{ "code": "SASDWG4", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Structure and Dynamics of Macrophage Infectivity Potentiator Proteins from Pathogenic Bacteria and Protozoans Bound to Fluorinated Pipecolic Acid Inhibitors.", "publication": { "title": "Structure and Dynamics of Macrophage Infectivity Potentiator Proteins from Pathogenic Bacteria and Protozoans Bound to Fluorinated Pipecolic Acid Inhibitors.", "author_list": "Pérez Carrillo VH, Whittaker JJ, Wiedemann C, Harder JM, Lohr T, Jamithireddy AK, Dajka M, Goretzki B, Joseph B, Guskov A, Harmer NJ, Holzgrabe U, Hellmich UA", "journal": "J Med Chem", "doi": "10.1021/acs.jmedchem.5c00134", "pmid": "39976355", "published_date": "2025 Feb 20" }, "status": "released", "submitted_date": "2025-01-08", "released_date": "2025-03-03" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDWG4.out", "intensities_data": 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"xray_energy": null, "beam_profile_ah": null, "beam_profile_al": null }, "sample": { "molecule": [ { "long_name": "Outer membrane protein MIP", "short_name": "LpMIP", "sequence": "ATDATSLATDKDKLSYSIGADLGKNFKNQGIDVNPEAMAK\r\nGMQDAMSGAQLALTEQQMKDVLNKFQKDLMAKRTAEFNKKADENKVKGEAFLTENKNKPG\r\nVVVLPSGLQYKVINSGNGVKPGKSDTVTVEYTGRLIDGTVFDSTEKTGKPATFQVSQVIP\r\nGWTEALQLMPAGSTWEIYVPSGLAYGPRSVGGPIGPNETLIFKIHLISVKKSS", "organism": "Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)", "uniprot_code": "Q5ZXE0", "uniprot_range_first": 21, "uniprot_range_last": 233, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MKMKLVTAAVMGLAMSTAMAATDATSLATDKDKLSYSIGADLGKNFKNQGIDVNPEAMAK\nGMQDAMSGAQLALTEQQMKDVLNKFQKDLMAKRTAEFNKKADENKVKGEAFLTENKNKPG\nVVVLPSGLQYKVINSGNGVKPGKSDTVTVEYTGRLIDGTVFDSTEKTGKPATFQVSQVIP\nGWTEALQLMPAGSTWEIYVPSGLAYGPRSVGGPIGPNETLIFKIHLISVKKSS", "mw": 22.842, "total_mw": 45.684, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" }, { "long_name": "(2S)‐3‐(4‐fluorophenyl)‐2‐{[(2S)‐1‐[(4‐ fluorophenyl)methanesulfonyl]piperidin‐2‐ yl]formamido}‐N‐[(pyridin‐3‐yl)methyl]propanamide", "short_name": "NJS227", "sequence": "C28H30F2N4O4S", "organism": null, "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "other", "uniprot_sequence": "", "mw": 0.557, "total_mw": 0.557, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "NJS227: https://pubchem.ncbi.nlm.nih.gov/compound/169192343" } ], "buffer": { "name": "20 mM Tris, 150 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Outer membrane protein MIP from Legionella pneumophila (LpMIP) in complex with inhibitor NJS227", "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": "Friedrich-Schiller-University Jena", "webpage": null } ], "contributor_name": "Jean-Martin", "contributor_surname": "Harder", "orcid": "https://orcid.org/0000-0002-2322-5371" } ], "concentration_method": null, "concentration_unit": null, "date": "2021-11-22", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 0.095, "number_of_frames": 2400, "wavelength": 0.124, "sample_detector_distance": 3.0, "concentration_min": null, "concentration_max": 5.0, "sample_volume": null, "flow_rate": null, "s_min": 0.024, "s_max": 7.371, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWG4_fit1_model1_img.png", "software": "SREFLEX", "pdb_link": [], "model_title": 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"chi_square_value": 1.169, "p_value": 0.5776, "fit_residual_plot": "SASDWG4_fit3_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWG4_fit3.fit", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWG4_fit4_model1_img.png", "software": "SREFLEX", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "3.2.1", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDWG4_fit4_model1.pdb", "model_mw": 44.02, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 1169 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWG4_fit4_fixed_fit_img.png", "software": "SREFLEX", "chi_square_value": 1.191, "p_value": 0.0264, "fit_residual_plot": "SASDWG4_fit4_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWG4_fit4.fit", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWG4_fit5_model1_img.png", "software": "SREFLEX", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "3.2.1", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDWG4_fit5_model1.pdb", "model_mw": 44.02, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 1169 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWG4_fit5_fixed_fit_img.png", "software": "SREFLEX", "chi_square_value": 1.208, "p_value": 0.3493, "fit_residual_plot": "SASDWG4_fit5_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWG4_fit5.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": "NJS227: https://pubchem.ncbi.nlm.nih.gov/compound/169192343", "experiment_description": "Synchrotron SAXS data from solutions of outer membrane protein MIP in complex with inhibitor NJS227 in 20 mM Tris, 150 mM NaCl, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 5.00 mg/ml was measured at 20°C. 11 successive 0.095 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": 42.0, "experimental_mw_error": null, "guinier_i0_mw": 37.0, "guinier_i0_mw_error": 2.8, "porod_mw": 40.8, "porod_mw_error": null, "pddf_i0": 0.1724, "pddf_i0_error": 0.0002, "guinier_i0": 0.1717, "guinier_i0_error": 0.0003, "pddf_rg": 3.002, "pddf_rg_error": 0.006, "guinier_rg": 2.953, "guinier_rg_error": 0.096, "pddf_dmax": 10.01, "pddf_dmax_error": null, "porod_volume": 65.4, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 31, "guinier_point_last": 148, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDWG4_datloglog_img.png", "symmetry": null, "last_modified": "2025-03-03T15:29:42.991874+01:00", "bragg_peak": [] }