SASDCU3

Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) 7.0 mg/mL

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2026-05-18T10:07:06.737546+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) 7.0 mg/mL

Concentration— – 7.0 Buffer / pH50 mM Tris (pH 7.8), 50 mM NaCl, 0.5 mM Tris(2-carboxyethyl)phosphine, and 5% (v/v) glycerol / 7.8
Experimental temperature— Facility / beamlineAdvanced Light Source (ALS) / 12.3.1 (SIBYLS)
Wavelength— nmExposure— s × —

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Proline dehydrogenase
View sequence
GHMPNIPPPFTAPYAPDDAEIAARLLPASHLSPPQEARIHRTATRLIEAIRKRDDRLGGVEDMLREFALSTKEGLALMVLAEALLRVPDARTADQFIEDKLGEGDFIHHETKSTAFLVNASAWALGLSARVIQPGETPDGTIGRLVKRLGAPAVRTATRQAMRLMGNHFVLGETIEQALERGKPRSGQKTRYSFDMLGEGARTAADARRYFDAYASAIETIGKAAGNHALPDRPGISVKLSALHPRFEAISRARVMVELVPQLLDLAQRAKAHDLNFTVDAEEADRLELSLDVIAATLADPSLKGWDGFGLAIQAYQKRASAVIDYVDALARAHDRKLMVRLVKGAYWDTEIKRAQERGLDGYPVFTRKAMTDLNYVACASKLLALRPRIFPQFATHNALTVATVLEMAEGSSGFEFQRLHGMGEALYEQLAKDHADIAYRTYAPVGSHRDLLAYLVRRLLENGANSSFVAQAADYRVPVPALLQRPADAIVRPQAAAHPRIPLPCDLFAPERRNSRGVEFGARTALDQLLTDVKAETGDLKPIADATPDQAHAAVAAARAGFAGWSRTPAGIRAAALEQAAHLLESRSAHFIALLQREGGKTLDDALSELREAADFCRYYAAQGRKLFGSETAMPGPTGESNALTMRGRGVFVAISPWNFPLAIFLGQVTAALMAGNSVVAKPAEQTPRIAREAVALLHEAGIPKSALYLVTGDGRIGAALTAHPDIAGVVFTGSTEVARSINRALAAKDGPIVPLIAETGGINAMIADATALPEQVADDVVTSAFRSAGQRCSALRLLFVQEDVADRMIEMVAGAARELKIGDPSDVATHVGPVIDVEAKQRLDAHIARMKTEARLHFAGPAPEGCFVAPHIFELTEAGQLTEEVFGPILHVVRYRPENLERVLRAIERTGYGLTLGVHSRIDDSIEAIIDRVQVGNIYVNRNMIGAVVGVQPFGGNGLSGTGPKAGGPHYLARFATEQTVTINTAAAGGNAALLAGEE
proteinBradyrhizobium diazoefficiensQ89E26—–—tetramerMolecule count 4107.558 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1513[3]0.013075–0.324398 1/AHas uncertainty columnMissing 00sasbdb/entries/u3/sasdcu3/source/SASDCU3.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)13.7—Å
i0Guinier607.37.38—
i0P(r)612.70.7—
mwExperimental429.0—kDa
porod_volumePorod560.0—ų
rgGuinier5.190.07Å
rgP(r)5.150.02Å

