SASDEU6

Polyglutamine-binding protein 1 p.Arg153Serfs*41 (PQBP-1 XLID mutant R153Sfs*41)

Data type: SASBDB experimental data Status: Published Curve type: Merged Last updated: 2023-05-25T11:22:08.798758+02:00

The entry displays the EOM ensemble Rg distributions and the fit to the data of the refined ensemble. The full EOM ensemble and log file describing the associated volume fractions is available for download in the full entry zip-archive.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Polyglutamine-binding protein 1 p.Arg153Serfs*41 (PQBP-1 XLID mutant R153Sfs*41)

Concentration1.0 – 7.3 Buffer / pHPhosphate-buffered saline / 7.4
Experimental temperature10.0 Facility / beamlineDORIS III, DESY / EMBL X33
Wavelength0.124 nmExposure0.045 s × —

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Polyglutamine-binding protein 1 p.Arg153Serfs*41
View sequence
>SP|O60828|PQBP1_HUMANPOLYGLUTAMINE-BINDINGPROTEIN1OS=HOMOSAPIENSGPMPLPVALQTRLAKRGILKHLEPEPEEEIIAEDYDDDPVDYEATRLEGLPPSWYKVFDPSCGLPYYWNADTDLVSWLSPHDPNSVVTKSAKKLRSSNADAEEKLDRSHDKSDRGHDKSDRSHEKLDRGHDKSDRGHDKSDRDRERGYDKVDRESETGNGIGTAGMTRQTGKRAKNGATIAGRSWLPIPRARRQ
proteinHomo sapiensO608281–154dimerMolecule count 221.914 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11546[3]0.0813365–4.18161 1/nmHas uncertainty columnMissing 00sasbdb/entries/u6/sasdeu6/source/SASDEU6.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)13.01.0nm
i0Guinier3006.9916.14arbitrary
i0P(r)2971.09.293arbitrary
mwExperimental45.49—kDa
mwGuinier I(0)45.49—kDa
porod_volumePorod100.0—nm³
rgGuinier3.610.19nm
rgP(r)3.610.01nm

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 namePhosphate-buffered salineBuffer concentration—
pH7.4Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2013-02-15Storage / measurement temperature— / 10.0
Exposure time0.045Frames—
Wavelength0.124Sample-to-detector distance3.0
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlineDORIS III, DESY / EMBL X33 · Hamburg, Germany
q range0.081 – 4.182Sample 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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All source fields (unfiltered)

