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{
"code": "SASDD93",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "The antibiotic cyclomarin blocks arginine-phosphate-induced millisecond dynamics in the N-terminal domain of ClpC1 from <i>Mycobacterium tuberculosis</i>.",
"publication": {
"title": "The antibiotic cyclomarin blocks arginine-phosphate-induced millisecond dynamics in the N-terminal domain of ClpC1 from <i>Mycobacterium tuberculosis</i>.",
"author_list": "Weinhäupl K, Brennich M, Kazmaier U, Lelievre J, Ballell L, Goldberg A, Schanda P, Fraga H",
"journal": "J Biol Chem",
"doi": "10.1074/jbc.RA118.002251",
"pmid": "29632076",
"published_date": "2018 Jun 1"
},
"status": "released",
"submitted_date": "2018-01-24",
"released_date": "2018-06-12"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDD93.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD93.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD93_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD93_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD93_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD93_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDD93.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "ESRF",
"city": "Grenoble",
"country": "France",
"beamline_name": "BM29",
"beam_geometry": "",
"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-dependent Clp protease ATP-binding subunit ClpC1",
"short_name": "ClpC1",
"sequence": "MFERFTDRARRVVVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKSLESLGISLEGVR\r\nSQVEEIIGQGQQAPSGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA\r\nAQVLVKLGAELTRVRQQVIQLLSGYQGKEAAEAGTGGRGGESGSPSTSLVLDQFGRNLTA\r\nAAMEGKLDPVIGREKEIERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIVHGEVPE\r\nTLKDKQLYTLDLGSLVAGSRYRGDFEERLKKVLKEINTRGDIILFIDELHTLVGAGAAEG\r\nAIDAASILKPKLARGELQTIGATTLDEYRKYIEKDAALERRFQPVQVGEPTVEHTIEILK\r\nGLRDRYEAHHRVSITDAAMVAAATLADRYINDRFLPDKAIDLIDEAGARMRIRRMTAPPD\r\nLREFDEKIAEARREKESAIDAQDFEKAASLRDREKTLVAQRAEREKQWRSGDLDVVAEVD\r\nDEQIAEVLGNWTGIPVFKLTEAETTRLLRMEEELHKRIIGQEDAVKAVSKAIRRTRAGLK\r\nDPKRPSGSFIFAGPSGVGKTELSKALANFLFGDDDALIQIDMGEFHDRFTASRLFGAPPG\r\nYVGYEEGGQLTEKVRRKPFSVVLFDEIEKAHQEIYNSLLQVLEDGRLTDGQGRTVDFKNT\r\nVLIFTSNLGTSDISKPVGLGFSKGGGENDYERMKQKVNDELKKHFRPEFLNRIDDIIVFH\r\nQLTREEIIRMVDLMISRVAGQLKSKDMALVLTDAAKALLAKRGFDPVLGARPLRRTIQRE\r\nIEDQLSEKILFEEVGPGQVVTVDVDNWDGEGPGEDAVFTFTGTRKPPAEPDLAKAGAHSA\r\nGGPEPAARGSHHHHHH",
"organism": "Mycobacterium tuberculosis",
"uniprot_code": "P9WPC9",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "unknown",
"molecular_type": "protein",
"uniprot_sequence": "MFERFTDRARRVVVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKSLESLGISLEGVR\nSQVEEIIGQGQQAPSGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA\nAQVLVKLGAELTRVRQQVIQLLSGYQGKEAAEAGTGGRGGESGSPSTSLVLDQFGRNLTA\nAAMEGKLDPVIGREKEIERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIVHGEVPE\nTLKDKQLYTLDLGSLVAGSRYRGDFEERLKKVLKEINTRGDIILFIDELHTLVGAGAAEG\nAIDAASILKPKLARGELQTIGATTLDEYRKYIEKDAALERRFQPVQVGEPTVEHTIEILK\nGLRDRYEAHHRVSITDAAMVAAATLADRYINDRFLPDKAIDLIDEAGARMRIRRMTAPPD\nLREFDEKIAEARREKESAIDAQDFEKAASLRDREKTLVAQRAEREKQWRSGDLDVVAEVD\nDEQIAEVLGNWTGIPVFKLTEAETTRLLRMEEELHKRIIGQEDAVKAVSKAIRRTRAGLK\nDPKRPSGSFIFAGPSGVGKTELSKALANFLFGDDDALIQIDMGEFHDRFTASRLFGAPPG\nYVGYEEGGQLTEKVRRKPFSVVLFDEIEKAHQEIYNSLLQVLEDGRLTDGQGRTVDFKNT\nVLIFTSNLGTSDISKPVGLGFSKGGGENDYERMKQKVNDELKKHFRPEFLNRIDDIIVFH\nQLTREEIIRMVDLMISRVAGQLKSKDMALVLTDAAKALLAKRGFDPVLGARPLRRTIQRE\nIEDQLSEKILFEEVGPGQVVTVDVDNWDGEGPGEDAVFTFTGTRKPPAEPDLAKAGAHSA\nGGPEPAAR",
"mw": 94.518,
"total_mw": 94.518,
"number_molecules": 0,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "Hepes 50 mM pH 7.5, KCl 100 mM, glycerol 10%, MgCl2 4 mM and ATP 1 mM",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "ATP-dependent Clp protease ATP-binding subunit ClpC1",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL",
"address": "Grenoble, France",
"full_name": "European Molecular Biology Laboratory (EMBL) - Grenoble Outstation",
"webpage": "https://www.embl.fr/"
}
],
"contributor_name": "Martha",
"contributor_surname": "Brennich",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-09-18",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 49,
"wavelength": 0.099,
"sample_detector_distance": 2.867,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.09,
"s_max": 2.383,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD93_fit1_model1_img.png",
"software": "Other",
"pdb_link": [
{
"pdb_code": "6em9",
"ext_code": "6EM9",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDD93_fit1_model1.pdb",
"model_mw": 348.2,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 119
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD93_fit1_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 3.337,
"p_value": 0.0,
"fit_residual_plot": "SASDD93_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD93_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Ca_C1ClpCresting_full3_modified_685504.log",
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD93_fit2_model1_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/SASDD93_fit2_model1.pdb",
"model_mw": 1190.0,
"bead_radius": 4.2,
"log": null,
"symmetry": null,
"comment": null,
"user": 119
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD93_fit2_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.59,
"p_value": 0.967615,
"fit_residual_plot": "SASDD93_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD93_fit2.fir",
"fit_log": null,
"software_version": null,
"description": null
}
],
"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-dependent Clp protease ATP-binding subunit ClpC1 in 50 mM HEPES, pH 7.5, 100 mM KCl, 10% v/v glycerol, 4 mM MgCl2 and 1 mM ATP were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Size-exclusion chromatography SEC-SAXS was performed on a sample at at 20°C. 49 successive 1 second frames were collected through the corresponding SEC elution peak. Each data frame was normalized to the intensity of the transmitted beam and radially averaged (2D- to 1D data reduction). The scattering of the solvent-blank (reduced data obtained from the elution buffer) was subtracted from each sample frame and the resulting subtracted SAXS profiles were scaled and averaged to generate the data displayed in this entry.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 1250.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 1250.0,
"porod_mw_error": null,
"pddf_i0": 44.73,
"pddf_i0_error": 0.1,
"guinier_i0": 44.59,
"guinier_i0_error": 0.13,
"pddf_rg": 7.702,
"pddf_rg_error": 0.02,
"guinier_rg": 7.64,
"guinier_rg_error": 0.03,
"pddf_dmax": 25.0,
"pddf_dmax_error": null,
"porod_volume": 2156.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 17,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDD93_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
