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{
"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": []
}
