SASDAT4

uPAR wild-type

Data type: SASBDB experimental data Status: Published Curve type: Merged Last updated: 2023-05-25T11:21:52.654103+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · uPAR wild-type

Concentration1.5 – 4.4 mg/mlBuffer / pH25 mM Sodium Phosphate 5 % Glycerol 50 mM NaSO4 / 7.2
Experimental temperature10.0 Facility / beamlineDORIS III, DESY / EMBL X33
Wavelength0.15 nmExposure30.0 s × 4

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Urokinase plasminogen activator surface receptor
View sequence
>SP|Q03405|UPAR_HUMANUROKINASEPLASMINOGENACTIVATORSURFACERECEPTOROS=HOMOSAPIENSGN=PLAURPE=1SV=1MGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT
proteinHomo sapiensQ03405—–—monomerMolecule count 136.98 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
12277[3]0.233861–6.34517 1/nmHas uncertainty columnMissing 00sasbdb/entries/t4/sasdat4/source/SASDAT4.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)9.7—nm
i0Guinier49.3——
mwExperimental47.0—kDa
mwGuinier I(0)47.0—kDa
porod_volumePorod69.0—nm³
rgGuinier2.8—nm
rgP(r)2.9—nm

These values are reported by SASBDB; SAXSdb did not recalculate them from the experimental curve.

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3. Source Fits and Models Source Fits & Models

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4. Source File Index Source Files

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5. Experiment Description and Publication Experiment & Publication

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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.

Open the original SASBDB entry

Buffer and Sample Properties

Buffer name25 mM Sodium Phosphate 5 % Glycerol 50 mM NaSO4Buffer concentration25.0 mM
pH7.2AdditivesGlycerol 5.000 %, NaSO4 50.000 mM
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2010-06-10Storage / measurement temperature10.0 / 10.0
Exposure time30.0Frames4
Wavelength0.15Sample-to-detector distance2.7
SourceX-ray synchrotronDetectorPilatus 1M-W
Facility / beamlineDORIS III, DESY / EMBL X33 · Hamburg, Germany
q range0.234 – 6.345Sample volume / flow rate— / —

Original SASBDB Plots

Experimental I(q)
Experimental I(q)
Experimental I(q), log-log
Experimental I(q), log-log
Guinier plot
Guinier plot
Kratky plot
Kratky plot
P(r) plot
P(r) plot

Downloadable Files

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pddfsasbdb/entries/t4/sasdat4/source/SASDAT4.outdownloaded419533316d16cf8c87f2c29372d8f7861dfe63ba865e36e80114accd844ce09e837cbDownloadView source fileSource site
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full_entry_zip:source record and ZIP contents (6 items)
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pddf:source record
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sascif:source record
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summary:source record
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All source fields (unfiltered)

Every source field is expanded here, including empty values, list members and fields already shown above.

