{ "code": "SASDE52", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "A structural and biochemical comparison of Ribonuclease E homologues from pathogenic bacteria highlights species-specific properties.", "publication": { "title": "A structural and biochemical comparison of Ribonuclease E homologues from pathogenic bacteria highlights species-specific properties.", "author_list": "Mardle CE, Shakespeare TJ, Butt LE, Goddard LR, Gowers DM, Atkins HS, Vincent HA, Callaghan AJ", "journal": "Sci Rep", "doi": "10.1038/s41598-019-44385-y", "pmid": "31138855", "published_date": "2019 May 28" }, "status": "released", "submitted_date": "2018-07-30", "released_date": "2019-05-28" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDE52.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDE52.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE52_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE52_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDE52_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE52_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDE52.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": "Endoribonuclease E", "short_name": "RNase E", "sequence": "HHHHHHHHHHSSGHIEGRHMKRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEETPTLSYMLPKLHEEAMALPSEEEFAERKRPEQPAL", "organism": "Escherichia coli", "uniprot_code": "P21513", "uniprot_range_first": 1, "uniprot_range_last": 529, "oligomerization": "tetramer", "molecular_type": "protein", "uniprot_sequence": "MKRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDY\nGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFI\nSLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEAL\nQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELA\nRQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALT\nAIDINSARATRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVE\nNRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLS\nLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQME\nTPHYHVLRVRKGEETPTLSYMLPKLHEEAMALPSEEEFAERKRPEQPALATFAMPDVPPA\nPTPAEPAAPVVAPAPKAAPATPAAPAQPGLLSRFFGALKALFSGGEETKPTEQPAPKAEA\nKPERQQDRRKPRQNNRRDRNERRDTRSERTEGSDNREENRRNRRQAQQQTAETRESRQQA\nEVTEKARTADEQQAPRRERSRRRNDDKRQAQQEAKALNVEEQSVQETEQEERVRPVQPRR\nKQRQLNQKVRYEQSVAEEAVVAPVVEETVAAEPIVQEAPAPRTELVKVPLPVVAQTAPEQ\nQEENNADNRDNGGMPRRSRRSPRHLRVSGQRRRRYRDERYPTQSPMPLTVACASPELASG\nKVWIRYPIVRPQDVQVEEQREQEEVHVQPMVTEVPVAAAIEPVVSAPVVEEVAGVVEAPV\nQVAEPQPEVVETTHPEVIAAAVTEQPQVITESDVAVAQEVAEQAEPVVEPQEETADIEEV\nVETAEVVVAEPEVVAQPAAPVVAEVAAEVETVAAVEPEVTVEHNHATAPMTRAPAPEYVP\nEAPRHSDWQRPTFAFEGKGAAGGHTATHHASAAPARPQPVE", "mw": 61.84, "total_mw": 247.36, "number_molecules": 4, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "10 mM DTT, 10 mM MgCl2, 0.5 M NaCl, 20 mM Tris", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Ribonuclease E from Escherichia coli", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Portsmouth, UK", "full_name": "University of Portsmouth", "webpage": "https://www.port.ac.uk" } ], "contributor_name": "A", "contributor_surname": "Callaghan", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2017-02-11", "storage_temperature": 21.0, "cell_temperature": 15.0, "exposure_time": 3.0, "number_of_frames": 640, "wavelength": 0.1, "sample_detector_distance": 4.014, "concentration_min": null, "concentration_max": 6.58, "sample_volume": null, "flow_rate": null, "s_min": 0.04, "s_max": 4.42, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDE52_fit1_model1_img.png", "software": "DAMFILT", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDE52_fit1_model1.pdb", "model_mw": 320.174, "bead_radius": 5.0, "log": "https://www.sasbdb.org/media/log_files/damsel_vJsG2E3.log", "symmetry": "P222", "comment": null, "user": 338 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDE52_fit1_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.054, "p_value": 0.000144, "fit_residual_plot": "SASDE52_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDE52_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Ec_Rne_5.log", "software_version": "5", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "4.6", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Ribonuclease E from Escherichia coli in 10 mM DTT, 10 mM MgCl2, 0.5 M NaCl, 20 mM Tris, pH 8 were collected on the B21 beam line at the Diamond Light Source (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 6.58 mg/ml was measured at 15°C. 640 successive 3 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": 276.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 290.0, "porod_mw_error": null, "pddf_i0": 0.04441, "pddf_i0_error": null, "guinier_i0": 0.04445, "guinier_i0_error": 6.8e-05, "pddf_rg": 5.01, "pddf_rg_error": null, "guinier_rg": 5.031, "guinier_rg_error": 0.215, "pddf_dmax": 16.1, "pddf_dmax_error": null, "porod_volume": 468.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 16, "guinier_point_last": 91, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDE52_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }