{
"code": "SASDEQ6",
"status": "Published",
"type_of_curve": "Extrapolated to infinite dilution",
"angular_unit": "1/nm",
"project": {
"title": "Molecular Fingerprints for a Novel Enzyme Family in Actinobacteria with Glucosamine Kinase Activity.",
"publication": {
"title": "Molecular Fingerprints for a Novel Enzyme Family in Actinobacteria 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"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEQ6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEQ6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEQ6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEQ6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEQ6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEQ6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEQ6.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"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,
"line_collimation_slitlength": null,
"line_collimation_integrationwidth": null,
"xray_energy": null,
"beam_profile_ah": null,
"beam_profile_al": null
},
"sample": {
"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",
"mw": 48.377,
"total_mw": 48.377,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris-HCl, 150 mM NaCl, 10 mM MgCl2, 5 mM DTT, 50 mM D-glucose",
"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 in presence of 50 mM D-glucose",
"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": "2018-04-13",
"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,
"concentration_max": 10.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.147,
"s_max": 4.928,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEQ6_fit1_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "6hwj",
"ext_code": "6HWJ",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEQ6_fit1_model1.pdb",
"model_mw": 45.17,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "Volume fraction for this structure was of 1.0 as determined OLIGOMER",
"user": 320
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/gluk01_50mM_glucose_zero_OLIGOMER_SASBDB_fit_img.png",
"software": "OLIGOMER",
"chi_square_value": 39.62,
"p_value": 0.0,
"fit_residual_plot": "gluk01_50mM_glucose_zero_OLIGOMER_SASBDB_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEQ6_fit1.fit",
"fit_log": null,
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Streptacidiphilus jiangxiensis glucosamine kinase in presence of 50 mM glucose 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 < 4.928 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.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 41.0,
"experimental_mw_error": null,
"guinier_i0_mw": 41.0,
"guinier_i0_mw_error": null,
"porod_mw": 45.8,
"porod_mw_error": null,
"pddf_i0": 37.17,
"pddf_i0_error": null,
"guinier_i0": 37.34,
"guinier_i0_error": 0.05,
"pddf_rg": 2.614,
"pddf_rg_error": null,
"guinier_rg": 2.62,
"guinier_rg_error": 0.04,
"pddf_dmax": 8.0,
"pddf_dmax_error": null,
"porod_volume": 73.25,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 29,
"guinier_point_last": 75,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEQ6_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}