summary.json:179 field values
Field pathRaw value
codeSASDAT4
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleA flexible multidomain structure drives the function of the urokinase-type plasminogen activator receptor (uPAR).
project.publication.titleA flexible multidomain structure drives the function of the urokinase-type plasminogen activator receptor (uPAR).
project.publication.author_listMertens HD, Kjaergaard M, Mysling S, Gårdsvoll H, Jørgensen TJ, Svergun DI, Ploug M
project.publication.journalJ Biol Chem
project.publication.doi10.1074/jbc.M112.398404
project.publication.pmid22896701
project.publication.published_date2012 Oct 5
project.statusreleased
project.submitted_datenull
project.released_date2015-07-07
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intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT4_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDAT4.sascif
experiment.instrument.detector.typeCustom-built
experiment.instrument.detector.namePilatus 1M-W
experiment.instrument.detector.resolution0.172
experiment.instrument.nameDORIS III, DESY
experiment.instrument.cityHamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL X33
experiment.instrument.beam_geometry0.60
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
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experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameUrokinase plasminogen activator surface receptor
experiment.sample.molecule[0].short_nameuPAR
experiment.sample.molecule[0].sequence>sp|Q03405|UPAR_HUMAN Urokinase plasminogen activator surface receptor OS=Homo sapiens GN=PLAUR PE=1 SV=1 MGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL ELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC GSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG FHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP MNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV QYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeQ03405
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL ELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC GSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG FHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP MNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV QYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT
experiment.sample.molecule[0].mw36.98
experiment.sample.molecule[0].total_mw36.98
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_statenull
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.buffer.name25 mM Sodium Phosphate 5 % Glycerol 50 mM NaSO4
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additiveGlycerol 5.000 %, NaSO4 50.000 mM
experiment.sample.buffer.concentration25.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.2
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameuPAR wild-type
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
experiment.sample.deuterationnull
experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_nameEMBL-Hamburg
experiment.contributor[0].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[0].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[0].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[0].contributor_nameHaydyn
experiment.contributor[0].contributor_surnameMertens
experiment.contributor[0].orcidnull
experiment.concentration_methodA280
experiment.concentration_unitmg/ml
experiment.date2010-06-10
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time30.0
experiment.number_of_frames4
experiment.wavelength0.15
experiment.sample_detector_distance2.7
experiment.concentration_min1.5
experiment.concentration_max4.4
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.234
experiment.s_max6.345
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].softwarenull
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fits[0].p_value0.000911
fits[0].fit_residual_plotSASDAT4_fit1_fitresiduals_img.png
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fits[1].softwarenull
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fits[1].p_value0.0
fits[1].fit_residual_plotfit4columns71_fitresiduals_img.png
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fits[1].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardBSA
descriptionnull
experiment_descriptionnull
tags[0]X33
intensity_unitnull
experimental_mw47.0
experimental_mw_errornull
guinier_i0_mw47.0
guinier_i0_mw_errornull
porod_mwnull
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pddf_i0null
pddf_i0_errornull
guinier_i049.3
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guinier_rg2.8
guinier_rg_errornull
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estimated_volume_errornull
guinier_point_first1
guinier_point_last90
pddf_point_first1
pddf_point_last1200
i0_calibration_standard_datanull
intensities_log_log_plotSASDAT4_datloglog_img.png
symmetrynull
last_modified2023-05-25T11:21:52.654103+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDAT4
statussuccess
started_at2026-08-11T14:30:39.298847+00:00
finished_at2026-08-11T14:30:49.432782+00:00
source_last_modified2023-05-25T11:21:52.654103+02:00
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View the complete summary.json source
{
  "code": "SASDAT4",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "A flexible multidomain structure drives the function of the urokinase-type plasminogen activator receptor (uPAR).",
    "publication": {
      "title": "A flexible multidomain structure drives the function of the urokinase-type plasminogen activator receptor (uPAR).",
      "author_list": "Mertens HD, Kjaergaard M, Mysling S, Gårdsvoll H, Jørgensen TJ, Svergun DI, Ploug M",
      "journal": "J Biol Chem",
      "doi": "10.1074/jbc.M112.398404",
      "pmid": "22896701",
      "published_date": "2012 Oct 5"
    },
    "status": "released",
    "submitted_date": null,
    "released_date": "2015-07-07"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDAT4.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDAT4.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT4_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT4_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAT4_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT4_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAT4.sascif",
  "experiment": {
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        "name": "Pilatus 1M-W",
        "resolution": 0.172
      },
      "name": "DORIS III, DESY",
      "city": "Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL X33",
      "beam_geometry": "0.60",
      "type_of_source": "X-ray synchrotron",
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    },
    "sample": {
      "molecule": [
        {
          "long_name": "Urokinase plasminogen activator surface receptor",
          "short_name": "uPAR",
          "sequence": ">sp|Q03405|UPAR_HUMAN Urokinase plasminogen activator surface receptor OS=Homo sapiens GN=PLAUR PE=1 SV=1\nMGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL\nELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC\nGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG\nFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP\nMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV\nQYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT\n\n",
          "organism": "Homo sapiens",
          "uniprot_code": "Q03405",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
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