SASDEA3

Labeled thioredoxin (TRX-Alexa488/Alexa594) with denaturant

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

The protein contains a penultimate non-canonical amino acid p-acetylphenylalanine (207 Da) that is represented as U (selenocysteine, 168 Da) in the amino acid sequence for the entry. Therefore, the calculated MW from sequence (MW(expected)) must be adjusted accordingly (ca. 40 Da).

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Labeled thioredoxin (TRX-Alexa488/Alexa594) with denaturant

Concentration— – 10.0 Buffer / pHPBS, 10 mM DTT, 6 M urea, 0.3 M KCl / 7.4
Experimental temperature23.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.1 nmExposure0.05 s × 20

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Thioredoxin 1
View sequence
>U=P-ACETYLPHENYLALANINE.CWASLABELEDWITHALEXAFLUOR594C5MALEIMIDE.UWASLABELEDWITHALEXAFLUOR488C5HYDROXYLAMINEGCDKIIHLTDDSFDTDVLKADGAILVDFWAEWSGPSKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANUA
proteinEscherichia coliP0AA252–106monomerMolecule count 111.753 kDa
Alexa Fluor™ 594 C5 Maleimideother———–—monomerMolecule count 10.886 kDa
Alexa Fluor™ 488 C5 Hydroxylamineother———–—monomerMolecule count 10.7 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11714[3]0.0767596–4.58324 1/nmHas uncertainty columnMissing 04sasbdb/entries/a3/sasdea3/source/SASDEA3.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)13.88—nm
i0Guinier315.41.6arbitrary
i0P(r)320.71.7arbitrary
mwExperimental9.5—kDa
porod_volumePorod30.9—nm³
rgGuinier3.20.08nm
rgP(r)3.4660.05nm

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

This entry has no source fit record.

