SASDDB9

Structure of Halobacterium salinarum VNG0258H/RosR in the presence of 2 M NaBr

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

Individual (top) and spatially averaged (DAMFILT, bottom) ab initio models are displayed.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Structure of Halobacterium salinarum VNG0258H/RosR in the presence of 2 M NaBr

Concentration— – 3.0 Buffer / pH50 mM HEPES, 2 M NaBr, 0.02% NaN3 / 7.0
Experimental temperature20.0 Facility / beamlineESRF / BM29
Wavelength0.09919 nmExposure1.0 s × 10

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
VNG0258H/RosR
View sequence
>VNG0258H/ROSRMSEAQPDARSDARDLTAFQKNILTVLGEEARYGLAIKRELEEYYGEEVNHGRLYPNLDDLVNKGLVEKSELDKRTNEYALTNEGFDAVVDDLEWTLSKFVADADRRERVETIVADDAAALEHHHHHH
proteinHalobacterium salinarum NRC-1Q9HSF41–116dimerMolecule count 214.533 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11043[3]0.03642828–4.911624 1/nmHas uncertainty columnMissing 01sasbdb/entries/b9/sasddb9/source/SASDDB9.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)8.1—nm
i0Guinier18.040.066—
i0P(r)17.34——
mwExperimental33.4—kDa
mwPorod37.0—kDa
porod_volumePorod59.0—nm³
rgGuinier2.540.31nm
rgP(r)2.43—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 name50 mM HEPES, 2 M NaBr, 0.02% NaN3Buffer concentration—
pH7.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2015-09-26Storage / measurement temperature20.0 / 20.0
Exposure time1.0Frames10
Wavelength0.09919Sample-to-detector distance2.869
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineESRF / BM29 · Grenoble, France
q range0.036 – 4.912Sample 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
codeSASDDB9
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleThe 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell.
project.publication.titleThe 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell.
project.publication.author_listKutnowski N, Shmuely H, Dahan I, Shmulevich F, Davidov G, Shahar A, Eichler J, Zarivach R, Shaanan B
project.publication.journalJ Struct Biol
project.publication.doi10.1016/j.jsb.2018.08.008
project.publication.pmid30110657
project.publication.published_date2018 Aug 12
project.statusreleased
project.submitted_date2018-06-29
project.released_date2018-08-15
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experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
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experiment.sample.molecule[0].sequence>VNG0258H/RosR MSEAQPDARSDARDLTAFQKNILTVLGEEARYGLAIKRELEEYYGEEVNHGRLYPNLDDL VNKGLVEKSELDKRTNEYALTNEGFDAVVDDLEWTLSKFVADADRRERVETIVADDAAAL EHHHHHH
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experiment.sample.molecule[0].uniprot_codeQ9HSF4
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last116
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
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experiment_descriptionSynchrotron SAXS data from solutions Halobacterium salinarum VNG0258H/RosR in 50 mM HEPES, 2 M NaBr, 0.02% NaN3, pH 7 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09919 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.00 mg/ml was measured at 20°C. 10 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.
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symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
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codeSASDDB9
statussuccess
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View the complete summary.json source
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  "status": "Published",
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  "angular_unit": "1/nm",
  "project": {
    "title": "The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell.",
    "publication": {
      "title": "The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell.",
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      "pmid": "30110657",
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View the complete manifest.json source
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