SASDDQ3

Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) collected by SEC-SAXS

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2019-12-06T13:07:15.624532+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) collected by SEC-SAXS

Concentration— – — Buffer / pH50 mM Tris, 50 mM NaCl, 0.5 mM TCEP, 5% (v/v) glycerol / 7.8
Experimental temperature22.0 Facility / beamlineAdvanced Photon Source (APS), Argonne National Laboratory / BioCAT 18ID
Wavelength0.103 nmExposure— s × —

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Bifunctional protein PutA
View sequence
>BJPUTAGHMPNIPPPFTAPYAPDDAEIAARLLPASHLSPPQEARIHRTATRLIEAIRKRDDRLGGVEDMLREFALSTKEGLALMVLAEALLRVPDARTADQFIEDKLGEGDFIHHETKSTAFLVNASAWALGLSARVIQPGETPDGTIGRLVKRLGAPAVRTATRQAMRLMGNHFVLGETIEQALERGKPRSGQKTRYSFDMLGEGARTAADARRYFDAYASAIETIGKAAGNHALPDRPGISVKLSALHPRFEAISRARVMVELVPQLLDLAQRAKAHDLNFTVDAEEADRLELSLDVIAATLADPSLKGWDGFGLAIQAYQKRASAVIDYVDALARAHDRKLMVRLVKGAYWDTEIKRAQERGLDGYPVFTRKAMTDLNYVACASKLLALRPRIFPQFATHNALTVATVLEMAEGSSGFEFQRLHGMGEALYEQLAKDHADIAYRTYAPVGSHRDLLAYLVRRLLENGANSSFVAQAADYRVPVPALLQRPADAIVRPQAAAHPRIPLPCDLFAPERRNSRGVEFGARTALDQLLTDVKAETGDLKPIADATPDQAHAAVAAARAGFAGWSRTPAGIRAAALEQAAHLLESRSAHFIALLQREGGKTLDDALSELREAADFCRYYAAQGRKLFGSETAMPGPTGESNALTMRGRGVFVAISPWNFPLAIFLGQVTAALMAGNSVVAKPAEQTPRIAREAVALLHEAGIPKSALYLVTGDGRIGAALTAHPDIAGVVFTGSTEVARSINRALAAKDGPIVPLIAETGGINAMIADATALPEQVADDVVTSAFRSAGQRCSALRLLFVQEDVADRMIEMVAGAARELKIGDPSDVATHVGPVIDVEAKQRLDAHIARMKTEARLHFAGPAPEGCFVAPHIFELTEAGQLTEEVFGPILHVVRYRPENLERVLRAIERTGYGLTLGVHSRIDDSIEAIIDRVQVGNIYVNRNMIGAVVGVQPFGGNGLSGTGPKAGGPHYLARFATEQTVTINTAAAGGNAALLAGEE
proteinBradyrhizobium diazoefficiensQ89E26—–—tetramerMolecule count 4107.558 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11266[3]0.00569995–0.383203 1/AHas uncertainty columnMissing 0291sasbdb/entries/q3/sasddq3/source/SASDDQ3.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)14.23—Å
i0Guinier461.01.0arbitrary
i0P(r)463.2—arbitrary
mwExperimental433.8—kDa
porod_volumePorod582.0—ų
rgGuinier5.220.02Å
rgP(r)5.2—Å