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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 namePBS, 10 mM DTT, 6 M urea, 0.3 M KClBuffer concentration—
pH7.4Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2013-06-15Storage / measurement temperature— / 23.0
Exposure time0.05Frames20
Wavelength0.1Sample-to-detector distance3.0
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.077 – 4.583Sample 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
codeSASDEA3
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleDecoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.
project.publication.titleDecoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.
project.publication.author_listFuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, Kachala M, Estrada Girona G, Milles S, Mishra A, Onck PR, Gräter F, Esteban-Martín S, Pappu RV, Svergun DI, Lemke EA
project.publication.journalProc Natl Acad Sci U S A
project.publication.doi10.1073/pnas.1704692114
project.publication.pmid28716919
project.publication.published_date2017 Aug 1
project.statusreleased
project.submitted_date2018-08-16
project.released_date2018-08-18
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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_nameThioredoxin 1
experiment.sample.molecule[0].short_nameTRX-488/594
experiment.sample.molecule[0].sequence> U=p-acetylphenylalanine. C was labeled with Alexa Fluor 594 C5 maleimide. U was labeled with Alexa Fluor 488 C5 hydroxylamine GCDKIIHLTDDSFDTDVLKADGAILVDFWAEWSGPSKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANUA
experiment.sample.molecule[0].organismEscherichia coli
experiment.sample.molecule[0].uniprot_codeP0AA25
experiment.sample.molecule[0].uniprot_range_first2
experiment.sample.molecule[0].uniprot_range_last106
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLN IDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA
experiment.sample.molecule[0].mw11.753
experiment.sample.molecule[0].total_mw11.753
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
experiment.sample.molecule[1].long_nameAlexa Fluor™ 594 C5 Maleimide
experiment.sample.molecule[1].short_nameAlexa594
experiment.sample.molecule[1].sequencenull
experiment.sample.molecule[1].organismnull
experiment.sample.molecule[1].uniprot_codenull
experiment.sample.molecule[1].uniprot_range_firstnull
experiment.sample.molecule[1].uniprot_range_lastnull
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeother
experiment.sample.molecule[1].uniprot_sequencenull
experiment.sample.molecule[1].mw0.886
experiment.sample.molecule[1].total_mw0.886
experiment.sample.molecule[1].number_molecules1
experiment.sample.molecule[1].complex_statenull
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.molecule[2].long_nameAlexa Fluor™ 488 C5 Hydroxylamine
experiment.sample.molecule[2].short_nameAlexa488
experiment.sample.molecule[2].sequencenull
experiment.sample.molecule[2].organismnull
experiment.sample.molecule[2].uniprot_codenull
experiment.sample.molecule[2].uniprot_range_firstnull
experiment.sample.molecule[2].uniprot_range_lastnull
experiment.sample.molecule[2].oligomerizationmonomer
experiment.sample.molecule[2].molecular_typeother
experiment.sample.molecule[2].uniprot_sequencenull
experiment.sample.molecule[2].mw0.7
experiment.sample.molecule[2].total_mw0.7
experiment.sample.molecule[2].number_molecules1
experiment.sample.molecule[2].complex_stateFalse
experiment.sample.molecule[2].deuterationnull
experiment.sample.molecule[2].molecule_sourcebiological
experiment.sample.molecule[2].molecule_descriptionnull
experiment.sample.buffer.namePBS, 10 mM DTT, 6 M urea, 0.3 M KCl
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
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameLabeled thioredoxin (TRX-Alexa488/Alexa594) with denaturant
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].addressPrague, Czech Republic
experiment.contributor[0].affiliation[0].full_nameInstitute of Biotechnology CAS v.v.i.
experiment.contributor[0].affiliation[0].webpagehttp://www.ibt.cas.cz/
experiment.contributor[0].contributor_nameGustavo
experiment.contributor[0].contributor_surnameFuertes Vives
experiment.contributor[0].orcidhttps://orcid.org/0000-0002-8564-8644
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2013-06-15
experiment.storage_temperaturenull
experiment.cell_temperature23.0
experiment.exposure_time0.05
experiment.number_of_frames20
experiment.wavelength0.1
experiment.sample_detector_distance3.0
experiment.concentration_minnull
experiment.concentration_max10.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.077
experiment.s_max4.583
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[]
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionThe protein contains a penultimate non-canonical amino acid p-acetylphenylalanine (207 Da) that is represented as U (selenocysteine, 168 Da) in the amino acid sequence for the entry. Therefore, the calculated MW from sequence (MW(expected)) must be adjusted accordingly (ca. 40 Da).
experiment_descriptionnull
tags[0]idp
intensity_unitarbitrary
experimental_mw9.5
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i0320.7
pddf_i0_error1.7
guinier_i0315.4
guinier_i0_error1.6
pddf_rg3.466
pddf_rg_error0.05
guinier_rg3.2
guinier_rg_error0.08
pddf_dmax13.88
pddf_dmax_errornull
porod_volume30.9
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first5
guinier_point_last126
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDEA3_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDEA3
statussuccess
started_at2026-08-11T13:55:59.155789+00:00
finished_at2026-08-11T13:56:07.600535+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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View the complete summary.json source
{
  "code": "SASDEA3",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.",
    "publication": {
      "title": "Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.",
      "author_list": "Fuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, Kachala M, Estrada Girona G, Milles S, Mishra A, Onck PR, Gräter F, Esteban-Martín S, Pappu RV, Svergun DI, Lemke EA",
      "journal": "Proc Natl Acad Sci U S A",
      "doi": "10.1073/pnas.1704692114",
      "pmid": "28716919",
      "published_date": "2017 Aug 1"
    },
    "status": "released",
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    "released_date": "2018-08-18"
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    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Prague, Czech Republic",
            "full_name": "Institute of Biotechnology CAS v.v.i.",
            "webpage": "http://www.ibt.cas.cz/"
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        ],
        "contributor_name": "Gustavo",
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      }
    ],
    "concentration_method": null,
    "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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