{ "code": "SASDVV6", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Dynamic Interchange of Local Residue-Residue Interactions in the Largely Extended Single Alpha-Helix in Drebrin", "publication": { "title": "Dynamic Interchange of Local Residue-Residue Interactions in the Largely Extended Single Alpha-Helix in Drebrin", "author_list": "Varga S, Péterfia B, Dudola D, Farkas V, Jeffries C, Permi P, Gáspári Z", "journal": "Biochemical Journal", "doi": "10.1042/BCJ20253036", "pmid": null, "published_date": "2025 Apr 01" }, "status": "released", "submitted_date": "2024-12-14", "released_date": "2025-04-08" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVV6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVV6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVV6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVV6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVV6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVV6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVV6.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": "Drebrin", "short_name": "SAH", "sequence": "GSHMKDPMKRINREQFWEQAKKEEELRKEEERKKALDERLRFEQERMEQERQEQEERERRYREREQQIEEHRRK", "organism": "Homo sapiens", "uniprot_code": "Q16643", "uniprot_range_first": 173, "uniprot_range_last": 238, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MAGVSFSGHRLELLAAYEEVIREESAADWALYTYEDGSDDLKLAASGEGGLQELSGHFEN\nQKVMYGFCSVKDSQAALPKYVLINWVGEDVPDARKCACASHVAKVAEFFQGVDVIVNASS\nVEDIDAGAIGQRLSNGLARLSSPVLHRLRLREDENAEPVGTTYQKTDAAVEMKRINREQF\nWEQAKKEEELRKEEERKKALDERLRFEQERMEQERQEQEERERRYREREQQIEEHRRKQQ\nTLEAEEAKRRLKEQSIFGDHRDEEEETHMKKSESEVEEAAAIIAQRPDNPREFFKQQERV\nASASAGSCDVPSPFNHRPGSHLDSHRRMAPTPIPTRSPSDSSTASTPVAEQIERALDEVT\nSSQPPPLPPPPPPAQETQEPSPILDSEETRAAAPQAWAGPMEEPPQAQAPPRGPGSPAED\nLMFMESAEQAVLAAPVEPATADATEIHDAADTIETDTATADTTVANNVPPAATSLIDLWP\nGNGEGASTLQGEPRAPTPPSGTEVTLAEVPLLDEVAPEPLLPAGEGCATLLNFDELPEPP\nATFCDPEEVEGESLAAPQTPTLPSALEELEQEQEPEPHLLTNGETTQKEGTQASEGYFSQ\nSQEEEFAQSEELCAKAPPPVFYNKPPEIDITCWDADPVPEEEEGFEGGD", "mw": 9.728, "total_mw": 9.728, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "The protein construct used for SAXS contains an additional eight non-native amino acids at the N-terminus (gshmkdpm) derived from the remnants of a protein affinity tag, post TEV cleavage." } ], "buffer": { "name": "17 mM NaH2PO4, 3 mM Na2HPO4, 50 mM NaCl", "concentration_unit": null, "comment": "20 mM phosphate", "additive": null, "concentration": null, "pka": null, "ph": 6.0, "deuteration": null }, "purity_method": null, "name": "Extended single alpha-helix (SAH) region of Drebrin", "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": "Cy M", "contributor_surname": "Jeffries", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2023-07-07", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 0.1, "number_of_frames": 20, "wavelength": 0.123982, "sample_detector_distance": 3.0, "concentration_min": null, "concentration_max": 3.2, "sample_volume": null, "flow_rate": null, "s_min": 0.023, "s_max": 4.433, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": null, "software": "Other [static image]", "pdb_link": [], "model_title": null, "type_of_model": "other", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVV6_fit1_model1.png", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 9 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVV6_fit1_fixed_fit_img.png", "software": "Pepsi-SAXS", "chi_square_value": 1.0741, "p_value": 0.0014, "fit_residual_plot": "SASDVV6_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVV6_fit1.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": "The single alpha helix ensemble displayed in this entry consists of 60 individual models informed by NMR chemical-shift results and are made available for download in the full-entry zip archive. For display purposes, the models have been aligned relative to amino acids 190-223 (UniProt amino acid numbering. Alternatively, amino acids 26-59, NMR model numbering). The fit to the SAXS data of the ensemble was determined using Pepsi-SAXS. Batch SAXS data spanning a three point concentration series (where the data have been normalised to protein concentration) at 0.82, 1.64 and 3.2 mg/ml are also provided in the full-entry zip archive in addition to SEC-MALLS/RI measurements. NOTE: The experimental molecular weight quoted in this entry is derived from this SEC-MALLS/RI analysis (11 kDa).", "experiment_description": "Synchrotron SAXS data from solutions of the single alpha-helix (SAH) region of Drebrin in 17 mM NaH2PO4, 3 mM Na2HPO4, 50 mM NaCl, pH 6 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123982 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.20 mg/ml was measured at 20°C. 20 successive 0.100 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": "1/cm", "experimental_mw": 10.99, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 11.0, "porod_mw_error": null, "pddf_i0": 0.03564, "pddf_i0_error": null, "guinier_i0": 0.0350399, "guinier_i0_error": null, "pddf_rg": 3.144, "pddf_rg_error": null, "guinier_rg": 2.95, "guinier_rg_error": 0.02, "pddf_dmax": 12.0, "pddf_dmax_error": null, "porod_volume": 18.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 26, "guinier_point_last": 134, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVV6_datloglog_img.png", "symmetry": null, "last_modified": "2025-04-08T09:16:52.466844+02:00", "bragg_peak": [] }