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 (pH 7.8), 50 mM NaCl, 0.5 mM Tris(2-carboxyethyl)phosphine, and 5% (v/v) glycerolBuffer concentration—
pH7.8Additives—
Buffer descriptionBjPutA buffer
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2016-12-12Storage / measurement temperature— / —
Exposure time—Frames—
Wavelength—Sample-to-detector distance—
SourceX-ray synchrotronDetectorPilatus3 X 2M
Facility / beamlineAdvanced Light Source (ALS) / 12.3.1 (SIBYLS) · Berkeley, CA, USA
q range0.131 – 3.244Sample 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:169 field values
Field pathRaw value
codeSASDCU3
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleBiophysical investigation of type A PutAs reveals a conserved core oligomeric structure.
project.publication.titleBiophysical investigation of type A PutAs reveals a conserved core oligomeric structure.
project.publication.author_listKorasick DA, Singh H, Pemberton TA, Luo M, Dhatwalia R, Tanner JJ
project.publication.journalFEBS J
project.publication.doi10.1111/febs.14165
project.publication.pmid28710792
project.publication.published_date2017 Sep
project.statusreleased
project.submitted_date2017-05-19
project.released_date2017-07-17
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experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus3 X 2M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameAdvanced Light Source (ALS)
experiment.instrument.cityBerkeley, CA
experiment.instrument.countryUSA
experiment.instrument.beamline_name12.3.1 (SIBYLS)
experiment.instrument.beam_geometry
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_nameProline dehydrogenase
experiment.sample.molecule[0].short_nameBjPutA wild-type
experiment.sample.molecule[0].sequenceGHMPNIPPPFTAPYAPDDAEIAARLLPASHLSPPQEARIHRTATRLIEAIRKRDDRLGGVEDMLREFALSTKEGLALMVL AEALLRVPDARTADQFIEDKLGEGDFIHHETKSTAFLVNASAWALGLSARVIQPGETPDGTIGRLVKRLGAPAVRTATRQ AMRLMGNHFVLGETIEQALERGKPRSGQKTRYSFDMLGEGARTAADARRYFDAYASAIETIGKAAGNHALPDRPGISVKL SALHPRFEAISRARVMVELVPQLLDLAQRAKAHDLNFTVDAEEADRLELSLDVIAATLADPSLKGWDGFGLAIQAYQKRA SAVIDYVDALARAHDRKLMVRLVKGAYWDTEIKRAQERGLDGYPVFTRKAMTDLNYVACASKLLALRPRIFPQFATHNAL TVATVLEMAEGSSGFEFQRLHGMGEALYEQLAKDHADIAYRTYAPVGSHRDLLAYLVRRLLENGANSSFVAQAADYRVPV PALLQRPADAIVRPQAAAHPRIPLPCDLFAPERRNSRGVEFGARTALDQLLTDVKAETGDLKPIADATPDQAHAAVAAAR AGFAGWSRTPAGIRAAALEQAAHLLESRSAHFIALLQREGGKTLDDALSELREAADFCRYYAAQGRKLFGSETAMPGPTG ESNALTMRGRGVFVAISPWNFPLAIFLGQVTAALMAGNSVVAKPAEQTPRIAREAVALLHEAGIPKSALYLVTGDGRIGA ALTAHPDIAGVVFTGSTEVARSINRALAAKDGPIVPLIAETGGINAMIADATALPEQVADDVVTSAFRSAGQRCSALRLL FVQEDVADRMIEMVAGAARELKIGDPSDVATHVGPVIDVEAKQRLDAHIARMKTEARLHFAGPAPEGCFVAPHIFELTEA GQLTEEVFGPILHVVRYRPENLERVLRAIERTGYGLTLGVHSRIDDSIEAIIDRVQVGNIYVNRNMIGAVVGVQPFGGNG LSGTGPKAGGPHYLARFATEQTVTINTAAAGGNAALLAGEE
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 (pH 7.8), 50 mM NaCl, 0.5 mM Tris(2-carboxyethyl)phosphine, and 5% (v/v) glycerol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentBjPutA buffer
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) 7.0 mg/mL
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_nameJohn
experiment.contributor[0].contributor_surnameTanner
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-12-12
experiment.storage_temperaturenull
experiment.cell_temperaturenull
experiment.exposure_timenull
experiment.number_of_framesnull
experiment.wavelengthnull
experiment.sample_detector_distancenull
experiment.concentration_minnull
experiment.concentration_max7.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.131
experiment.s_max3.244
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].comment
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fits[0].p_value0.0
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estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from a solution of Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) in 50 mM Tris (pH 7.8), 50 mM NaCl, 0.5 mM Tris(2-carboxyethyl)phosphine, and 5% (v/v) glycerol, pH 7.8 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS; Berkeley, CA, USA) using a Pilatus3 X 2M detector. One solute concentration of 7 mg/ml was measured. The data were normalized to the intensity of the transmitted beam and radially averaged. The radially averaged scattering of the solvent-blank was subtracted.
tags[]
intensity_unitnull
experimental_mw429.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i0612.7
pddf_i0_error0.7
guinier_i0607.3
guinier_i0_error7.38
pddf_rg5.15
pddf_rg_error0.02
guinier_rg5.19
guinier_rg_error0.07
pddf_dmax13.7
pddf_dmax_errornull
porod_volume560.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first2
guinier_point_last20
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDCU3_datloglog_img.png
symmetrynull
last_modified2026-05-18T10:07:06.737546+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDCU3
statussuccess
started_at2026-08-11T14:07:39.143985+00:00
finished_at2026-08-11T14:07:52.369250+00:00
source_last_modified2026-05-18T10:07:06.737546+02:00
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View the complete summary.json source
{
  "code": "SASDCU3",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure.",
    "publication": {
      "title": "Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure.",
      "author_list": "Korasick DA, Singh H, Pemberton TA, Luo M, Dhatwalia R, Tanner JJ",
      "journal": "FEBS J",
      "doi": "10.1111/febs.14165",
      "pmid": "28710792",
      "published_date": "2017 Sep"
    },
    "status": "released",
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