Extended single alpha-helix (SAH) region of Drebrin
Data type: SASBDB experimental dataStatus: PublishedCurve type: Single concentrationLast updated: 2025-04-08T09:16:52.466844+02:00
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).
▼
1. Samples, Components and Experimental Conditions Sample & Experiment
Sample 1 · Extended single alpha-helix (SAH) region of Drebrin
5. Experiment Description and Publication Experiment & Publication
Original 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.
Related Publication
Title
Dynamic Interchange of Local Residue-Residue Interactions in the Largely Extended Single Alpha-Helix in Drebrin
Authors
Varga S, Péterfia B, Dudola D, Farkas V, Jeffries C, Permi P, Gáspári Z
DOI / PMID
10.1042/BCJ20253036 / —
▼
6. Complete Source Record Complete Source Record
The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
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.
experiment.sample.buffer.name
17 mM NaH2PO4, 3 mM Na2HPO4, 50 mM NaCl
experiment.sample.buffer.concentration_unit
null
experiment.sample.buffer.comment
20 mM phosphate
experiment.sample.buffer.additive
null
experiment.sample.buffer.concentration
null
experiment.sample.buffer.pka
null
experiment.sample.buffer.ph
6.0
experiment.sample.buffer.deuteration
null
experiment.sample.purity_method
null
experiment.sample.name
Extended single alpha-helix (SAH) region of Drebrin
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.
{
"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": []
}
