{ "code": "SASDF93", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/nm", "project": { "title": "The archaeal LDH-like malate dehydrogenase from Ignicoccus islandicus displays dual substrate recognition, hidden allostery and a non-canonical tetrameric oligomeric organization", "publication": { "title": "The archaeal LDH-like malate dehydrogenase from Ignicoccus islandicus displays dual substrate recognition, hidden allostery and a non-canonical tetrameric oligomeric organization", "author_list": "Roche J, Girard E, Mas C, Madern D", "journal": "Journal of Structural Biology", "doi": "/10.1016/j.jsb.2019.07.006", "pmid": null, "published_date": "2019 Jul" }, "status": "released", "submitted_date": "2019-02-20", "released_date": "2019-07-11" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDF93.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF93.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF93_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF93_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF93_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF93_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF93.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": "Malate dehydrogenase", "short_name": null, "sequence": "MARIPYKVAVIGTGRVGATFAYTMAVVPGIARMTLVDVVPGLAKGVMEDIKHAAAVFRRSITVEAFEDVSKVENADAIVITAGKPRKADMSRRDLANVNAQIIRDIGDKLRDRNPGALYVVVTNPVDVMTMVLDDVIGSKGTVIGTGTSLDTFRFRAAVSELLNVPIVAVDGYVVGEHGEEAFVAWSTVTIKGIHIDQYIKERNINISREQIEKYVKDVAASIIASQGATIWGPAATFQEIVVSHLANESKIIPISLPQNIEGVGRVAVSVPTIISGRLKPLVQLLNEEEQERLKRAAKAIRNVYESILT", "organism": "Ignicoccus islandicus DSM 13165", "uniprot_code": "A0A0U3FQH7", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "tetramer", "molecular_type": "protein", "uniprot_sequence": "MARIPYKVAVIGTGRVGATFAYTMAVVPGIARMTLVDVVPGLAKGVMEDIKHAAAVFRRS\nITVEAFEDVSKVENADAIVITAGKPRKADMSRRDLANVNAQIIRDIGDKLRDRNPGALYV\nVVTNPVDVMTMVLDDVIGSKGTVIGTGTSLDTFRFRAAVSELLNVPIVAVDGYVVGEHGE\nEAFVAWSTVTIKGIHIDQYIKERNINISREQIEKYVKDVAASIIASQGATIWGPAATFQE\nIVVSHLANESKIIPISLPQNIEGVGRVAVSVPTIISGRLKPLVQLLNEEEQERLKRAAKA\nIRNVYESILT", "mw": 33.552, "total_mw": 134.208, "number_molecules": 4, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM Tris-HCl 50 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Ignicoccus islandicus malate dehydrogenase", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "IBS", "address": "Grenoble, France", "full_name": "Institut de Biologie Structurale", "webpage": "" } ], "contributor_name": "Jennifer", "contributor_surname": "Roche", "orcid": "https://orcid.org/0000-0002-6234-1340" } ], "concentration_method": null, "concentration_unit": null, "date": "2018-09-05", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 10, "wavelength": 0.125, "sample_detector_distance": 2.85, "concentration_min": 0.39, "concentration_max": 9.31, "sample_volume": null, "flow_rate": null, "s_min": 0.045, "s_max": 4.946, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF93_fit1_model1_img.png", "software": "PDB (Protein Data Bank)", "pdb_link": [ { "pdb_code": "6qss", "ext_code": "6QSS", "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/SASDF93_fit1_model1.pdb", "model_mw": 135.2, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 419 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/refine00_fit_img.png", "software": "CRYSOL", "chi_square_value": 1.678, "p_value": 0.0, "fit_residual_plot": "refine00_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF93_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/refine00.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 I. islandicus malate dehydrogenase in 50 mM Tris-HCl 50 mM NaCl, pH 7.4 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.125 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.4 and 9.3 mg/ml were measured at 20°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 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": 118.75, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 124.0, "porod_mw_error": null, "pddf_i0": 107.7, "pddf_i0_error": null, "guinier_i0": 109.12, "guinier_i0_error": 0.61, "pddf_rg": 3.163, "pddf_rg_error": null, "guinier_rg": 3.26, "guinier_rg_error": 0.03, "pddf_dmax": 8.96, "pddf_dmax_error": null, "porod_volume": 198.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 17, "guinier_point_last": 75, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDF93_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }