{ "code": "SASDEF5", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Crystal structure of a xylulose 5-phosphate phosphoketolase. insights into the substrate specificity for xylulose 5-phosphate.", "publication": { "title": "Crystal structure of a xylulose 5-phosphate phosphoketolase. insights into the substrate specificity for xylulose 5-phosphate.", "author_list": "Scheidig AJ, Horvath D, Szedlacsek SE", "journal": "J Struct Biol", "doi": "10.1016/j.jsb.2019.04.017", "pmid": "31059775", "published_date": "2019 May 3" }, "status": "released", "submitted_date": "2018-09-30", "released_date": "2019-05-08" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEF5.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEF5.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEF5_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEF5_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEF5_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEF5_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEF5.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "PETRA III", "city": "DESY; Hamburg", "country": "Germany", "beamline_name": "EMBL P12", "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": "Probable phosphoketolase", "short_name": null, "sequence": "MSHHHHHHSMDIEFVDLEGSMTEYNSEAYLKKLDKWWRAATYLGAGMIFLKENPLFSVTGTPIKAENL\r\nKANPIGHWGTVSGQTFLYAHANRLINKYDQKMFYMGGPGHGGQAMVVPSYLDGSYTEAY\r\nPEITQDLEGMSRLFKRFSFPGGIGSHMTAQTPGSLHEGGELGYVLSHATGAILDQPEQI\r\nAFAVVGDGEAETGPLMTSWHSIKFINPKNDGAILPILDLNGFKISNPTLFARTSDVDIR\r\nKFFEGLGYSPRYIENDDIHDYMAYHKLAAEVFDKAIEDIHQIQKDAREDNRYQNGEIPA\r\nWPIVIARLPKGWGGPRYNDWSGPKFDGKGMPIEHSFRAHQVPLPLSSKNMGTLPEFVKW\r\nMTSYQPETLFNADGSLKEELRDFAPKGEMRMASNPVTNGGVDSSNLVLPDWQEFANPIS\r\nENNRGKLLPDTNDNMDMNVLSKYFAEIVKLNPTRFRLFGPDETMSNRFWEMFKVTNRQW\r\nMQVIKNPNDEFISPEGRIIDSQLSEHQAEGWLEGYTLTGRTGAFASYESFLRVVDSMLT\r\nQHFKWIRQAADQKWRHDYPSLNVISTSTVFQQDHNGYTHQDPGMLTHLAEKKSDFIRQY\r\nLPADGNTLLAVFDRAFQDRSKINHIVASKQPRQQWFTKEEAEKLATDGIATIDWASTAK\r\nDGEAVDLVFASAGAEPTIETLAALHLVNEVFPQAKFRYVNVVELGRLQKKKGALNQERE\r\nLSDEEFEKYFGPSGTPVIFGFHGYEDLIESIFYQRGHDGLIVHGYREDGDITTTYDMRV\r\nYSELDRFHQAIDAMQVLYVNRKVNQGLAKAFIDRMKRTLVKHFEVTRNEGVDIPDFTEW\r\nVWSDLKK", "organism": "Lactococcus lactis subsp. lactis", "uniprot_code": "Q9CFH4", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MTEYNSEAYLKKLDKWWRAATYLGAGMIFLKENPLFSVTGTPIKAENLKANPIGHWGTVS\nGQTFLYAHANRLINKYDQKMFYMGGPGHGGQAMVVPSYLDGSYTEAYPEITQDLEGMSRL\nFKRFSFPGGIGSHMTAQTPGSLHEGGELGYVLSHATGAILDQPEQIAFAVVGDGEAETGP\nLMTSWHSIKFINPKNDGAILPILDLNGFKISNPTLFARTSDVDIRKFFEGLGYSPRYIEN\nDDIHDYMAYHKLAAEVFDKAIEDIHQIQKDAREDNRYQNGEIPAWPIVIARLPKGWGGPR\nYNDWSGPKFDGKGMPIEHSFRAHQVPLPLSSKNMGTLPEFVKWMTSYQPETLFNADGSLK\nEELRDFAPKGEMRMASNPVTNGGVDSSNLVLPDWQEFANPISENNRGKLLPDTNDNMDMN\nVLSKYFAEIVKLNPTRFRLFGPDETMSNRFWEMFKVTNRQWMQVIKNPNDEFISPEGRII\nDSQLSEHQAEGWLEGYTLTGRTGAFASYESFLRVVDSMLTQHFKWIRQAADQKWRHDYPS\nLNVISTSTVFQQDHNGYTHQDPGMLTHLAEKKSDFIRQYLPADGNTLLAVFDRAFQDRSK\nINHIVASKQPRQQWFTKEEAEKLATDGIATIDWASTAKDGEAVDLVFASAGAEPTIETLA\nALHLVNEVFPQAKFRYVNVVELGRLQKKKGALNQERELSDEEFEKYFGPSGTPVIFGFHG\nYEDLIESIFYQRGHDGLIVHGYREDGDITTTYDMRVYSELDRFHQAIDAMQVLYVNRKVN\nQGLAKAFIDRMKRTLVKHFEVTRNEGVDIPDFTEWVWSDLKK", "mw": 95.727, "total_mw": 191.454, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20mM potassium phosphate 150mM NaCl 0.007 %(w/v) β-octyl