SASDE44

Tryparedoxin W39A, oxidized state

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2020-11-27T11:54:22.541849+01:00

SEC column type: GE Healthcare S75 3.2/300; Sample Injection Concentration = 10 mg/mL; Column flow-rate = 0.1 mL/min.

▼

1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Tryparedoxin W39A, oxidized state

Concentration— – — Buffer / pH10 mM HEPES pH 7.5, 50 mM NaCl / 7.5
Experimental temperature20.0 Facility / beamlineESRF / BM29
Wavelength0.099 nmExposure1.0 s × —

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Tryparedoxin W39A
View sequence
GSGLAKYLPGATNLLSKSGEVSLGSLVGKTVFLYFSASACPPCRGFTPVLAEFYEKHHVAKNFEVVLISWDENESDFHDYYGKMPWLALPFDQRSTVSELGKTFGVESIPTLITINADTGAIIGTQARTRVIEDPDGANFPWPN
proteinTrypanosoma brucei bruceiO774042–144monomerMolecule count 115.702 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11043[3]0.03725576–4.927891 1/nmHas uncertainty columnMissing 020sasbdb/entries/44/sasde44/source/SASDE44.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)5.53—nm
i0Guinier7.290.01—
i0P(r)7.292——
mwExperimental13.8—kDa
mwPorod13.8—kDa
porod_volumePorod23.4—nm³
rgGuinier1.560.01nm
rgP(r)1.557—nm

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

▼

3. Source Fits and Models Source Fits & Models

Fit 1 · OLIGOMER

χ²: 2.04CorMap p: 0.0Unit: 1/A

Fit to mixture of crystallographic monomer and dimer: 99.9% monomer

ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—atomicPDB (Protein Data Bank) —31.776GXYModel Image
2—atomicOther —15.88—Model Image
▶

4. Source File Index Source Files

▶

5. Experiment Description and Publication Experiment & Publication

▼

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 name10 mM HEPES pH 7.5, 50 mM NaClBuffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2018-05-31Storage / measurement temperature20.0 / 20.0
Exposure time1.0Frames—
Wavelength0.099Sample-to-detector distance2.869
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineESRF / BM29 · Grenoble, France
q range0.037 – 4.928Sample 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

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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:172 field values
Field pathRaw value
codeSASDE44
statusPublished
type_of_curveSEC-SAS
angular_unit1/nm
project.titleInhibitor-induced dimerization of an essential oxidoreductase from African Trypanosomes.
project.publication.titleInhibitor-induced dimerization of an essential oxidoreductase from African Trypanosomes.
project.publication.author_listWagner A, Le TA, Brennich M, Klein P, Bader N, Diehl E, Paszek D, Weickhmann AK, Dirdjaja N, Krauth-Siegel RL, Engels B, Opatz T, Schindelin H, Hellmich UA
project.publication.journalAngew Chem Int Ed Engl
project.publication.doi10.1002/anie.201810470
project.publication.pmid30605929
project.publication.published_date2019 Jan 3
project.statusreleased
project.submitted_date2018-09-06
project.released_date2019-01-08
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experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
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experiment.sample.molecule[0].long_nameTryparedoxin W39A
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceGSGLAKYLPGATNLLSKSGEVSLGSLVGKTVFLYFSASACPPCRG FTPVLAEFYEKHHVAKNFEVVLISWDENESDFHDYYGKMPWLALPFDQRSTVSELGKTFG VESIPTLITINADTGAIIGTQARTRVIEDPDGANFPWPN
experiment.sample.molecule[0].organismTrypanosoma brucei brucei
experiment.sample.molecule[0].uniprot_codeO77404
experiment.sample.molecule[0].uniprot_range_first2
experiment.sample.molecule[0].uniprot_range_last144
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMSGLAKYLPGATNLLSKSGEVSLGSLVGKTVFLYFSASWCPPCRGFTPVLAEFYEKHHVA KNFEVVLISWDENESDFHDYYGKMPWLALPFDQRSTVSELGKTFGVESIPTLITINADTG AIIGTQARTRVIEDPDGANFPWPN
experiment.sample.molecule[0].mw15.702
experiment.sample.molecule[0].total_mw15.702
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_stateFalse
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experiment.sample.molecule[0].molecule_sourcebiological
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experiment.sample.nameTryparedoxin W39A, oxidized state
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
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experiment.sample.absorbptionnull
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experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_nameEMBL
experiment.contributor[0].affiliation[0].addressGrenoble, France
experiment.contributor[0].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Grenoble Outstation
experiment.contributor[0].affiliation[0].webpagehttps://www.embl.fr/
experiment.contributor[0].contributor_nameMartha
experiment.contributor[0].contributor_surnameBrennich
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experiment.concentration_unitnull
experiment.date2018-05-31
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experiment.cell_temperature20.0
experiment.exposure_time1.0
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estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionSEC column type: GE Healthcare S75 3.2/300; Sample Injection Concentration = 10 mg/mL; Column flow-rate = 0.1 mL/min.
experiment_descriptionSynchrotron SAXS data from solutions of Tryparedoxin W39A, oxidized state in 10 mM HEPES pH 7.5, 50 mM NaCl, pH 7.5 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Dectris Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The data were collected using in-line size exclusion chromatography (SEC)-SAXS at 20°C.
tags[]
intensity_unitnull
experimental_mw13.8
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw13.8
porod_mw_errornull
pddf_i07.292
pddf_i0_errornull
guinier_i07.29
guinier_i0_error0.01
pddf_rg1.557
pddf_rg_errornull
guinier_rg1.56
guinier_rg_error0.01
pddf_dmax5.53
pddf_dmax_errornull
porod_volume23.4
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first27
guinier_point_last171
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDE44_datloglog_img.png
symmetrynull
last_modified2020-11-27T11:54:22.541849+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDE44
statussuccess
started_at2026-08-11T14:13:26.124572+00:00
finished_at2026-08-11T14:13:35.356112+00:00
source_last_modified2020-11-27T11:54:22.541849+01:00
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View the complete summary.json source
{
  "code": "SASDE44",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "Inhibitor-induced dimerization of an essential oxidoreductase from African Trypanosomes.",
    "publication": {
      "title": "Inhibitor-induced dimerization of an essential oxidoreductase from African Trypanosomes.",
      "author_list": "Wagner A, Le TA, Brennich M, Klein P, Bader N, Diehl E, Paszek D, Weickhmann AK, Dirdjaja N, Krauth-Siegel RL, Engels B, Opatz T, Schindelin H, Hellmich UA",
      "journal": "Angew Chem Int Ed Engl",
      "doi": "10.1002/anie.201810470",
      "pmid": "30605929",
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      "name": "Tryparedoxin W39A, oxidized state",
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View the complete manifest.json source
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