{ "code": "SASDVJ6", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Computational study of DPP8 and DPP9: fundamental insights and inhibitor design", "publication": { "title": "Computational study of DPP8 and DPP9: fundamental insights and inhibitor design", "author_list": "Olivier Beyens, Yann Sterckx", "journal": "University of Antwerp PhD thesis", "doi": null, "pmid": null, "published_date": "2024 Nov 06" }, "status": "released", "submitted_date": "2024-08-26", "released_date": "2025-01-14" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVJ6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVJ6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVJ6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVJ6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVJ6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVJ6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVJ6.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Eiger 4M", "resolution": 75.0 }, "name": "SOLEIL", "city": "Saint-Aubin", "country": "France", "beamline_name": "SWING", "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": "Isoform 1 of Dipeptidyl peptidase 8", "short_name": null, "sequence": "MWKRSEQMKIKSGKCNMAAAMETEQLGVEIFETADCEENIESQDRPKLEPFYVERYSWSQLKKLLADTRKYHGYMMAKAPHDFMFVKRNDPDGPHSDRIYYLAMSGENRENTLFYSEIPKTINRAAVLMLSWKPLLDLFQATLDYGMYSREEELLRERKRIGTVGIASYDYHQGSGTFLFQAGSGIYHVKDGGPQGFTQQPLRPNLVETSCPNIRMDPKLCPADPDWIAFIHSNDIWISNIVTREERRLTYVHNELANMEEDARSAGVATFVLQEEFDRYSGYWWCPKAETTPSGGKILRILYEENDESEVEIIHVTSPMLETRRADSFRYPKTGTANPKVTFKMSEIMIDAEGRIIDVIDKELIQPFEILFEGVEYIARAGWTPEGKYAWSILLDRSQTRLQIVLISPELFIPVEDDVMERQRLIESVPDSVTPLIIYEETTDIWINIHDIFHVFPQSHEEEIEFIFASECKTGFRHLYKITSILKESKYKRSSGGLPAPSDFKCPIKEEIAITSGEWEVLGRHGSNIQVDEVRRLVYFEGTKDSPLEHHLYVVSYVNPGEVTRLTDRGYSHSCCISQHCDFFISKYSNQKNPHCVSLYKLSSPEDDPTCKTKEFWATILDSAGPLPDYTPPEIFSFESTTGFTLYGMLYKPHDLQPGKKYPTVLFIYGGPQVQLVNNRFKGVKYFRLNTLASLGYVVVVIDNRGSCHRGLKFEGAFKYKMGQIEIDDQVEGLQYLASRYDFIDLDRVGIHGWSYGGYLSLMALMQRSDIFRVAIAGAPVTLWIFYDTGYTERYMGHPDQNEQGYYLGSVAMQAEKFPSEPNRLLLLHGFLDENVHFAHTSILLSFLVRAGKPYDLQIYPQERHSIRVPESGEHYELHLLHYLQENLGSRIAALKVIHHHHHH", "organism": "Homo sapiens", "uniprot_code": "Q6V1X1", "uniprot_range_first": 1, "uniprot_range_last": 898, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MWKRSEQMKIKSGKCNMAAAMETEQLGVEIFETADCEENIESQDRPKLEPFYVERYSWSQ\nLKKLLADTRKYHGYMMAKAPHDFMFVKRNDPDGPHSDRIYYLAMSGENRENTLFYSEIPK\nTINRAAVLMLSWKPLLDLFQATLDYGMYSREEELLRERKRIGTVGIASYDYHQGSGTFLF\nQAGSGIYHVKDGGPQGFTQQPLRPNLVETSCPNIRMDPKLCPADPDWIAFIHSNDIWISN\nIVTREERRLTYVHNELANMEEDARSAGVATFVLQEEFDRYSGYWWCPKAETTPSGGKILR\nILYEENDESEVEIIHVTSPMLETRRADSFRYPKTGTANPKVTFKMSEIMIDAEGRIIDVI\nDKELIQPFEILFEGVEYIARAGWTPEGKYAWSILLDRSQTRLQIVLISPELFIPVEDDVM\nERQRLIESVPDSVTPLIIYEETTDIWINIHDIFHVFPQSHEEEIEFIFASECKTGFRHLY\nKITSILKESKYKRSSGGLPAPSDFKCPIKEEIAITSGEWEVLGRHGSNIQVDEVRRLVYF\nEGTKDSPLEHHLYVVSYVNPGEVTRLTDRGYSHSCCISQHCDFFISKYSNQKNPHCVSLY\nKLSSPEDDPTCKTKEFWATILDSAGPLPDYTPPEIFSFESTTGFTLYGMLYKPHDLQPGK\nKYPTVLFIYGGPQVQLVNNRFKGVKYFRLNTLASLGYVVVVIDNRGSCHRGLKFEGAFKY\nKMGQIEIDDQVEGLQYLASRYDFIDLDRVGIHGWSYGGYLSLMALMQRSDIFRVAIAGAP\nVTLWIFYDTGYTERYMGHPDQNEQGYYLGSVAMQAEKFPSEPNRLLLLHGFLDENVHFAH\nTSILLSFLVRAGKPYDLQIYPQERHSIRVPESGEHYELHLLHYLQENLGSRIAALKVI", "mw": 