{ "code": "SASDG36", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase.", "publication": { "title": "Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase.", "author_list": "Majdi Yazdi M, Saran S, Mrozowich T, Lehnert C, Patel TR, Sanders DAR, Palmer DRJ", "journal": "J Struct Biol", "doi": "10.1016/j.jsb.2019.107409", "pmid": "31678256", "published_date": "2019 Oct 31" }, "status": "released", "submitted_date": "2019-09-29", "released_date": "2019-11-17" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDG36.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDG36.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG36_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG36_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDG36_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG36_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDG36.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "Diamond Light Source", "city": "Didcot", "country": "UK", "beamline_name": "B21", "beam_geometry": "1 x 5 mm", "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": "4-hydroxy-tetrahydrodipicolinate synthase (N84D mutant)", "short_name": "HTPA synthase N84D", "sequence": "MDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSDATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF", "organism": "Campylobacter jejuni", "uniprot_code": "Q9PPB4", "uniprot_range_first": 1, "uniprot_range_last": 298, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHR\nTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLY\nEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLA\nHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDEL\nYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF", "mw": 32.671, "total_mw": 65.342, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM Tris-HCl, 150 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "4-hydroxy-tetrahydrodipicolinate synthase (N84D mutant)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Lethbridge, AB, Canada", "full_name": "University of Lethbridge", "webpage": "http://www.uleth.ca/" } ], "contributor_name": "Trushar", "contributor_surname": "Patel", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2017-08-02", "storage_temperature": null, "cell_temperature": null, "exposure_time": 3.0, "number_of_frames": 619, "wavelength": 0.1, "sample_detector_distance": 4.0, "concentration_min": null, "concentration_max": 10.0, "sample_volume": 50.0, "flow_rate": 0.16, "s_min": 0.066, "s_max": 3.898, "total_exposure_time": null, "seccolumn": 1 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG36_fit1_model1_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "DAMFILT 5.0 (r9678)", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDG36_fit1_model1.pdb", "model_mw": 63.444, "bead_radius": 3.25, "log": null, "symmetry": null, "comment": null, "user": 239 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDG36_fit1_model2_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDG36_fit1_model2.pdb", "model_mw": 63.5, "bead_radius": 1.9, "log": null, "symmetry": "P1", "comment": null, "user": 239 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/untitled_2637_2_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.424, "p_value": 0.005573, "fit_residual_plot": "untitled_2637_2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDG36_fit1.fir", "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": "The models displayed in this entry represent: Top, the averaged (DAMFILT) model obtained from the spatial alignment of several individual DAMMIF models (volume and bead occupancy corrected) and; Bottom, and individual DAMMIF model representative and corresponding fit. Additional individual DAMMIF models (in P1 symmetry) are provided in the full entry zip archive.", "experiment_description": "Synchrotron SAXS data from solutions of N84D mutant 4-hydroxy-tetrahydrodipicolinate synthase in 20 mM Tris-HCl, 150 mM NaCl, pH 8 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Pilatus 2M detector at a sample-detector distance of 4 m and at a wavelength of λ = 0.1 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 10 mg/ml was injected at a 0.16 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column . 619 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": 78.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 54.0, "porod_mw_error": null, "pddf_i0": 0.07698, "pddf_i0_error": 3e-05, "guinier_i0": 0.077, "guinier_i0_error": 6e-05, "pddf_rg": 3.08, "pddf_rg_error": 0.02, "guinier_rg": 3.1, "guinier_rg_error": 0.04, "pddf_dmax": 9.5, "pddf_dmax_error": null, "porod_volume": 108.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 6, "guinier_point_last": 153, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDG36_datloglog_img.png", "symmetry": null, "last_modified": "2021-04-22T13:41:03.378678+02:00", "bragg_peak": [] }