SASDC56

Blue light receptor YtvA, dark/inactive state

Data type: SASBDB experimental data Status: Published Curve type: Extrapolated to infinite dilution Last updated: 2023-05-25T11:21:52.654103+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Blue light receptor YtvA, dark/inactive state

Concentration1.7 – 11.0 Buffer / pHPBS + 5 mM DTT / 7.4
Experimental temperature20.0 Facility / beamlineDORIS III, DESY / EMBL X33
Wavelength0.15 nmExposure30.0 s × 4

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
pfyP - Blue light photoreceptor
View sequence
GASFQSFGIPGQLEVIKKALDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPMEIEDKTYFVGIQNDITKQKEYEKLLEDSLTEITALSTPIVPIRNGISALPLVGNLTEERFNSIVCTLTNILSTSKDDYLIIDLSGLAQVNEQTADQIFKLSHLLKLTGTELIITGIKPELAMKMNKLDANFSSLKTYSNVKDAVKVLPIM
proteinBacillus subtilisO346272–261dimerMolecule count 229.12 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
12310[3]0.0774543–6.23701 1/nmHas uncertainty columnMissing 00sasbdb/entries/56/sasdc56/source/SASDC56.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)10.11.0nm
i0Guinier71.16——
i0P(r)69.98——
mwExperimental47.0—kDa
mwPorod47.0—kDa
porod_volumePorod75.0—nm³
rgGuinier3.20.1nm
rgP(r)3.2—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

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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 + 5 mM DTTBuffer concentration—
pH7.4Additives—
Buffer description10 mM phosphate buffer; 2.7 mM KCl; 137 mM NaCl; 5 mM DTT
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuterationFalse / —

Acquisition Conditions and Instrument

Measurement date2009-10-24Storage / measurement temperature4.0 / 20.0
Exposure time30.0Frames4
Wavelength0.15Sample-to-detector distance2.7
SourceX-ray synchrotronDetectorPilatus 1M-W
Facility / beamlineDORIS III, DESY / EMBL X33 · Hamburg, Germany
q range0.077 – 6.237Sample 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:225 field values
Field pathRaw value
codeSASDC56
statusPublished
type_of_curveExtrapolated to infinite dilution
angular_unit1/nm
project.titleThe switch that does not flip: the blue-light receptor YtvA from Bacillus subtilis adopts an elongated dimer conformation independent of the activation state as revealed by a combined AUC and SAXS study.
project.publication.titleThe switch that does not flip: the blue-light receptor YtvA from Bacillus subtilis adopts an elongated dimer conformation independent of the activation state as revealed by a combined AUC and SAXS study.
project.publication.author_listJurk M, Dorn M, Kikhney A, Svergun D, Gärtner W, Schmieder P
project.publication.journalJ Mol Biol
project.publication.doi10.1016/j.jmb.2010.08.036
project.publication.pmid20800068
project.publication.published_date2010 Oct 15
project.statusreleased
project.submitted_date2017-07-03
project.released_date2017-07-14
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experiment.instrument.detector.namePilatus 1M-W
experiment.instrument.detector.resolution0.172
experiment.instrument.nameDORIS III, DESY
experiment.instrument.cityHamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL X33
experiment.instrument.beam_geometry0.60
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_namepfyP - Blue light photoreceptor
experiment.sample.molecule[0].short_nameYtvA
experiment.sample.molecule[0].sequenceGASFQSFGIPGQLEVIKKALDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGK NCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPMEIEDKTYFV GIQNDITKQKEYEKLLEDSLTEITALSTPIVPIRNGISALPLVGNLTEERFNSIVCTLTN ILSTSKDDYLIIDLSGLAQVNEQTADQIFKLSHLLKLTGTELIITGIKPELAMKMNKLDA NFSSLKTYSNVKDAVKVLPIM
experiment.sample.molecule[0].organismBacillus subtilis
experiment.sample.molecule[0].uniprot_codeO34627
experiment.sample.molecule[0].uniprot_range_first2
experiment.sample.molecule[0].uniprot_range_last261
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMASFQSFGIPGQLEVIKKALDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGK NCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPMEIEDKTYFV GIQNDITKQKEYEKLLEDSLTEITALSTPIVPIRNGISALPLVGNLTEERFNSIVCTLTN ILSTSKDDYLIIDLSGLAQVNEQTADQIFKLSHLLKLTGTELIITGIKPELAMKMNKLDA NFSSLKTYSNVKDAVKVLPIM
experiment.sample.molecule[0].mw29.12
experiment.sample.molecule[0].total_mw58.24
experiment.sample.molecule[0].number_molecules2
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.namePBS + 5 mM DTT
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.comment10 mM phosphate buffer; 2.7 mM KCl; 137 mM NaCl; 5 mM DTT
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.nameBlue light receptor YtvA, dark/inactive state
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
experiment.sample.deuterationnull
experiment.sample.mixtureFalse
experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressBerlin, Germany
experiment.contributor[0].affiliation[0].full_nameLeibniz-Institut für Molekulare Pharmakologie
experiment.contributor[0].affiliation[0].webpagehttp://www.leibniz-fmp.de
experiment.contributor[0].contributor_nameMarcel
experiment.contributor[0].contributor_surnameJurk
experiment.contributor[0].orcidnull
experiment.contributor[1].affiliation[0].short_nameEMBL-Hamburg
experiment.contributor[1].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[1].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[1].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[1].contributor_nameAl
experiment.contributor[1].contributor_surnameKikhney
experiment.contributor[1].orcidhttps://orcid.org/0000-0003-1321-3956
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experiment.concentration_unitnull
experiment.date2009-10-24
experiment.storage_temperature4.0
experiment.cell_temperature20.0
experiment.exposure_time30.0
experiment.number_of_frames4
experiment.wavelength0.15
experiment.sample_detector_distance2.7
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experiment.concentration_max11.0
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last_modified2023-05-25T11:21:52.654103+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDC56
statussuccess
started_at2026-08-11T15:01:51.045723+00:00
finished_at2026-08-11T15:02:07.006329+00:00
source_last_modified2023-05-25T11:21:52.654103+02:00
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View the complete summary.json source
{
  "code": "SASDC56",
  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "angular_unit": "1/nm",
  "project": {
    "title": "The switch that does not flip: the blue-light receptor YtvA from Bacillus subtilis adopts an elongated dimer conformation independent of the activation state as revealed by a combined AUC and SAXS study.",
    "publication": {
      "title": "The switch that does not flip: the blue-light receptor YtvA from Bacillus subtilis adopts an elongated dimer conformation independent of the activation state as revealed by a combined AUC and SAXS study.",
      "author_list": "Jurk M, Dorn M, Kikhney A, Svergun D, Gärtner W, Schmieder P",
      "journal": "J Mol Biol",
      "doi": "10.1016/j.jmb.2010.08.036",
      "pmid": "20800068",
      "published_date": "2010 Oct 15"
    },
    "status": "released",
    "submitted_date": "2017-07-03",
    "released_date": "2017-07-14"
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