SASDBP2

Human linear triubiquitin

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2020-08-28T15:27:40.482221+02:00

Note: The displayed results show a merged data set derived from a concentration series. Data were normalised to protein concentration and the high angle data from highest concentration and low angle data from lowest concentration were merged to generate final SAXS profile. Because of the flexibility of linear-triubiquitin molecule, ensemble optimisation method, EOM, was performed. The models shown above are two triubiquitin examples from the final EOM output. All EOM models, the radius of gyration distribution and maximum particle dimension distribution can be found in the full entry zip archive.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Human linear triubiquitin

Concentration1.05 – 4.2 mg/mlBuffer / pH50 mM Tris 150mM NaCl 0.5 mM EDTA / 7.5
Experimental temperature— Facility / beamlinePohang Accelerator Laboratory / 5C
Wavelength1.907 nmExposure60.0 s × 5

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Human linear tri-ubiquitin
View sequence
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
proteinHomo sapiensQ5U5U6—–—monomerMolecule count 125.658 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1221[3]0.228731–2.23993 1/nmHas uncertainty columnMissing 00sasbdb/entries/p2/sasdbp2/source/SASDBP2.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)8.63—nm
i0Guinier402.71.8—
i0P(r)409.55.6—
mwExperimental27.05—kDa
porod_volumePorod35.9—nm³
rgGuinier2.450.04nm
rgP(r)2.60.05nm

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

Fit 1 · —

χ²: 0.56CorMap p: 0.0Unit: 1/A
ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—mixEOM/RANCH —25.67—Model Image
2—mixEOM/RANCH —25.67—Model Image
▶

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 150mM NaCl 0.5 mM EDTABuffer concentration50.0 mM
pH7.5Additives150mM NaCl, 0.5 mM EDTA
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2014-11-03Storage / measurement temperature22.0 / —
Exposure time60.0Frames5
Wavelength1.907Sample-to-detector distance1.4
SourceX-ray synchrotronDetectorADSC Quantum 315
Facility / beamlinePohang Accelerator Laboratory / 5C · Pohang, South Korea
q range0.229 – 2.24Sample 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 (8 items)
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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:176 field values
Field pathRaw value
codeSASDBP2
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleNew conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin.
project.publication.titleNew conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin.
project.publication.author_listThach TT, Shin D, Han S, Lee S
project.publication.journalActa Crystallogr D Struct Biol
project.publication.doi10.1107/S2059798316001510
project.publication.pmid27050132
project.publication.published_date2016 Apr
project.statusreleased
project.submitted_date2015-10-16
project.released_date2016-04-07
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experiment.instrument.detector.typeCCD
experiment.instrument.detector.nameADSC Quantum 315
experiment.instrument.detector.resolution315.0
experiment.instrument.namePohang Accelerator Laboratory
experiment.instrument.cityPohang
experiment.instrument.countrySouth Korea
experiment.instrument.beamline_name5C
experiment.instrument.beam_geometry
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_nameHuman linear tri-ubiquitin
experiment.sample.molecule[0].short_nameTriubiquitin
experiment.sample.molecule[0].sequenceMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeQ5U5U6
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_sequenceMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKA KIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGC
experiment.sample.molecule[0].mw25.658
experiment.sample.molecule[0].total_mw25.658
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
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experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive150mM NaCl, 0.5 mM EDTA
experiment.sample.buffer.concentration50.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameHuman linear triubiquitin
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].addressSeoul, SK
experiment.contributor[0].affiliation[0].full_nameSungkyunkwan University
experiment.contributor[0].affiliation[0].webpagehttp://www.skku.edu/eng_home/index.jsp
experiment.contributor[0].contributor_nameDonghyuk
experiment.contributor[0].contributor_surnameShin
experiment.contributor[0].orcidnull
experiment.contributor[1].affiliation[0].short_namenull
experiment.contributor[1].affiliation[0].addressSeoul, SK
experiment.contributor[1].affiliation[0].full_nameSungkyunkwan University
experiment.contributor[1].affiliation[0].webpagehttp://www.skku.edu/eng_home/index.jsp
experiment.contributor[1].contributor_nameTrung
experiment.contributor[1].contributor_surnameThanh Thach
experiment.contributor[1].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitmg/ml
experiment.date2014-11-03
experiment.storage_temperature22.0
experiment.cell_temperaturenull
experiment.exposure_time60.0
experiment.number_of_frames5
experiment.wavelength1.907
experiment.sample_detector_distance1.4
experiment.concentration_min1.05
experiment.concentration_max4.2
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experiment.flow_ratenull
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experiment.s_max2.24
experiment.total_exposure_time300.0
experiment.seccolumnnull
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fits[0].models[0].bead_radius1.9
fits[0].models[0].lognull
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fits[0].models[0].comment
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fits[0].softwarenull
fits[0].chi_square_value0.56
fits[0].p_value0.0
fits[0].fit_residual_plotnull
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fits[0].fit_lognull
fits[0].software_versionnull
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionNote: The displayed results show a merged data set derived from a concentration series. Data were normalised to protein concentration and the high angle data from highest concentration and low angle data from lowest concentration were merged to generate final SAXS profile. Because of the flexibility of linear-triubiquitin molecule, ensemble optimisation method, EOM, was performed. The models shown above are two triubiquitin examples from the final EOM output. All EOM models, the radius of gyration distribution and maximum particle dimension distribution can be found in the full entry zip archive.
experiment_descriptionnull
tags[]
intensity_unitnull
experimental_mw27.05
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i0409.5
pddf_i0_error5.6
guinier_i0402.7
guinier_i0_error1.8
pddf_rg2.6
pddf_rg_error0.05
guinier_rg2.45
guinier_rg_error0.04
pddf_dmax8.63
pddf_dmax_errornull
porod_volume35.9
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first3
guinier_point_last34
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDBP2_datloglog_img.png
symmetrynull
last_modified2020-08-28T15:27:40.482221+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDBP2
statussuccess
started_at2026-08-11T13:42:51.813084+00:00
finished_at2026-08-11T13:43:00.070684+00:00
source_last_modified2020-08-28T15:27:40.482221+02:00
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View the complete summary.json source
{
  "code": "SASDBP2",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "New conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin.",
    "publication": {
      "title": "New conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin.",
      "author_list": "Thach TT, Shin D, Han S, Lee S",
      "journal": "Acta Crystallogr D Struct Biol",
      "doi": "10.1107/S2059798316001510",
      "pmid": "27050132",
      "published_date": "2016 Apr"
    },
    "status": "released",
    "submitted_date": "2015-10-16",
    "released_date": "2016-04-07"
  },
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    "sample": {
      "molecule": [
        {
          "long_name": "Human linear tri-ubiquitin",
          "short_name": "Triubiquitin",
          "sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG\r\n",
          "organism": "Homo sapiens",
          "uniprot_code": "Q5U5U6",
          "uniprot_range_first": null,
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  "last_modified": "2020-08-28T15:27:40.482221+02:00",
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}
View the complete manifest.json source
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