{
"code": "SASDDH9",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "Arabidopsis and Chlamydomonas phosphoribulokinase crystal structures complete the redox structural proteome of the Calvin-Benson cycle.",
"publication": {
"title": "Arabidopsis and Chlamydomonas phosphoribulokinase crystal structures complete the redox structural proteome of the Calvin-Benson cycle.",
"author_list": "Gurrieri L, Del Giudice A, Demitri N, Falini G, Pavel NV, Zaffagnini M, Polentarutti M, Crozet P, Marchand CH, Henri J, Trost P, Lemaire SD, Sparla F, Fermani S",
"journal": "Proc Natl Acad Sci U S A",
"doi": "10.1073/pnas.1820639116",
"pmid": "30923119",
"published_date": "2019 Apr 16"
},
"status": "released",
"submitted_date": "2018-07-05",
"released_date": "2019-03-13"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDH9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDH9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDH9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDH9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDH9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDH9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDH9.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": "Phosphoribulokinase, chloroplastic",
"short_name": "CrPRK",
"sequence": "GSHMDKDKTVVIGLAADSGCGKSTFMRRMTSIFGGVPKPPAGG\r\nNPDSNTLISDMTTVICLDDYHCLDRNGRKVKGVTALAPEAQNFDLMYNQVKALKEGKSVDKPIYNHVSGL\r\nIDAPEKIESPPILVIEGLHPFYDKRVAELLDFKIYLDISDDIKFAWKIQRDMAERGHSLESIKSSIAARK\r\nPDFDAYIDPQKKDADMIIQVLPTQLVPDDKGQYLRVRLIMKEGSKMFDPVYLFDEGSTISWIPCGRKLTC\r\nSFPGIKMFYGPDTWYGQEVSVLEMDGQFDKLEELIYVESHLSNTSAKFYGEITQQMLKNSGFPGSNNGTG\r\nLFQTIVGLKVREVYERIVKKDVVPV",
"organism": "Chlamydomonas reinhardtii",
"uniprot_code": "P19824",
"uniprot_range_first": 32,
"uniprot_range_last": 375,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MAFTMRAPAPRATAQSRVTANRARRSLVVRADKDKTVVIGLAADSGCGKSTFMRRMTSIF\nGGVPKPPAGGNPDSNTLISDMTTVICLDDYHCLDRNGRKVKGVTALAPEAQNFDLMYNQV\nKALKEGKSVDKPIYNHVSGLIDAPEKIESPPILVIEGLHPFYDKRVAELLDFKIYLDISD\nDIKFAWKIQRDMAERGHSLESIKSSIAARKPDFDAYIDPQKKDADMIIQVLPTQLVPDDK\nGQYLRVRLIMKEGSKMFDPVYLFDEGSTISWIPCGRKLTCSFPGIKMFYGPDTWYGQEVS\nVLEMDGQFDKLEELIYVESHLSNTSAKFYGEITQQMLKNSGFPGSNNGTGLFQTIVGLKV\nREVYERIVKKDVVPV",
"mw": 38.908,
"total_mw": 77.816,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "Tris-HCl 50 mM 150 mM KCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Chloroplastic phosphoribulokinase (collected using SEC-SAXS)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "Sapienza",
"address": "Rome, Italy",
"full_name": "Sapienza University Rome",
"webpage": "http://www.uniroma1.it/"
}
],
"contributor_name": "Alessandra",
"contributor_surname": "Del Giudice",
"orcid": "https://orcid.org/0000-0002-1916-8300"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2016-02-15",
"storage_temperature": 4.0,
"cell_temperature": 4.0,
"exposure_time": 1.0,
"number_of_frames": 80,
"wavelength": 0.099,
"sample_detector_distance": 2.872,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.122,
"s_max": 3.502,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDH9_fit1_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "6h7g",
"ext_code": "6H7G",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDDH9_fit1_model1.pdb",
"model_mw": 75.89,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 341
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/6h7g01_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.222,
"p_value": 2.1e-05,
"fit_residual_plot": "6h7g01_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDH9_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/6h7g01.log",
"software_version": "CRYSOL_30",
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "Additional SEC parameters: Column type: Superdex 200 10/300 GL (GE Healthcare); Flow rate: 0.5 ml/min; Sample injection concentration: 6.1 mg/ml; Injection volume: 100 µl.",
"experiment_description": "Synchrotron SAXS data from solutions of chloroplastic phosphoribulokinase (collected using SEC-SAXS) in Tris-HCl 50 mM 150 mM KCl, pH 7.5 were collected on the BM29 beam line at the ESRF (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). SEC-SAXS was performed at 4°C. 80 successive 1 second frames were collected through the SEC-elution profile. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of an appropriate solvent-blank (eluate SEC-buffer) was subtracted.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 70.0,
"experimental_mw_error": null,
"guinier_i0_mw": 70.0,
"guinier_i0_mw_error": 0.2,
"porod_mw": 72.0,
"porod_mw_error": null,
"pddf_i0": 42.42,
"pddf_i0_error": 0.06,
"guinier_i0": 42.0,
"guinier_i0_error": 0.1,
"pddf_rg": 3.548,
"pddf_rg_error": 0.008,
"guinier_rg": 3.43,
"guinier_rg_error": 0.01,
"pddf_dmax": 11.3,
"pddf_dmax_error": null,
"porod_volume": 115.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 55,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDDH9_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}