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

summary.json:168 field values
Field pathRaw value
codeSASDEU6
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleFrameshift PQBP-1 mutants K192S<sup>fs*7</sup> and R153S<sup>fs*41</sup> implicated in X-linked intellectual disability form stable dimers.
project.publication.titleFrameshift PQBP-1 mutants K192S<sup>fs*7</sup> and R153S<sup>fs*41</sup> implicated in X-linked intellectual disability form stable dimers.
project.publication.author_listRahman SK, Okazawa H, Chen YW
project.publication.journalJ Struct Biol
project.publication.doi10.1016/j.jsb.2019.04.003
project.publication.pmid30951824
project.publication.published_date2019 Apr 2
project.statusreleased
project.submitted_date2018-10-23
project.released_date2019-04-08
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experiment.instrument.detector.namePilatus 2M
experiment.instrument.detector.resolutionnull
experiment.instrument.nameDORIS III, DESY
experiment.instrument.cityHamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL X33
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_namePolyglutamine-binding protein 1 p.Arg153Serfs*41
experiment.sample.molecule[0].short_nameR153Sfs*41
experiment.sample.molecule[0].sequence>sp|O60828|PQBP1_HUMAN Polyglutamine-binding protein 1 OS=Homo sapiens GPMPLPVALQTRLAKRGILKHLEPEPEEEIIAEDYDDDPVDYEATRLEGLPP SWYKVFDPSCGLPYYWNADTDLVSWLSPHDPNSVVTKSAKKLRSSNADAE EKLDRSHDKSDRGHDKSDRSHEKLDRGHDKSDRGHDKSDRDRERGYDKVD RESETGNGIGTAGMTRQTGKRAKNGATIAGRSWLPIPRARRQ
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeO60828
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last154
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMPLPVALQTRLAKRGILKHLEPEPEEEIIAEDYDDDPVDYEATRLEGLPPSWYKVFDPSC GLPYYWNADTDLVSWLSPHDPNSVVTKSAKKLRSSNADAEEKLDRSHDKSDRGHDKSDRS HEKLDRGHDKSDRGHDKSDRDRERGYDKVDRERERDRERDRDRGYDKADREEGKERRHHR REELAPYPKSKKAVSRKDEELDPMDPSSYSDAPRGTWSTGLPKRNEAKTGADTTAAGPLF QQRPYPSPGAVLRANAEASRTKQQD
experiment.sample.molecule[0].mw21.914
experiment.sample.molecule[0].total_mw43.828
experiment.sample.molecule[0].number_molecules2
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.namePhosphate-buffered saline
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.4
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experiment.sample.purity_methodnull
experiment.sample.namePolyglutamine-binding protein 1 p.Arg153Serfs*41 (PQBP-1 XLID mutant R153Sfs*41)
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
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experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressLondon, UK
experiment.contributor[0].affiliation[0].full_nameKing's College London
experiment.contributor[0].affiliation[0].webpagehttps://www.kcl.ac.uk
experiment.contributor[0].contributor_nameYu Wai
experiment.contributor[0].contributor_surnameChen
experiment.contributor[0].orcidhttp://orcid.org/0000-0001-7833-7533
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2013-02-15
experiment.storage_temperaturenull
experiment.cell_temperature10.0
experiment.exposure_time0.045
experiment.number_of_framesnull
experiment.wavelength0.124
experiment.sample_detector_distance3.0
experiment.concentration_min1.0
experiment.concentration_max7.3
experiment.sample_volumenull
experiment.flow_ratenull
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experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].p_value0.005645
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fits[1].softwareEOM/GAJOE
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fits[1].p_value0.023111
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fits[1].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version4.5a
i0_calibration_standardnull
descriptionThe entry displays the EOM ensemble Rg distributions and the fit to the data of the refined ensemble. The full EOM ensemble and log file describing the associated volume fractions is available for download in the full entry zip-archive.
experiment_descriptionSynchrotron SAXS data from solutions of polyglutamine-binding protein 1 p.Arg153Serfs*41 in phosphate-buffered saline, pH 7.4 were collected on the EMBL X33 beam line at the DORIS III storage ring (DESY, Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1 and 7.3 mg/ml were measured at 10°C using an X-ray exposure time of 45 ms. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.
tags[0]idp
tags[1]X33
intensity_unitarbitrary
experimental_mw45.49
experimental_mw_errornull
guinier_i0_mw45.49
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i02971.0
pddf_i0_error9.293
guinier_i03006.99
guinier_i0_error16.14
pddf_rg3.61
pddf_rg_error0.01
guinier_rg3.61
guinier_rg_error0.19
pddf_dmax13.0
pddf_dmax_error1.0
porod_volume100.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first8
guinier_point_last106
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDEU6_datloglog_img.png
symmetrynull
last_modified2023-05-25T11:22:08.798758+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDEU6
statussuccess
started_at2026-08-11T15:15:53.740516+00:00
finished_at2026-08-11T15:16:07.704979+00:00
source_last_modified2023-05-25T11:22:08.798758+02:00
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View the complete summary.json source
{
  "code": "SASDEU6",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "Frameshift PQBP-1 mutants K192S<sup>fs*7</sup> and R153S<sup>fs*41</sup> implicated in X-linked intellectual disability form stable dimers.",
    "publication": {
      "title": "Frameshift PQBP-1 mutants K192S<sup>fs*7</sup> and R153S<sup>fs*41</sup> implicated in X-linked intellectual disability form stable dimers.",
      "author_list": "Rahman SK, Okazawa H, Chen YW",
      "journal": "J Struct Biol",
      "doi": "10.1016/j.jsb.2019.04.003",
      "pmid": "30951824",
      "published_date": "2019 Apr 2"
    },
    "status": "released",
    "submitted_date": "2018-10-23",
    "released_date": "2019-04-08"
  },
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        {
          "long_name": "Polyglutamine-binding protein 1 p.Arg153Serfs*41",
          "short_name": "R153Sfs*41",
          "sequence": ">sp|O60828|PQBP1_HUMAN Polyglutamine-binding protein 1 OS=Homo sapiens\r\nGPMPLPVALQTRLAKRGILKHLEPEPEEEIIAEDYDDDPVDYEATRLEGLPP \r\nSWYKVFDPSCGLPYYWNADTDLVSWLSPHDPNSVVTKSAKKLRSSNADAE \r\nEKLDRSHDKSDRGHDKSDRSHEKLDRGHDKSDRGHDKSDRDRERGYDKVD \r\nRESETGNGIGTAGMTRQTGKRAKNGATIAGRSWLPIPRARRQ",
          "organism": "Homo sapiens",
          "uniprot_code": "O60828",
          "uniprot_range_first": 1,
          "uniprot_range_last": 154,
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          "molecular_type": "protein",
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View the complete manifest.json source
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