SASDER3

Senescence-associated E3 ubiquitin ligase 1, 1.8 mg/ml

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2023-06-21T07:56:39.492710+02:00

Monomer:tetramer fractions by volume: 60:40. The rigid bodies used for the SASREF MX tetramer model were predicted by I-TASSER.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Senescence-associated E3 ubiquitin ligase 1, 1.8 mg/ml

Concentration— – 1.8 Buffer / pH50 mM Tris, 250 mM NaCl / 9.0
Experimental temperature10.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.123987 nmExposure0.05 s × 20

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Senescence-associated E3 ubiquitin ligase 1
View sequence
GPLGSMVGSSDGDQSDDSSHFERGVDHIYEAFICPLTKEVMHDPVTLENGRTFEREAIEKWFKECRDSGRPPSCPLTSQELTSTDVSASIALRNTIEEWRSRNDAAKLDIARQSLFLGNAETDILQALMHVRQICRTIRSNRHGVRNSQLIHMIIDMLKSTSHRVRYKALQTLQVVVEGDDESKAIVAEGDTVRTLVKFLSHEPSKGREAAVSLLFELSKSEALCEKIGSIHGALILLVGLTSSNSENVSIVEKADRTLENMERSEEIVRQMASYGRLQPLLGKLLEGSPETKLSMASFLGELPLNNDVKVLVAQTVGSSLVDLMRSGDMPQREAALKALNKISSFEGSAKVLISKGILPPLIKDLFYVGPNNLPIRLKEVSATILANIVNIGYDFDKATLVSENRVENLLHLISNTGPAIQCKLLEVLVGLTSCPKTVPKVVYAIKTSGAIISLVQFIEVRENDDLRLASIKLLHNLSPFMSEELAKALCGTAGQLGSLVAIISEKTPITEEQAAAAGLLAELPDRDLGLTQEMLEVGAFEKIISKVFGIRQGDIKGMRFVNPFLEGLVRILARITFVFNKEARAINFCREHDVASLFLHLLQSNGQDNIQMVSAMALENLSLESIKLTRMPDPPPVNYCGSIFSCVRKPHVVNGLCKIHQGICSLRETFCLVEGGAVEKLVALLDHENVKVVEAALAALSSLLEDGLDVEKGVKILDEADGIRHILNVLRENRTERLTRRAVWMVERILRIEDIAREVAEEQSLSAALVDAFQNADFRTRQIAENALKHIDKIPNFSSIFPNIA
proteinArabidopsis thalianaQ9LM76—–—tetramerMolecule count 488.79 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11808[3]0.0269502–4.80121 1/nmHas uncertainty columnMissing 0250sasbdb/entries/r3/sasder3/source/SASDER3.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)23.0—nm
i0Guinier7557.4—arbitrary
mwExperimental199.0—kDa
mwPorod199.0—kDa
rgGuinier5.92—nm
rgP(r)6.238—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

