SASDAB9

EcPaaA2-HisEcParE2 construct

Data type: SASBDB experimental data Status: Published Curve type: Merged Last updated: 2019-12-06T13:07:15.624532+01:00

Use of SAXS to validate the oligomer state of the obtained crystal structure and to model missing afinity tags

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · EcPaaA2-HisEcParE2 construct

Concentration1.0 – 10.0 mg/mlBuffer / pH50 mM Tris-HCl 500 mM NaCl / 7.5
Experimental temperature10.0 Facility / beamlineSOLEIL / SWING
Wavelength0.1 nmExposure0.75 s × 750

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Plasmid stabilization protein ParE
View sequence
MGSSHHHHHHSSGLVPRGSHLPVLWLESADTDLDDITSYIARFDIDAAERLWQRLRGCVLPLSEHPYLYPPSDRVPGLREIVAHPNYIILYRVTTSSVEVVNVIHARRQFP
proteinEscherichia coliA0A0D7C2L12–92octamerMolecule count 812.693 kDa
Uncharacterized protein (Antitoxin)
View sequence
MDYKDDDDKNRALSPMVSEFETIEQENSYNEWLRAKVATSLADPRPAIPHDEVERRMAERFAKMRKERSKQ
proteinEscherichia coliA0A0F6F6Q914–75octamerMolecule count 88.458 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1802[3]0.2222031–4.002615 1/nmHas uncertainty columnMissing 00sasbdb/entries/b9/sasdab9/source/SASDAB9.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)15.28—nm
i0Guinier0.175042——
i0P(r)0.18——
mwExperimental100.0—kDa
mwGuinier I(0)100.0—kDa
mwPorod97.74—kDa
porod_volumePorod166.16—nm³
rgGuinier3.255—nm
rgP(r)3.408—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