104.18, "total_mw": 208.36, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "The protein construct used for SAXS contains an additional C-terminal polyhistidine tag (HHHHHH)." } ], "buffer": { "name": "25 mM HEPES, 150 mM NaCl, 2 mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "apo Dipeptidyl peptidase 8 (DPP8 apo)", "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": "University of Antwerp", "webpage": null } ], "contributor_name": "Yann", "contributor_surname": "Sterckx", "orcid": "https://orcid.org/0000-0002-7420-0983" } ], "concentration_method": null, "concentration_unit": null, "date": "2023-10-14", "storage_temperature": 10.0, "cell_temperature": 20.0, "exposure_time": 0.99, "number_of_frames": 870, "wavelength": 0.099, "sample_detector_distance": 2.0, "concentration_min": null, "concentration_max": 11.9, "sample_volume": 40.0, "flow_rate": 0.2, "s_min": 0.119, "s_max": 5.543, "total_exposure_time": null, "seccolumn": 43 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVJ6_fit1_model1_img.png", "software": "BILBOMD", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVJ6_fit1_model1.pdb", "model_mw": 207.4, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 488 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVJ6_fit1_fitfoxs_img.png", "software": "Other", "chi_square_value": 1.77, "p_value": 0.0, "fit_residual_plot": null, "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVJ6_fit1.dat", "fit_log": null, "software_version": "Bilbo-MD", "description": "" }, { "models": [ { "model_plot": null, "software": "DENSS", "pdb_link": [], "model_title": null, "type_of_model": "density", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVJ6_fit2_model1.mrc", "model_mw": null, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 488 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVJ6_fit2_fixed_fit_img.png", "software": "DENSS", "chi_square_value": 2.2209, "p_value": 0.9886, "fit_residual_plot": "SASDVJ6_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVJ6_fit2.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": null, "experiment_description": "Synchrotron SAXS data from solutions of DPP8 apo in 25 mM HEPES, 150 mM NaCl, 2 mM DTT, pH 7.5 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a Eiger 4M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.099 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 40.00 μl sample at 11.9 mg/ml was injected at a 0.20 ml/min flow rate onto a Shodex KW404-4F column at 20°C. 870 successive 0.990 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": 206.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 169.0, "porod_mw_error": null, "pddf_i0": 0.1726, "pddf_i0_error": null, "guinier_i0": 0.172482, "guinier_i0_error": null, "pddf_rg": 4.24, "pddf_rg_error": null, "guinier_rg": 4.217, "guinier_rg_error": 0.03, "pddf_dmax": 13.6, "pddf_dmax_error": null, "porod_volume": 271.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 3, "guinier_point_last": 42, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVJ6_datloglog_img.png", "symmetry": null, "last_modified": "2025-01-14T14:58:09.605963+01:00", "bragg_peak": [] }