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 name50 mM Tris, 50 mM NaCl, 0.5 mM TCEP, 5% (v/v) glycerolBuffer concentration—
pH7.8Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2017-07-16Storage / measurement temperature— / 22.0
Exposure time—Frames—
Wavelength0.103Sample-to-detector distance3.5
SourceX-ray synchrotronDetectorPilatus 100K
Facility / beamlineAdvanced Photon Source (APS), Argonne National Laboratory / BioCAT 18ID · Lemont, IL, USA
q range0.057 – 3.832Sample 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:159 field values
Field pathRaw value
codeSASDDQ3
statusPublished
type_of_curveSEC-SAS
angular_unit1/A
project.titleRedox Modulation of Oligomeric State in Proline Utilization A.
project.publication.titleRedox Modulation of Oligomeric State in Proline Utilization A.
project.publication.author_listKorasick DA, Campbell AC, Christgen SL, Chakravarthy S, White TA, Becker DF, Tanner JJ
project.publication.journalBiophys J
project.publication.doi10.1016/j.bpj.2018.04.046
project.publication.pmid29925020
project.publication.published_date2018 Jun 19
project.statusreleased
project.submitted_date2018-02-26
project.released_date2018-06-22
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experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 100K
experiment.instrument.detector.resolution172.0
experiment.instrument.nameAdvanced Photon Source (APS), Argonne National Laboratory
experiment.instrument.cityLemont, IL
experiment.instrument.countryUSA
experiment.instrument.beamline_nameBioCAT 18ID
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_nameBifunctional protein PutA
experiment.sample.molecule[0].short_nameBjPutA
experiment.sample.molecule[0].sequence>BjPutA GHMPNIPPPFTAPYAPDDAEIAARLLPASHLSPPQEARIHRTATRLIEAIRKRDDRLGGVEDMLREFALSTKEGLALMVLAEALLRVPDARTADQFIEDKLGEGDFIHHETKSTAFLVNASAWALGLSARVIQPGETPDGTIGRLVKRLGAPAVRTATRQAMRLMGNHFVLGETIEQALERGKPRSGQKTRYSFDMLGEGARTAADARRYFDAYASAIETIGKAAGNHALPDRPGISVKLSALHPRFEAISRARVMVELVPQLLDLAQRAKAHDLNFTVDAEEADRLELSLDVIAATLADPSLKGWDGFGLAIQAYQKRASAVIDYVDALARAHDRKLMVRLVKGAYWDTEIKRAQERGLDGYPVFTRKAMTDLNYVACASKLLALRPRIFPQFATHNALTVATVLEMAEGSSGFEFQRLHGMGEALYEQLAKDHADIAYRTYAPVGSHRDLLAYLVRRLLENGANSSFVAQAADYRVPVPALLQRPADAIVRPQAAAHPRIPLPCDLFAPERRNSRGVEFGARTALDQLLTDVKAETGDLKPIADATPDQAHAAVAAARAGFAGWSRTPAGIRAAALEQAAHLLESRSAHFIALLQREGGKTLDDALSELREAADFCRYYAAQGRKLFGSETAMPGPTGESNALTMRGRGVFVAISPWNFPLAIFLGQVTAALMAGNSVVAKPAEQTPRIAREAVALLHEAGIPKSALYLVTGDGRIGAALTAHPDIAGVVFTGSTEVARSINRALAAKDGPIVPLIAETGGINAMIADATALPEQVADDVVTSAFRSAGQRCSALRLLFVQEDVADRMIEMVAGAARELKIGDPSDVATHVGPVIDVEAKQRLDAHIARMKTEARLHFAGPAPEGCFVAPHIFELTEAGQLTEEVFGPILHVVRYRPENLERVLRAIERTGYGLTLGVHSRIDDSIEAIIDRVQVGNIYVNRNMIGAVVGVQPFGGNGLSGTGPKAGGPHYLARFATEQTVTINTAAAGGNAALLAGEE
experiment.sample.molecule[0].organismBradyrhizobium diazoefficiens
experiment.sample.molecule[0].uniprot_codeQ89E26
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationtetramer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMPNIPPPFTAPYAPDDAEIAARLLPASHLSPPQEARIHRTATRLIEAIRKRDDRLGGVED MLREFALSTKEGLALMVLAEALLRVPDARTADQFIEDKLGEGDFIHHETKSTAFLVNASA WALGLSARVIQPGETPDGTIGRLVKRLGAPAVRTATRQAMRLMGNHFVLGETIEQALERG KPRSGQKTRYSFDMLGEGARTAADARRYFDAYASAIETIGKAAGNHALPDRPGISVKLSA LHPRFEAISRARVMVELVPQLLDLAQRAKAHDLNFTVDAEEADRLELSLDVIAATLADPS LKGWDGFGLAIQAYQKRASAVIDYVDALARAHDRKLMVRLVKGAYWDTEIKRAQERGLDG YPVFTRKAMTDLNYVACASKLLALRPRIFPQFATHNALTVATVLEMAEGSSGFEFQRLHG MGEALYEQLAKDHADIAYRTYAPVGSHRDLLAYLVRRLLENGANSSFVAQAADYRVPVPA LLQRPADAIVRPQAAAHPRIPLPCDLFAPERRNSRGVEFGARTALDQLLTDVKAETGDLK PIADATPDQAHAAVAAARAGFAGWSRTPAGIRAAALEQAAHLLESRSAHFIALLQREGGK TLDDALSELREAADFCRYYAAQGRKLFGSETAMPGPTGESNALTMRGRGVFVAISPWNFP LAIFLGQVTAALMAGNSVVAKPAEQTPRIAREAVALLHEAGIPKSALYLVTGDGRIGAAL TAHPDIAGVVFTGSTEVARSINRALAAKDGPIVPLIAETGGINAMIADATALPEQVADDV VTSAFRSAGQRCSALRLLFVQEDVADRMIEMVAGAARELKIGDPSDVATHVGPVIDVEAK QRLDAHIARMKTEARLHFAGPAPEGCFVAPHIFELTEAGQLTEEVFGPILHVVRYRPENL ERVLRAIERTGYGLTLGVHSRIDDSIEAIIDRVQVGNIYVNRNMIGAVVGVQPFGGNGLS GTGPKAGGPHYLARFATEQTVTINTAAAGGNAALLAGEE
