{"code":"SASDEA2","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/A","project":{"title":"Structure of a nucleotide pyrophosphatase/phosphodiesterase (NPP) from Euphorbia characias latex characterized by small-angle X-ray scattering: clues for the general organization of plant NPPs.","publication":{"title":"Structure of a nucleotide pyrophosphatase/phosphodiesterase (NPP) from Euphorbia characias latex characterized by small-angle X-ray scattering: clues for the general organization of plant NPPs.","author_list":"Sabatucci A, Pintus F, Cabras T, Vincenzoni F, Maccarrone M, Medda R, Dainese E","journal":"Acta Crystallogr D Struct Biol","doi":"10.1107/S2059798320010207","pmid":"32876061","published_date":"2020 Sep 1"},"status":"released","submitted_date":"2018-07-31","released_date":"2020-11-17"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDEA2.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDEA2.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEA2_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEA2_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEA2_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEA2_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDEA2.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus 2M","resolution":null},"name":"Diamond Light Source","city":"Didcot","country":"UK","beamline_name":"B21","beam_geometry":"1 x 5 mm","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":"nucleotide pyrophosphatase/phosphodiesterase from E. characias latex partially sequenced","short_name":"ELNPP","sequence":"LIANGTEAELGLIPVFPTLTFPNHYSIVTGLYPPYHGIINNHFVDPHtGESFtMKSHEPKWWLGEPLWEtPLWETVVNHGLKLLFLEELAPWIEVKADWVLSRtPLLAIRPPDGIsPsEVVAK","organism":"Euphorbia characias","uniprot_code":null,"uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"dimer","molecular_type":"protein","uniprot_sequence":null,"mw":13.887,"total_mw":27.774,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"50 mM potassium phosphate","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.0,"deuteration":null},"purity_method":null,"name":"ELNPP -  nucleotide pyrophosphatase/phosphodiesterase from Euphorbia characias latex","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Italy","full_name":"Università degli studi di Teramo","webpage":"https://www.unite.it"}],"contributor_name":"Annalaura","contributor_surname":"Sabatucci","orcid":"https://orcid.org/0000-0002-8004-2547"}],"concentration_method":null,"concentration_unit":null,"date":"2016-02-20","storage_temperature":null,"cell_temperature":10.0,"exposure_time":3.0,"number_of_frames":5,"wavelength":0.1,"sample_detector_distance":4.0,"concentration_min":null,"concentration_max":6.0,"sample_volume":50.0,"flow_rate":0.16,"s_min":0.111,"s_max":4.074,"total_exposure_time":null,"seccolumn":19},"fits":[],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"Additional SEC parameters: Column type, Shodex KW403; Flow rate, 0.160  ml/min; Sample injection concentration, 6 mg/ml (as determined by Bradford assay); Injection volume, 50 µl. Note. There is an apparent discrepancy noted between the expected molecular weight (calculated from the deposited amino acid sequence) and the experimental molecular weight (assessed from the SAXS data: Porod volume/2 = 50 kDa; datmw = 60-66 kDa). At present, only a partial amino acid sequence of the protein is available and consequently not all amino acids are taken into account when calculating the expected molecular weight from the deposited amino acid sequence.","experiment_description":"Synchrotron SAXS data, I(s) vs s (where s = 4πsinθ/λ, 2θ is the scattering angle and λ the X-ray wavelength), were collected from the nucleotide pyrophosphatase/phosphodiesterase from Euphorbia characias latex using continuous-flow size-exclusion chromatography SAXS (SEC-SAXS) on the B21 beam line at the Diamond Light Source (Oxfordshire, UK). Data were collected using a Pilatus 2M detector at a sample-detector distance of 4 m at a wavelength of λ = 0.1 nm. The SEC mobile phase consisted of 50 mM potassium phosphate, pH 7, (10°C). The SAXS data measured from the SEC-elution sample peak (5 successive 3 s frames) were normalized to the intensity of the transmitted beam and radially averaged. The scattering of an appropriate solvent-blank was subtracted from the sample frames to produce the scaled and averaged data displayed in this entry.","tags":[],"intensity_unit":"arbitrary","experimental_mw":51.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":64.0,"porod_mw_error":null,"pddf_i0":0.01051,"pddf_i0_error":null,"guinier_i0":0.01059,"guinier_i0_error":3e-05,"pddf_rg":3.01,"pddf_rg_error":0.01,"guinier_rg":3.035,"guinier_rg_error":0.149,"pddf_dmax":10.4,"pddf_dmax_error":0.01,"porod_volume":102.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":23,"guinier_point_last":116,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDEA2_datloglog_img.png","symmetry":null,"last_modified":"2020-11-17T11:17:16.472708+01:00","bragg_peak":[]}