查看完整 summary.json 原文
{
"code": "SASDD53",
"status": "Published",
"type_of_curve": "Extrapolated to infinite dilution",
"angular_unit": "1/A",
"project": {
"title": "Crystal structure of the flexible tandem repeat domain of bacterial cellulose synthesis subunit C.",
"publication": {
"title": "Crystal structure of the flexible tandem repeat domain of bacterial cellulose synthesis subunit C.",
"author_list": "Nojima S, Fujishima A, Kato K, Ohuchi K, Shimizu N, Yonezawa K, Tajima K, Yao M",
"journal": "Sci Rep",
"doi": "10.1038/s41598-017-12530-0",
"pmid": "29026093",
"published_date": "2017 Oct 12"
},
"status": "released",
"submitted_date": "2018-01-17",
"released_date": "2018-01-17"
},
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"name": "Pilatus3 2M",
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},
"name": "Photon Factory (PF), High Energy Accelerator Research Organization (KEK)",
"city": "Tsukuba",
"country": "Japan",
"beamline_name": "BL-10C",
"beam_geometry": null,
"type_of_source": "X-ray synchrotron",
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},
"sample": {
"molecule": [
{
"long_name": "Bacterial cellulose synthesis subunit C",
"short_name": "BcsC-TPR",
"sequence": "GHMDEPTAQQQLLSQVRLGEATKREDLVRQSLYRLELIDPDNPDVIAARFRYLLRQGDNAGAQKQLDRMKQLAPDSAAYKSSVTSMTLSGAEGRQALQQARLQATTGHVPEALAAYDALFKGNPPEGDLAVEYWALVAKVPARRSEAITQLKALNARNPGNAALQNSLAQLLFGEGRDAEAYAVLEQMAKSSAGREAAAGLWYQQIQRMPVSDASVKALQRFLTVFSSGDTVDSARTQLAAQQKQLADPAFRARATGLAAVDAGQGAKAVNELRQAVNANGTDSEAVGALGQAYSQSGDRARAVAQFEKAIAMDPTSGNRSKWDSLLKTNRYWLLIQQGDAALKANNPGEAERLYSQARRIDNTDSYAVLGLGDAAMARKDSHAAESFYRQALRMDSGNSNAVRGLANIYRARSPQEADTFIQSLSASQRRSIDDIERGLKNDRLAQQAEALENSGQWAQAAELQRQRLALDPGSVWVTYRLASDLRQAGEPREADAHMQRLAALKPGDPEQVYAYGLYLSGNNQEMAALNQLNALPKAQWNSNIQELAERLQTNRLLDNANRLRDSGHEEQARALLAQQPASTRIDLTLADWAQQGGDSASAQHYFNRVLEREPNNQDALLGLAELYAADGNKMAARAQLAKLLEHHHHHH",
"organism": "Enterobacter sp. CJF-002",
"uniprot_code": "K0J1W8",
"uniprot_range_first": 24,
"uniprot_range_last": 664,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MRKFTVSLLCLSLVLALTPATQADEPTAQQQLLSQVRLGEATKREDLVRQSLYRLELIDP\nDNPDVIAARFRYLLRQGDNAGAQKQLDRMKQLAPDSAAYKSSVTSMTLSGAEGRQALQQA\nRLQATTGHVPEALAAYDALFKGNPPEGDLAVEYWALVAKVPARRSEAITQLKALNARNPG\nNAALQNSLAQLLFGEGRDAEAYAVLEQMAKSSAGREAAAGLWYQQIQRMPVSDASVKALQ\nRFLTVFSSGDTVDSARTQLAAQQKQLADPAFRARATGLAAVDAGQGAKAVNELRQAVNAN\nGTDSEAVGALGQAYSQSGDRARAVAQFEKAIAMDPTSGNRSKWDSLLKTNRYWLLIQQGD\nAALKANNPGEAERLYSQARRIDNTDSYAVLGLGDAAMARKDSHAAESFYRQALRMDSGNS\nNAVRGLANIYRARSPQEADTFIQSLSASQRRSIDDIERGLKNDRLAQQAEALENSGQWAQ\nAAELQRQRLALDPGSVWVTYRLASDLRQAGEPREADAHMQRLAALKPGDPEQVYAYGLYL\nSGNNQEMAALNQLNALPKAQWNSNIQELAERLQTNRLLDNANRLRDSGHEEQARALLAQQ\nPASTRIDLTLADWAQQGGDSASAQHYFNRVLEREPNNQDALLGLAELYAADGNKMAARAQ\nLAKLPAPTAAQPQSINTQRRLALVQAALGDTDSARQTFSRIMPQAKAQPPSMESALVLRD\nAARFQAQQGEPQQALETWKDAMVASGVTTTPPADNDTFTRLTRNNAKDDWLKRGIRSDAA\nDLYRQQDINVTLQHDYWGSSGTGGYSDLKAHTTLVQADAPLADGRMFFRTDVVNMNVGSF\nDTTDDVYDPNWGTCSATPCRGNTSQKANGASLAVGWQNGTWSGDIGTTPMGFDVVDVVGG\nLSYSSDLGPLGYTVNVHRRPISSSLLAFGGQKDPNTGVTWGGVRATGGGVSLSYDKGEAN\nGVWSSLNADSLTGKNVADNWRIRWMTGYYYKLINKDNERLTVGLNNMLWHYDKDLSDYTL\nGQGGYYSPQQYISFAVPVVWRKRTANWSWELGASGSWSHSKTDGIKRYPLQNLIPDNQFF\nANGDRMFLDKDNSSTSSSSNGFGYTARALVERRVTSHWFVGAGVDIQQAKDYTPSHALIY\nVRYSGAGWQGDMDMPPQTLTPYADW",
"mw": 71.298,
"total_mw": 71.298,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
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"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Tetratrico peptide repeat domain of Bacterial cellulose synthesis subunit C",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "KEK",