glucoside 1mM DTT 1mM MgCl 1mM thiaminpyrophosphate 2 %(v/v) glycerol", "concentration_unit": null, "comment": "SEC11 buffer", "additive": null, "concentration": null, "pka": null, "ph": 7.0, "deuteration": null }, "purity_method": null, "name": "Phosphoketolase (L. lactis) with 1 mM thiaminpyrophosphate and 2% v/v glycerol at pH 7.0", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Germany", "full_name": "Kiel University", "webpage": "https://www.uni-kiel.de" } ], "contributor_name": "Axel", "contributor_surname": "Scheidig", "orcid": "https://orcid.org/0000-0002-2382-8818" } ], "concentration_method": null, "concentration_unit": null, "date": "2017-09-07", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 0.045, "number_of_frames": 29, "wavelength": 0.124, "sample_detector_distance": 3.0, "concentration_min": null, "concentration_max": 8.0, "sample_volume": null, "flow_rate": null, "s_min": 0.025, "s_max": 5.064, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEF5_fit1_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "6gua", "ext_code": "6GUA", "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/SASDEF5_fit1_model1.pdb", "model_mw": 186.9, "bead_radius": null, "log": null, "symmetry": "P2", "comment": "PDB-ID 6GUA is a tetramer of dimers; the dimer is supposed to be the biological assembly in solution", "user": 366 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/pk7_ref82_AB_fit_img.png", "software": "CRYSOL", "chi_square_value": 3.244, "p_value": 0.0, "fit_residual_plot": "pk7_ref82_AB_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEF5_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/pk7_ref82_AB.log", "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEF5_fit2_model1_img.png", "software": "SASREF", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEF5_fit2_model1.pdb", "model_mw": 187.1, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/PKLl2mop.log", "symmetry": "P1", "comment": null, "user": 366 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/PKLl2mop-1_fit_img.png", "software": "SASREF", "chi_square_value": 1.9, "p_value": 0.0, "fit_residual_plot": "PKLl2mop-1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEF5_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/PKLl2mop.log", "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 phosphoketolase in 20mM potassium phosphate, 150mM NaCl, 0.007 %(w/v) β-octyl glucoside, 1mM DTT, 1mM MgCl2, 1mM thiaminpyrophosphate, 2 % v/v glycerol, pH 7 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 8.00 mg/ml was measured at 20°C. 29 successive 0.045 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": "1/cm", "experimental_mw": 164.0, "experimental_mw_error": null, "guinier_i0_mw": 146.0, "guinier_i0_mw_error": null, "porod_mw": 148.0, "porod_mw_error": null, "pddf_i0": 21180.0, "pddf_i0_error": null, "guinier_i0": 21282.0, "guinier_i0_error": 14.3, "pddf_rg": 3.387, "pddf_rg_error": null, "guinier_rg": 3.44, "guinier_rg_error": 0.55, "pddf_dmax": 10.15, "pddf_dmax_error": null, "porod_volume": 237.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 34, "guinier_point_last": 128, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEF5_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:56:39.492710+02:00", "bragg_peak": [] }