▶

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 name50 mM Tris, 250 mM NaClBuffer concentration—
pH9.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2015-06-02Storage / measurement temperature10.0 / 10.0
Exposure time0.05Frames20
Wavelength0.123987Sample-to-detector distance3.0
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.027 – 4.801Sample 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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full_entry_zip:source record and ZIP contents (5 items)
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pddf:source record
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sascif: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:171 field values
Field pathRaw value
codeSASDER3
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleSenescence-associated ubiquitin ligase 1 (SAUL1)
project.publicationnull
project.statusreleased
project.submitted_date2017-07-21
project.released_date2021-09-13
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDER3.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDER3.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDER3_dat_img.png
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pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDER3_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDER3_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDER3.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 2M
experiment.instrument.detector.resolutionnull
experiment.instrument.namePETRA III
experiment.instrument.cityDESY; Hamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL P12
experiment.instrument.beam_geometrynull
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
experiment.instrument.line_collimation_slitlengthnull
experiment.instrument.line_collimation_integrationwidthnull
experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameSenescence-associated E3 ubiquitin ligase 1
experiment.sample.molecule[0].short_nameSAUL1
experiment.sample.molecule[0].sequenceGPLGS MVGSSDGDQSDDSSHFERGVDHIYEAFICPLTKEVMHDPVTLENGRTFEREAIEKWFKEC RDSGRPPSCPLTSQELTSTDVSASIALRNTIEEWRSRNDAAKLDIARQSLFLGNAETDIL QALMHVRQICRTIRSNRHGVRNSQLIHMIIDMLKSTSHRVRYKALQTLQVVVEGDDESKA IVAEGDTVRTLVKFLSHEPSKGREAAVSLLFELSKSEALCEKIGSIHGALILLVGLTSSN SENVSIVEKADRTLENMERSEEIVRQMASYGRLQPLLGKLLEGSPETKLSMASFLGELPL NNDVKVLVAQTVGSSLVDLMRSGDMPQREAALKALNKISSFEGSAKVLISKGILPPLIKD LFYVGPNNLPIRLKEVSATILANIVNIGYDFDKATLVSENRVENLLHLISNTGPAIQCKL LEVLVGLTSCPKTVPKVVYAIKTSGAIISLVQFIEVRENDDLRLASIKLLHNLSPFMSEE LAKALCGTAGQLGSLVAIISEKTPITEEQAAAAGLLAELPDRDLGLTQEMLEVGAFEKII SKVFGIRQGDIKGMRFVNPFLEGLVRILARITFVFNKEARAINFCREHDVASLFLHLLQS NGQDNIQMVSAMALENLSLESIKLTRMPDPPPVNYCGSIFSCVRKPHVVNGLCKIHQGIC SLRETFCLVEGGAVEKLVALLDHENVKVVEAALAALSSLLEDGLDVEKGVKILDEADGIR HILNVLRENRTERLTRRAVWMVERILRIEDIAREVAEEQSLSAALVDAFQNADFRTRQIA ENALKHIDKIPNFSSIFPNIA
experiment.sample.molecule[0].organismArabidopsis thaliana
experiment.sample.molecule[0].uniprot_codeQ9LM76
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationtetramer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMVGSSDGDQSDDSSHFERGVDHIYEAFICPLTKEVMHDPVTLENGRTFEREAIEKWFKEC RDSGRPPSCPLTSQELTSTDVSASIALRNTIEEWRSRNDAAKLDIARQSLFLGNAETDIL QALMHVRQICRTIRSNRHGVRNSQLIHMIIDMLKSTSHRVRYKALQTLQVVVEGDDESKA IVAEGDTVRTLVKFLSHEPSKGREAAVSLLFELSKSEALCEKIGSIHGALILLVGLTSSN SENVSIVEKADRTLENMERSEEIVRQMASYGRLQPLLGKLLEGSPETKLSMASFLGELPL NNDVKVLVAQTVGSSLVDLMRSGDMPQREAALKALNKISSFEGSAKVLISKGILPPLIKD LFYVGPNNLPIRLKEVSATILANIVNIGYDFDKATLVSENRVENLLHLISNTGPAIQCKL LEVLVGLTSCPKTVPKVVYAIKTSGAIISLVQFIEVRENDDLRLASIKLLHNLSPFMSEE LAKALCGTAGQLGSLVAIISEKTPITEEQAAAAGLLAELPDRDLGLTQEMLEVGAFEKII SKVFGIRQGDIKGMRFVNPFLEGLVRILARITFVFNKEARAINFCREHDVASLFLHLLQS NGQDNIQMVSAMALENLSLESIKLTRMPDPPPVNYCGSIFSCVRKPHVVNGLCKIHQGIC SLRETFCLVEGGAVEKLVALLDHENVKVVEAALAALSSLLEDGLDVEKGVKILDEADGIR HILNVLRENRTERLTRRAVWMVERILRIEDIAREVAEEQSLSAALVDAFQNADFRTRQIA ENALKHIDKIPNFSSIFPNIA
experiment.sample.molecule[0].mw88.79
experiment.sample.molecule[0].total_mw355.16
experiment.sample.molecule[0].number_molecules4
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.buffer.name50 mM Tris, 250 mM NaCl
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph9.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameSenescence-associated E3 ubiquitin ligase 1, 1.8 mg/ml
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_namenull
experiment.contributor[0].affiliation[0].addressHamburg, Germany
experiment.contributor[0].affiliation[0].full_nameUniversity of Hamburg
experiment.contributor[0].affiliation[0].webpagehttps://www.uni-hamburg.de/
experiment.contributor[0].contributor_nameHaifa
experiment.contributor[0].contributor_surnameEl Kilani
experiment.contributor[0].orcidnull
experiment.contributor[1].affiliation[0].short_nameEMBL-Hamburg
experiment.contributor[1].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[1].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[1].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[1].contributor_nameAl
experiment.contributor[1].contributor_surnameKikhney
