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{
"code": "SASDE56",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle.",
"publication": {
"title": "Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle.",
"author_list": "Verschueren KHG, Blanchet C, Felix J, Dansercoer A, De Vos D, Bloch Y, Van Beeumen J, Svergun D, Gutsche I, Savvides SN, Verstraete K",
"journal": "Nature",
"doi": "10.1038/s41586-019-1095-5",
"pmid": "30944476",
"published_date": "2019 Apr"
},
"status": "released",
"submitted_date": "2018-10-10",
"released_date": "2019-04-02"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDE56.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDE56.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE56_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE56_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDE56_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE56_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDE56.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus 6M",
"resolution": null
},
"name": "PETRA III",
"city": "DESY; Hamburg",
"country": "Germany",
"beamline_name": "EMBL P12",
"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": "ATP-citrate synthase",
"short_name": null,
"sequence": "MSAKAISEQTGKELLYKFICTTSAIQNRFKYARVTPDTDWARLLQDHPWLLSQNLVVKPDQLIKRRGKLGLVGVNLTLDGVKSWLKPRLGQEATVGKATGFLKNFLIEPFVPHSQAEEFYVCIYATREGDYVLFHHEGGVDVGDVDAKAQKLLVGVDEKLNPEDIKKHLLVHAPEDKKEILASFISGLFNFYEDLYFTYLEINPLVVTKDGVYVLDLAAKVDATADYICKVKWGDIEFPPPFGREAYPEEAYIADLDAKSGASLKLTLLNPKGRIWTMVAGGGASVVYSDTICDLGGVNELANYGEYSGAPSEQQTYDYAKTILSLMTREKHPDGKILIIGGSIANFTNVAATFKGIVRAIRDYQGPLKEHEVTIFVRRGGPNYQEGLRVMGEVGKTTGIPIHVFGTETHMTAIVGMALGHRPIPGKSTTLFSRHTKAIVWGMQTRAVQGMLDFDYVCSRDEPSVAAMVYPFTGDHKQKFYWGHKEILIPVFKNMADAMRKHPEVDVLINFASLRSAYDSTMETMNYAQIRTIAIIAEGIPEALTRKLIKKADQKGVTIIGPATVGGIKPGCFKIGNTGGMLDNILASKLYRPGSVAYVSRSGGMSNELNNIISRTTDGVYEGVAIGGDRYPGSTFMDHVLRYQDTPGVKMIVVLGEIGGTEEYKICRGIKEGRLTKPIVCWCIGTCATMFSSEVQFGHAGACANQASETAVAKNQALKEAGVFVPRSFDELGEIIQSVYEDLVANGVIVPAQEVPPPTVPMDYSWARELGLIRKPASFMTSICDERGQELIYAGMPITEVFKEEMGIGGVLGLLWFQKRLPKYSCQFIEMCLMVTADHGPAVSGAHNTIICARAGKDLVSSLTSGLLTIGDRFGGALDAAAKMFSKAFDSGIIPMEFVNKMKKEGKLIMGIGHRVKSINNPDMRVQILKDYVRQHFPATPLLDYALEVEKITTSKKPNLILNVDGLIGVAFVDMLRNCGSFTREEADEYIDIGALNGIFVLGRSMGFIGHYLDQKRLKQGLYRHPWDDISYVLPEHMSM",
"organism": "Homo sapiens",
"uniprot_code": "P53396",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "tetramer",
"molecular_type": "protein",
"uniprot_sequence": "MSAKAISEQTGKELLYKFICTTSAIQNRFKYARVTPDTDWARLLQDHPWLLSQNLVVKPD\nQLIKRRGKLGLVGVNLTLDGVKSWLKPRLGQEATVGKATGFLKNFLIEPFVPHSQAEEFY\nVCIYATREGDYVLFHHEGGVDVGDVDAKAQKLLVGVDEKLNPEDIKKHLLVHAPEDKKEI\nLASFISGLFNFYEDLYFTYLEINPLVVTKDGVYVLDLAAKVDATADYICKVKWGDIEFPP\nPFGREAYPEEAYIADLDAKSGASLKLTLLNPKGRIWTMVAGGGASVVYSDTICDLGGVNE\nLANYGEYSGAPSEQQTYDYAKTILSLMTREKHPDGKILIIGGSIANFTNVAATFKGIVRA\nIRDYQGPLKEHEVTIFVRRGGPNYQEGLRVMGEVGKTTGIPIHVFGTETHMTAIVGMALG\nHRPIPNQPPTAAHTANFLLNASGSTSTPAPSRTASFSESRADEVAPAKKAKPAMPQDSVP\nSPRSLQGKSTTLFSRHTKAIVWGMQTRAVQGMLDFDYVCSRDEPSVAAMVYPFTGDHKQK\nFYWGHKEILIPVFKNMADAMRKHPEVDVLINFASLRSAYDSTMETMNYAQIRTIAIIAEG\nIPEALTRKLIKKADQKGVTIIGPATVGGIKPGCFKIGNTGGMLDNILASKLYRPGSVAYV\nSRSGGMSNELNNIISRTTDGVYEGVAIGGDRYPGSTFMDHVLRYQDTPGVKMIVVLGEIG\nGTEEYKICRGIKEGRLTKPIVCWCIGTCATMFSSEVQFGHAGACANQASETAVAKNQALK\nEAGVFVPRSFDELGEIIQSVYEDLVANGVIVPAQEVPPPTVPMDYSWARELGLIRKPASF\nMTSICDERGQELIYAGMPITEVFKEEMGIGGVLGLLWFQKRLPKYSCQFIEMCLMVTADH\nGPAVSGAHNTIICARAGKDLVSSLTSGLLTIGDRFGGALDAAAKMFSKAFDSGIIPMEFV\nNKMKKEGKLIMGIGHRVKSINNPDMRVQILKDYVRQHFPATPLLDYALEVEKITTSKKPN\nLILNVDGLIGVAFVDMLRNCGSFTREEADEYIDIGALNGIFVLGRSMGFIGHYLDQKRLK\nQGLYRHPWDDISYVLPEHMSM",