experiment.sample.molecule[0].mw107.558
experiment.sample.molecule[0].total_mw430.232
experiment.sample.molecule[0].number_molecules4
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.name50 mM Tris, 50 mM NaCl, 0.5 mM TCEP, 5% (v/v) glycerol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.8
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameProline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) collected by SEC-SAXS
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_nameMizzou
experiment.contributor[0].affiliation[0].addressColumbia, MO, USA
experiment.contributor[0].affiliation[0].full_nameUniversity of Missouri-Columbia
experiment.contributor[0].affiliation[0].webpagehttp://missouri.edu/
experiment.contributor[0].contributor_nameDavid
experiment.contributor[0].contributor_surnameKorasick
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-07-16
experiment.storage_temperaturenull
experiment.cell_temperature22.0
experiment.exposure_timenull
experiment.number_of_framesnull
experiment.wavelength0.103
experiment.sample_detector_distance3.5
experiment.concentration_minnull
experiment.concentration_maxnull
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.057
experiment.s_max3.832
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwarePDB (Protein Data Bank)
fits[0].models[0].pdb_link[0].pdb_code3haz
fits[0].models[0].pdb_link[0].ext_code3HAZ
fits[0].models[0].pdb_link[0].ext_typepdb
fits[0].models[0].pdb_link[0].difference_with_modelidentical
fits[0].models[0].model_titlenull
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fits[0].models[0].model_mw424.8
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetrynull
fits[0].models[0].commentnull
fits[0].models[0].user290
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fits[0].softwareFoXS
fits[0].chi_square_value1.14276
fits[0].p_value0.0
fits[0].fit_residual_plotSASDDQ3_fit1_fitfoxsresiduals_img.png
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fits[0].fit_lognull
fits[0].software_versionnull
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) were collected using SEC-SAXS in 50 mM Tris, 50 mM NaCl, 0.5 mM TCEP, 5% (v/v) glycerol, pH 7.8 on the BioCAT 18ID beam line at the Advanced Photon Source (APS, Argonne, IL, USA) using a Pilatus 100K detector at a sample-detector distance of 3.5 m and at a wavelength of λ = 0.103 nm (l(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). The SEC-SAXS elution was collected at 22°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.
tags[]
intensity_unitarbitrary
experimental_mw433.8
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i0463.2
pddf_i0_errornull
guinier_i0461.0
guinier_i0_error1.0
pddf_rg5.2
pddf_rg_errornull
guinier_rg5.22
guinier_rg_error0.02
pddf_dmax14.23
pddf_dmax_errornull
porod_volume582.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last65
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDDQ3_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDDQ3
statussuccess
started_at2026-08-11T14:05:14.221280+00:00
finished_at2026-08-11T14:05:26.311170+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDDQ3",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Redox Modulation of Oligomeric State in Proline Utilization A.",
    "publication": {
      "title": "Redox Modulation of Oligomeric State in Proline Utilization A.",
      "author_list": "Korasick DA, Campbell AC, Christgen SL, Chakravarthy S, White TA, Becker DF, Tanner JJ",
      "journal": "Biophys J",
      "doi": "10.1016/j.bpj.2018.04.046",
      "pmid": "29925020",
      "published_date": "2018 Jun 19"
    },
    "status": "released",
    "submitted_date": "2018-02-26",
    "released_date": "2018-06-22"
  },
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View the complete manifest.json source
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