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{
"code": "SASDXB2",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Integrative Structural Characterization of <i>Candida glabrata</i>\n Phosphoglycerate Kinase by Small-Angle X-ray Scattering and AlphaFold: Implications for Therapeutic Targeting in Candidiasis",
"publication": {
"title": "Integrative Structural Characterization of <i>Candida glabrata</i>\n Phosphoglycerate Kinase by Small-Angle X-ray Scattering and AlphaFold: Implications for Therapeutic Targeting in Candidiasis",
"author_list": "Cuéllar-Cruz M, Maqueda Cabrera E, Siliqi D, Moreno A",
"journal": "ACS Omega",
"doi": "10.1021/acsomega.5c11751",
"pmid": null,
"published_date": "2026 Jan 21"
},
"status": "released",
"submitted_date": "2025-03-13",
"released_date": "2026-01-22"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDXB2.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDXB2.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXB2_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXB2_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDXB2_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXB2_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDXB2.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Eiger 4M",
"resolution": 75.0
},
"name": "Diamond Light Source",
"city": "Didcot",
"country": "UK",
"beamline_name": "B21",
"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,
"xray_energy": null,
"beam_profile_ah": null,
"beam_profile_al": null
},
"sample": {
"molecule": [
{
"long_name": "Phosphoglycerate kinase",
"short_name": "PgK",
"sequence": "MSLSSKLTVQDLELKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEHNPRYVVLASHLGRPNGE\r\nRNEKYSLAPVAEELQSLLGKPVTFLNDCVGSEVDSAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKA\r\nSAEDVAKFRKELCSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLTKELQYFGKALENPTRPFLAIL\r\nGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENAEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVL\r\nPVDFVIADAFSADANTKIVSDKEGIPAGWQGLDNGPESRKLFAATIAKAKTIVWNGPPGVFEFEKFASGT\r\nKAMLDEVVKSSTSGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKN",
"organism": "Nakaseomyces glabratus",
"uniprot_code": "A0A0W0EGC5",
"uniprot_range_first": 1,
"uniprot_range_last": 416,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MSLSSKLTVQDLELKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEHNPRYVVL\nASHLGRPNGERNEKYSLAPVAEELQSLLGKPVTFLNDCVGSEVDSAVKASAPGSVILLEN\nLRYHIEEEGSRKVDGQKVKASAEDVAKFRKELCSLADVYINDAFGTAHRAHSSMVGFDLP\nQRAAGFLLTKELQYFGKALENPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAF\nTFKKVLENAEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFVIADAFSADANTKIVS\nDKEGIPAGWQGLDNGPESRKLFAATIAKAKTIVWNGPPGVFEFEKFASGTKAMLDEVVKS\nSTSGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKN",
"mw": 44.617,
"total_mw": 44.617,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
}
],
"buffer": {
"name": "50 mM sodium phosphate, 500 mM NaCl, 500 mM imidazole, 1 mM phenylmethylsulfonyl fluoride (PMSF)",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.5,
"deuteration": null
},
"purity_method": null,
"name": "Phosphoglycerate kinase",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Bari, Italy",
"full_name": "CNR - Institute of Crystallography, Bari, Italy",
"webpage": "http://www.ba.ic.cnr.it"
}
],
"contributor_name": "Dritan",
"contributor_surname": "Siliqi",
"orcid": "https://orcid.org/0000-0003-1415-8725"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2025-02-13",
"storage_temperature": 4.0,
"cell_temperature": 15.0,
"exposure_time": 3.0,
"number_of_frames": 600,
"wavelength": 0.09464,
"sample_detector_distance": 3.733,
"concentration_min": null,
"concentration_max": 6.0,
"sample_volume": 50.0,
"flow_rate": 0.04,
"s_min": 0.045,
"s_max": 3.399,
"total_exposure_time": null,
"seccolumn": 1
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXB2_fit1_model1_img.png",
"software": "GASBOR",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDXB2_fit1_model1.cif",
"model_mw": null,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/GASBORon_2877.log",
"symmetry": null,
"comment": "Calpha model obtain from GASBOR",
"user": 396
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXB2_fit1_fixed_fit_img.png",
"software": "GASBOR",
"chi_square_value": 1.67,
"p_value": 0.0132,
"fit_residual_plot": "SASDXB2_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXB2_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/GASBORon_2877.log",
"software_version": null,
"description": "Gasbor Model"
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDXB2_fit2_model1_img.png",
"software": "AlphaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDXB2_fit2_model1.cif",
"model_mw": null,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "AlphaFold model",
"user": 396
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXB2_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 0.1,
"p_value": 0.0,
"fit_residual_plot": "SASDXB2_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDXB2_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/AF-A0A0W0EGC5-F1-model_v4_Zq1K1W7.log",
"software_version": null,
"description": "AlphaFold model"
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "4.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Phosphoglycerate kinase enzyme in 50 mM sodium phosphate, 500 mM NaCl, 500 mM imidazole, and 1 mM phenylmethylsulfonyl fluoride (PMSF) at pH 8.5 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.094 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 6 mg/ml was injected at a 0.07 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 15°C. 620 successive 3 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.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 47.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 46.5,
"porod_mw_error": null,
"pddf_i0": 0.05492,
"pddf_i0_error": null,
"guinier_i0": 0.0548792,
"guinier_i0_error": null,
"pddf_rg": 2.89,
"pddf_rg_error": null,
"guinier_rg": 2.86,
"guinier_rg_error": 0.179,
"pddf_dmax": 10.3,
"pddf_dmax_error": null,
"porod_volume": 79.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 3,
"guinier_point_last": 277,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDXB2_datloglog_img.png",
"symmetry": null,
"last_modified": "2026-01-22T09:29:53.275504+01:00",
"bragg_peak": []
}