Fit 1 · —

χ²: 3.439CorMap p: 0.0Unit: 1/A
ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—mixCRYSOL —84.58—Model Image
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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 name50 mM Tris-HCl 500 mM NaClBuffer concentration50.0 mM
pH7.5Additives500 mM NaCl
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2012-02-05Storage / measurement temperature— / 10.0
Exposure time0.75Frames750
Wavelength0.1Sample-to-detector distance1.82
SourceX-ray synchrotronDetectorAVIEX PCCD170170
Facility / beamlineSOLEIL / SWING · Saint-Aubin, France
q range0.222 – 4.003Sample 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:196 field values
Field pathRaw value
codeSASDAB9
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleA unique hetero-hexadecameric architecture displayed by the Escherichia coli O157 PaaA2-ParE2 antitoxin-toxin complex.
project.publication.titleA unique hetero-hexadecameric architecture displayed by the Escherichia coli O157 PaaA2-ParE2 antitoxin-toxin complex.
project.publication.author_listSterckx YG, Jové T, Shkumatov AV, Garcia-Pino A, Geerts L, De Kerpel M, Lah J, De Greve H, Van Melderen L, Loris R
project.publication.journalJ Mol Biol
project.publication.doi10.1016/j.jmb.2016.03.007
project.publication.pmid26996937
project.publication.published_date2016 Apr 24
project.statusreleased
project.submitted_date2015-08-24
project.released_date2016-03-18
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experiment.instrument.detector.nameAVIEX PCCD170170
experiment.instrument.detector.resolutionnull
experiment.instrument.nameSOLEIL
experiment.instrument.citySaint-Aubin
experiment.instrument.countryFrance
experiment.instrument.beamline_nameSWING
experiment.instrument.beam_geometry
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experiment.instrument.xray_energynull
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experiment.sample.molecule[0].long_namePlasmid stabilization protein ParE
experiment.sample.molecule[0].short_nameEcParE2
experiment.sample.molecule[0].sequenceMGSSHHHHHHSSGLVPRGSHLPVLWLESADTDLDDITSYIARFDIDAAERLWQRLRGCVLPLSEHPYLYPPSDRVPGLREIVAHPNYIILYRVTTSSVEVVNVIHARRQFP
experiment.sample.molecule[0].organismEscherichia coli
experiment.sample.molecule[0].uniprot_codeA0A0D7C2L1
experiment.sample.molecule[0].uniprot_range_first2
experiment.sample.molecule[0].uniprot_range_last92
experiment.sample.molecule[0].oligomerizationoctamer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMLPVLWLESADTDLDDITSYIARFDIDAAERLWQRLRGCVLPLSEHPYLYPPSDRVPGLR EIVAHPNYIILYRVTTSSVEVVNVIHARRQFP
experiment.sample.molecule[0].mw12.693
experiment.sample.molecule[0].total_mw101.546
experiment.sample.molecule[0].number_molecules8
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_nameUncharacterized protein (Antitoxin)
experiment.sample.molecule[1].short_nameEcPaaA2
experiment.sample.molecule[1].sequenceMDYKDDDDKNRALSPMVSEFETIEQENSYNEWLRAKVATSLADPRPAIPHDEVERRMAERFAKMRKERSKQ
experiment.sample.molecule[1].organismEscherichia coli
experiment.sample.molecule[1].uniprot_codeA0A0F6F6Q9
experiment.sample.molecule[1].uniprot_range_first14
experiment.sample.molecule[1].uniprot_range_last75
experiment.sample.molecule[1].oligomerizationoctamer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequencenull
experiment.sample.molecule[1].mw8.458
experiment.sample.molecule[1].total_mw67.667
experiment.sample.molecule[1].number_molecules8
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experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name50 mM Tris-HCl 500 mM NaCl
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive500 mM NaCl
experiment.sample.buffer.concentration50.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
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experiment.sample.purity_methodnull
experiment.sample.nameEcPaaA2-HisEcParE2 construct
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
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experiment.sample.absorbptionnull
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experiment.contributor[0].affiliation[0].short_nameVUB
experiment.contributor[0].affiliation[0].addressPleinlaan 2 1050 Brussel
experiment.contributor[0].affiliation[0].full_nameVrije Universiteit Brussel
experiment.contributor[0].affiliation[0].webpagehttp://www.vub.ac.be/
experiment.contributor[0].contributor_nameAlexander
experiment.contributor[0].contributor_surnameShkumatov
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitmg/ml
experiment.date2012-02-05
experiment.storage_temperaturenull
experiment.cell_temperature10.0
experiment.exposure_time0.75
experiment.number_of_frames750
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pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionUse of SAXS to validate the oligomer state of the obtained crystal structure and to model missing afinity tags
experiment_descriptionnull
tags[]
intensity_unitnull
experimental_mw100.0
experimental_mw_errornull
guinier_i0_mw100.0
guinier_i0_mw_errornull
porod_mw97.74
porod_mw_errornull
pddf_i00.18
pddf_i0_errornull
guinier_i00.175042
guinier_i0_errornull
pddf_rg3.408
pddf_rg_errornull
guinier_rg3.255
guinier_rg_errornull
pddf_dmax15.28
pddf_dmax_errornull
porod_volume166.16
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_firstnull
guinier_point_lastnull
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDAB9_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDAB9
statussuccess
started_at2026-08-11T16:34:23.487680+00:00
finished_at2026-08-11T16:34:36.463947+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDAB9",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "A unique hetero-hexadecameric architecture displayed by the Escherichia coli O157 PaaA2-ParE2 antitoxin-toxin complex.",
    "publication": {
      "title": "A unique hetero-hexadecameric architecture displayed by the Escherichia coli O157 PaaA2-ParE2 antitoxin-toxin complex.",
      "author_list": "Sterckx YG, Jové T, Shkumatov AV, Garcia-Pino A, Geerts L, De Kerpel M, Lah J, De Greve H, Van Melderen L, Loris R",
      "journal": "J Mol Biol",
      "doi": "10.1016/j.jmb.2016.03.007",
      "pmid": "26996937",
      "published_date": "2016 Apr 24"
    },
    "status": "released",
    "submitted_date": "2015-08-24",
    "released_date": "2016-03-18"
  },
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    },
    "sample": {
      "molecule": [
        {
          "long_name": "Plasmid stabilization protein ParE",
          "short_name": "EcParE2",
          "sequence": "MGSSHHHHHHSSGLVPRGSHLPVLWLESADTDLDDITSYIARFDIDAAERLWQRLRGCVLPLSEHPYLYPPSDRVPGLREIVAHPNYIILYRVTTSSVEVVNVIHARRQFP",
          "organism": "Escherichia coli",
          "uniprot_code": "A0A0D7C2L1",
          "uniprot_range_first": 2,
          "uniprot_range_last": 92,
          "oligomerization": "octamer",
          "molecular_type": "protein",
          "uniprot_sequence": "MLPVLWLESADTDLDDITSYIARFDIDAAERLWQRLRGCVLPLSEHPYLYPPSDRVPGLR\nEIVAHPNYIILYRVTTSSVEVVNVIHARRQFP",
          "mw": 12.693,
          "total_mw": 101.546,
          "number_molecules": 8,
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