查看完整 summary.json 原文
{
"code": "SASDAC7",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Modeling the ComD/ComE/comcde interaction network using small angle X-ray scattering.",
"publication": {
"title": "Modeling the ComD/ComE/comcde interaction network using small angle X-ray scattering.",
"author_list": "Sanchez D, Boudes M, van Tilbeurgh H, Durand D, Quevillon-Cheruel S",
"journal": "FEBS J",
"doi": "10.1111/febs.13240",
"pmid": "25702779",
"published_date": "2015 Apr"
},
"status": "released",
"submitted_date": "2015-01-12",
"released_date": "2015-07-07"
},
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"experiment": {
"instrument": {
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"name": "AVIEX PCCD170170",
"resolution": null
},
"name": "SOLEIL",
"city": "Saint-Aubin",
"country": "France",
"beamline_name": "SWING",
"beam_geometry": "",
"type_of_source": "X-ray synchrotron",
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"xray_energy": null,
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},
"sample": {
"molecule": [
{
"long_name": "comcde",
"short_name": null,
"sequence": "5’-AAGTACACTTTGGGAGAAAAAAATGACAGTTGAGAGAA-3’\r\n3’-TTCATGTGAAACCCTCTTTTTTTACTGTCAACTCTCTT-5'",
"organism": "Streptococcus pneumoniae",
"uniprot_code": null,
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"oligomerization": "other",
"molecular_type": "DNA",
"uniprot_sequence": null,
"mw": 23.5,
"total_mw": 23.5,
"number_molecules": 0,
"complex_state": null,
"deuteration": null,
"molecule_source": "biological",
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},
{
"long_name": "Response regulator",
"short_name": "LytTR",
"sequence": "VVDYFDYNYKGNDLKIPYHDILYIETTGVSHKLRIIGKNFAKE\r\nFYGTMTDIQEKDKHTQRFYSPHKSFLVNIGNIREIDRKNLEIVFYEDHRCPISRLKIRKL\r\nKDILEKKSQKHHHHHH",
"organism": "Streptococcus pneumoniae",
"uniprot_code": "Q8DMW5",
"uniprot_range_first": 138,
"uniprot_range_last": 250,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MKVLILEDVIEHQVRLERILDEISKESNIPISYKTTGKVREFEEYIENDEVNQLYFLDID\nIHGIEKKGFEVAQLIRHYNPYAIIVFITSRSEFATLTYKYQVSALDFVDKDINDEMFKKR\nIEQNIFYTKSMLLENEDVVDYFDYNYKGNDLKIPYHDILYIETTGVSHKLRIIGKNFAKE\nFYGTMTDIQEKDKHTQRFYSPHKSFLVNIGNIREIDRKNLEIVFYEDHRCPISRLKIRKL\nKDILEKKSQK",
"mw": 14.434,
"total_mw": 28.868,
"number_molecules": 2,
"complex_state": true,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM MES 500 mM NaCl 5% (v/v) Glycerol 5 mM β-mercaptoethanol",
"concentration_unit": "mM",
"comment": null,
"additive": "500 mM NaCl, 5% (vol/vol) glycerol, 5 mM β-mercaptoethanol",
"concentration": 50.0,
"pka": null,
"ph": 6.2,
"deuteration": null
},
"purity_method": "size-exclusion high-performance liquid chromatography (SEC-HPLC) column.",
"name": "Complex LytTR-comcde",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [],
"contributor_name": "Dominique",
"contributor_surname": "Durand",
"orcid": null
}
],
"concentration_method": "size-exclusion high-performance liquid chromatography (SEC-HPLC) column.",
"concentration_unit": "mg/ml",
"date": "2013-06-02",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 1.0,
"number_of_frames": 16,
"wavelength": 0.1,
"sample_detector_distance": 1.82,
"concentration_min": null,
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"s_min": 0.101,
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"seccolumn": null
},
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{
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{
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"software": "SASREF",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDAC7_fit1_model1.pdb",
"model_mw": 52.29,
"bead_radius": null,
"log": null,
"symmetry": "",
"comment": "",
"user": 40
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAC7_fit1_fit_img.png",
"software": null,
"chi_square_value": 1.094,
"p_value": 4e-06,
"fit_residual_plot": "fit4columns210_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAC7_fit1.fit",
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}
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"description": "Use of SAXS to describe the interaction between the LytTR domain of the response regulator ComE from S. pneumonia and the promoter region comcde.\r\nThe complex is constituted of two monomers of LytTR and one molecule of comcde.\r\nThe SAXS data were collected directly after elution through an on-line size-exclusion high-performance liquid chromatography (SEC-HPLC) column.\r\nThe molecular weight is not estimated from I(0) because the concentration of the complex cannot be accurately determined. It is obtained from the macromolecule volume using the method developed by Craievich’s team (the SAXS Mow program). ",
"experiment_description": "X-ray synchrotron radiation scattering data from solutions of complex LytTR-comcde in 50 mM MES 200 mM NaCl, 2% (vol/vol) glycerol, 5 mM β-mercaptoethanol were collected on the SWING beamline on the storage ring SOLEIL (Saint-Aubin, France) using a CCD AVIEX detector (s = 4π sin θ/λ, where 2θ is the scattering angle). The sample was loaded on a SE-HPLC column on line with the SAXS measuring cell. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The scattered intensities were displayed on an absolute scale (cm-1) using the scattering by water. Frames were examined individually and 16 identical frames were averaged and further processed. The corresponding concentration was 0.4 g/L.",
"tags": [],
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"experimental_mw": 56.0,
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"pddf_dmax": 12.5,
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"porod_volume": 74.0,
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"estimated_volume": null,
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"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDAC7_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}查看完整 manifest.json 原文
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