0.18,
"pddf_dmax": 8.43,
"pddf_dmax_error": null,
"porod_volume": 39.44,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 2,
"guinier_point_last": 11,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDH6_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-10-17T15:41:17.447524+02:00",
"bragg_peak": []
}查看完整 manifest.json 原文
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