"mw": 114.58,
"total_mw": 458.32,
"number_molecules": 4,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20mM HEPES, 150mM NaCl, 50mM Tris, 20mM citrate, 2mM CoA",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.2,
"deuteration": null
},
"purity_method": null,
"name": "Human ATP-citrate synthase (ACLY) in HBS + Citrate + Coenzyme-A",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL-Hamburg",
"address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
"full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
"webpage": "http://www.embl-hamburg.de/index.php"
}
],
"contributor_name": "Clement",
"contributor_surname": "Blanchet",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-05-05",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 900,
"wavelength": 0.124,
"sample_detector_distance": 3.1,
"concentration_min": null,
"concentration_max": 24.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.024,
"s_max": 7.297,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDE56_fit1_model1_img.png",
"software": "SASREF CV",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDE56_fit1_model1.pdb",
"model_mw": 454.9,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/coa_op_0.log",
"symmetry": "P222",
"comment": null,
"user": 43
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/h_coa_op_0-1_fit_img.png",
"software": "SASREF CV",
"chi_square_value": 7.25,
"p_value": 0.0,
"fit_residual_plot": "h_coa_op_0-1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDE56_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/coa_op_0.log",
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDE56_fit2_model1_img.png",
"software": "MultiFoXS",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDE56_fit2_model1.pdb",
"model_mw": 452.8,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 43
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDE56_e1_0_single_statehACL_AB_CoA_chi_2p76_fixed_fit_img.png",
"software": "MultiFoXS",
"chi_square_value": 2.756566,
"p_value": 0.0,
"fit_residual_plot": "SASDE56_e1_0_single_statehACL_AB_CoA_chi_2p76_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDE56_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 ATP-citrate synthase (ACLY) in 20mM HEPES, 150mM NaCl, 50mM Tris, 20mM citrate, 2mM coenzyme-A, pH 7.2 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Size-exclusion chromatography SAXS (SEC-SAXS) was employed using a sample injection concentration of 24.00 mg/ml. Data were measured at through the SEC elution at 20°C. 900 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of an appropriate solvent-blank was subtracted using the CHROMIXS SEC-SAXS analysis package.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 480.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 440.0,
"porod_mw_error": null,
"pddf_i0": 11900.0,
"pddf_i0_error": null,
"guinier_i0": 11832.0,
"guinier_i0_error": 10.0,
"pddf_rg": 5.768,
"pddf_rg_error": null,
"guinier_rg": 5.75,
"guinier_rg_error": 0.01,
"pddf_dmax": 16.5,
"pddf_dmax_error": null,
"porod_volume": 709.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 12,
"guinier_point_last": 74,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDE56_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:55:24.740692+02:00",
"bragg_peak": []
}