experiment.contributor[1].orcidhttps://orcid.org/0000-0003-1321-3956
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2015-06-02
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time0.05
experiment.number_of_frames20
experiment.wavelength0.123987
experiment.sample_detector_distance3.0
experiment.concentration_minnull
experiment.concentration_max1.8
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.027
experiment.s_max4.801
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDER3_fit1_model1_img.png
fits[0].models[0].softwareSASREF MX
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelatomic
fits[0].models[0].software_version
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fits[0].models[0].model_mw354.8
fits[0].models[0].bead_radius1.9
fits[0].models[0].lognull
fits[0].models[0].symmetryP222
fits[0].models[0].comment
fits[0].models[0].user4
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fits[0].models[1].softwareSASREF MX
fits[0].models[1].pdb_link[]
fits[0].models[1].model_titlenull
fits[0].models[1].type_of_modelatomic
fits[0].models[1].software_version
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fits[0].models[1].bead_radius1.9
fits[0].models[1].lognull
fits[0].models[1].symmetry
fits[0].models[1].comment
fits[0].models[1].user4
fits[0].fit_unit1/A
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fits[0].softwareOLIGOMER
fits[0].chi_square_value1.12
fits[0].p_value0.0028
fits[0].fit_residual_plotSASDER3_fit1_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDER3_fit1.fit
fits[0].fit_lognull
fits[0].software_version
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionMonomer:tetramer fractions by volume: 60:40. The rigid bodies used for the SASREF MX tetramer model were predicted by I-TASSER.
experiment_descriptionnull
tags[]
intensity_unitarbitrary
experimental_mw199.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw199.0
porod_mw_errornull
pddf_i0null
pddf_i0_errornull
guinier_i07557.4
guinier_i0_errornull
pddf_rg6.238
pddf_rg_errornull
guinier_rg5.92
guinier_rg_errornull
pddf_dmax23.0
pddf_dmax_errornull
porod_volumenull
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first24
guinier_point_last63
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDER3_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDER3
statussuccess
started_at2026-08-11T16:35:46.578610+00:00
finished_at2026-08-11T16:36:10.141381+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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View the complete summary.json source
{
  "code": "SASDER3",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Senescence-associated ubiquitin ligase 1 (SAUL1)",
    "publication": null,
    "status": "released",
    "submitted_date": "2017-07-21",
    "released_date": "2021-09-13"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDER3.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDER3.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDER3_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDER3_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDER3_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDER3_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDER3.sascif",
  "experiment": {
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        "name": "Pilatus 2M",
        "resolution": null
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      "city": "DESY; Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL P12",
      "beam_geometry": null,
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
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      "xray_energy": null,
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      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Senescence-associated E3 ubiquitin ligase 1",
          "short_name": "SAUL1",
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          "organism": "Arabidopsis thaliana",
          "uniprot_code": "Q9LM76",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "tetramer",
          "molecular_type": "protein",
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      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Hamburg, Germany",
            "full_name": "University of Hamburg",
            "webpage": "https://www.uni-hamburg.de/"
          }
        ],
        "contributor_name": "Haifa",
        "contributor_surname": "El Kilani",
        "orcid": null
      },
      {
        "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"
          }
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        "contributor_name": "Al",
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      }
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    "concentration_unit": null,
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  "last_modified": "2023-06-21T07:56:39.492710+02:00",
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}
View the complete manifest.json source
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