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.
View the complete summary.json source
{
"code": "SASDEL6",
"status": "Published",
"type_of_curve": "Extrapolated to infinite dilution",
"angular_unit": "1/nm",
"project": {
"title": "Molecular Fingerprints for a Novel Enzyme Family in <i>Actinobacteria</i> with Glucosamine Kinase Activity.",
"publication": {
"title": "Molecular Fingerprints for a Novel Enzyme Family in <i>Actinobacteria</i> with Glucosamine Kinase Activity.",
"author_list": "Manso JA, Nunes-Costa D, Macedo-Ribeiro S, Empadinhas N, Pereira PJB",
"journal": "MBio",
"doi": "10.1128/mBio.00239-19",
"pmid": "31088917",
"published_date": "2019 May 14"
},
"status": "released",
"submitted_date": "2018-10-15",
"released_date": "2019-05-09"
},
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"experiment": {
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"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "ESRF",
"city": "Grenoble",
"country": "France",
"beamline_name": "BM29",
"beam_geometry": "",
"type_of_source": "X-ray synchrotron",
"point_source": null,
"line_collimation": null,
"sample_path_length": null,
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"line_collimation_integrationwidth": null,
"xray_energy": null,
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},
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"molecule": [
{
"long_name": "Glucosamine kinase",
"short_name": null,
"sequence": "MTPNWSELVAAADPALVLPSGERRAEVAVPGPLRLDALLDLGEGHAVGVVRSADAARWTV\r\nPLVRDGAGGVRRSRPGDGTAEHLVAALARRGATPDAAFVLEAFTGAAPVTGERGIIVDQT\r\nNESVIVGECAVVKWAVRLPAEGEPGSPAAQRIAALARGGFTEMPRPWGLLTLAEGAQPVL\r\nLASVVAYLPGALDGWDWAVDDVRRLARGELTMDQALLPAAQLGTLTARMHAALAARGRTP\r\nATAADVAAWGVRMREELDEAVASVPGAEGERLKAWAPRIADVYAELDALAGTPLIDVHGD\r\nFHVGQILRADGRYAVVDFDGNPVLPADQRAARQPAALDVVGMTASLDHVGRVVVFRTPDV\r\nDPAPVRAWIAAAQRSFLDAYRTTLARLDADDLFDDRLLTPLRYAQEVREYLYAVRHLPHW\r\nVYVPDLSLTDLLPERLKDKKLAAALEHHHHHH",
"organism": "Streptacidiphilus jiangxiensis",
"uniprot_code": "A0A1H7TQR5",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MTPNWSELVAAADPALVLPSGERRAEVAVPGPLRLDALLDLGEGHAVGVVRSADAARWTV\nPLVRDGAGGVRRSRPGDGTAEHLVAALARRGATPDAAFVLEAFTGAAPVTGERGIIVDQT\nNESVIVGECAVVKWAVRLPAEGEPGSPAAQRIAALARGGFTEMPRPWGLLTLAEGAQPVL\nLASVVAYLPGALDGWDWAVDDVRRLARGELTMDQALLPAAQLGTLTARMHAALAARGRTP\nATAADVAAWGVRMREELDEAVASVPGAEGERLKAWAPRIADVYAELDALAGTPLIDVHGD\nFHVGQILRADGRYAVVDFDGNPVLPADQRAARQPAALDVVGMTASLDHVGRVVVFRTPDV\nDPAPVRAWIAAAQRSFLDAYRTTLARLDADDLFDDRLLTPLRYAQEVREYLYAVRHLPHW\nVYVPDLSLTDLLPERLKD",
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"total_mw": 48.377,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
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"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Glucosamine kinase from Streptacidiphilus jiangxiensis",
"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": "Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC-CSIC-Universidad de Cantabria)",
"webpage": null
}
],
"contributor_name": "Jose A",
"contributor_surname": "Manso",
"orcid": "https://orcid.org/0000-0002-2565-6239"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-11-24",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 1.0,
"number_of_frames": 10,
"wavelength": 0.09919,
"sample_detector_distance": 2.867,
"concentration_min": 1.25,
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"sample_volume": null,
"flow_rate": null,
"s_min": 0.091,
"s_max": 4.944,
"total_exposure_time": null,
"seccolumn": null
},
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"software": "PDB (Protein Data Bank)",
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"comment": "Volume fraction for this structure was of 0.96 as determined OLIGOMER",
"user": 320
},
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"software": "PDB (Protein Data Bank)",
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"symmetry": null,
"comment": "Volume fraction for this structure was of 0.04 as determined OLIGOMER",
"user": 320
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"fit_unit": "1/A",
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"software": "OLIGOMER",
"chi_square_value": 19.13,
"p_value": 0.0,
"fit_residual_plot": "gluk01_zero_OLIGOMER_SASBDB_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEL6_fit1.fit",
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"description": ""
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"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Streptacidiphilus jiangxiensis glucosamine kinase in 20 mM Tris-HCl (pH 8.0), 150 mM NaCl, 10 mM MgCl2 and 5 mM DTT were collected on the BM29 BIOSAXS beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.867 m and at a wavelength of λ = 0.0992 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle; s-range = 0.035 < s < 4.944 nm-1). Solute concentrations ranging between 1.25 and 10.0 mg/ml were measured at 10°C. 10 successive 1 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. The data were extrapolated to infinite dilution. The volume fractions for the structure above (open conformation) and below (closed conformation) were of 0.96 and 0.04 as determined by OLIGOMER, respectively.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 45.2,
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"pddf_i0": 40.04,
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"guinier_i0": 40.03,
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"pddf_rg": 2.59,
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"pddf_dmax": 8.0,
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"porod_volume": 71.79,
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"estimated_volume": null,
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"guinier_point_first": 11,
"guinier_point_last": 88,
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"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEL6_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}View the complete manifest.json source
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