"address": "Tsukuba, Japan",
"full_name": "High Energy Accelerater Research Organization (KEK)",
"webpage": "https://www.kek.jp"
}
],
"contributor_name": "Kento",
"contributor_surname": "Yonezawa",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-04-24",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 20.0,
"number_of_frames": 28,
"wavelength": 0.1,
"sample_detector_distance": 2.01,
"concentration_min": 0.71,
"concentration_max": 1.8,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.083,
"s_max": 4.001,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
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"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "ATSAS 2.7",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDD53_fit1_model1.pdb",
"model_mw": 71.9,
"bead_radius": 4.25,
"log": "https://www.sasbdb.org/media/log_files/desc_side-atsas.log",
"symmetry": "P1",
"comment": null,
"user": 275
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD53_fit1_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.906,
"p_value": 0.000126,
"fit_residual_plot": "SASDD53_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD53_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/desc_side-atsas_tdEKI48.log",
"software_version": "ATSAS 2.7",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Tetratrico peptide repeat domain of Bacterial cellulose synthesis subunit C in 50 mM HEPES, 100 mM KCl, pH 8 were collected on the beam line BL-10C at the Phton Factory (PF; Tsukuba, Ibaraki, Japan) using a Pilatus3 2M detector at a sample-detector distance of 2.01 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle).120 successive 20 second frames were collected at 20°C using size-exclusion chromatography SAXS. Sample was loaded to Superdex 200 increase 10/300 (GE healthcare). The flow rate was set at 0.05 mL/min. The data were normalized to the intensity of the incident beam and circularly averaged; the scattering of the solvent-blank was subtracted. Every five SAXS profiles were averaged to improve the signal-to-noise ratio of the data, and the extrapolated scattering profile at a concentration of zero was calculated with the data in the descent side of the peak (frames 91–118) by ALMERGE of ATSAS. In order to estimate the molecular mass from I(0), the partial specific volume, PSV, (0.7405 cm3/g) and the X-ray scattering contrast (Δρ = 2.949×10^10 cm-2) of this protein were calculated by using the PSV calculator of NucProt (http://www.molmovdb.org/cgi-bin/psv.cgi; Voss & Gerstein (2005) J. Mol. Biol. 346, 477–492) and the contrast module of MULCh (http://smb-research.smb.usyd.edu.au/NCVWeb/input.jsp; Whitten, et al., (2008) J. App. Crystallogr. 41, 222–226).",
"tags": [],
"intensity_unit": "1/cm",
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"guinier_i0_mw_error": 0.5,
"porod_mw": 72.1,
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"pddf_i0": 0.1035,
"pddf_i0_error": 0.0003,
"guinier_i0": 0.105,
"guinier_i0_error": 0.0004,
"pddf_rg": 5.13,
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"guinier_rg": 5.12,
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"pddf_dmax": 18.53,
"pddf_dmax_error": null,
"porod_volume": 115.3,
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"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 2,
"guinier_point_last": 59,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDD53_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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