SASDD73

Flavin reductase Pden_5119

Data type: SASBDB experimental data Status: Published Curve type: Merged Last updated: 2023-08-31T11:57:49.604042+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Flavin reductase Pden_5119

Concentration1.5 – 7.5 Buffer / pH50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole / 8.0
Experimental temperature4.0 Facility / beamlineCEITEC / Rigaku BioSAXS-1000
Wavelength0.154 nmExposure600.0 s × 30

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
NADPH-dependent FMN reductase
View sequence
MPGPRIVAFAGSWSRPSKTRSLVEEAARRAVARFGGSAHVFDIADLGPDFGSLRQPQDGPHTRHLDAFLAADALIVASPVYKGSYTGLFKHFIDLIEPVALVGKPVLLAATGGGDRHALVIEHQLRPVFGFFEAHTLATGLYVSASDFGPDGLASEAASTRLDRAVAQFAAHLSRHDAAPLLAVGLEHHHHHH
proteinParacoccus denitrificansA1BCD5—–—dimerMolecule count 220.596 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1200[3]0.0152168–0.301234 1/AHas uncertainty columnMissing 02sasbdb/entries/73/sasdd73/source/SASDD73.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)6.27—Å
i0Guinier0.140.0015arbitrary
i0P(r)0.1389—arbitrary
mwExperimental41.0—kDa
mwPorod43.6—kDa
porod_volumePorod69.8—ų
rgGuinier2.340.098Å
rgP(r)2.3—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 sodium phosphate buffer, 300 mM NaCl, 500 mM imidazoleBuffer concentration—
pH8.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2016-02-22Storage / measurement temperature4.0 / 4.0
Exposure time600.0Frames30
Wavelength0.154Sample-to-detector distance0.48
SourceX-ray in houseDetectorPilatus 100K
Facility / beamlineCEITEC / Rigaku BioSAXS-1000 · Brno, Czech Republic
q range0.152 – 3.012Sample 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:182 field values
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statusPublished
type_of_curveMerged
angular_unit1/A
project.titleStructural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans.
project.publication.titleStructural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans.
project.publication.author_listKryl M, Sedláček V, Kučera I
project.publication.journalInt J Mol Sci
project.publication.doi10.3390/ijms24043732
project.publication.pmid36835143
project.publication.published_date2023 Feb 13
project.statusreleased
project.submitted_date2018-01-23
project.released_date2023-08-31
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experiment.instrument.detector.resolution172.0
experiment.instrument.nameCEITEC
experiment.instrument.cityBrno
experiment.instrument.countryCzech Republic
experiment.instrument.beamline_nameRigaku BioSAXS-1000
experiment.instrument.beam_geometry
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experiment.instrument.point_sourcenull
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experiment.instrument.sample_path_lengthnull
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experiment.instrument.xray_energynull
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experiment.sample.molecule[0].short_namePden_5119
experiment.sample.molecule[0].sequenceMPGPRIVAFAGSWSRPSKTRSLVEEAARRAVARFGGSAHVFDIADLGPDFGSLRQPQDGP HTRHLDAFLAADALIVASPVYKGSYTGLFKHFIDLIEPVALVGKPVLLAATGGGDRHALV IEHQLRPVFGFFEAHTLATGLYVSASDFGPDGLASEAASTRLDRAVAQFAAHLSRHDAAP LLAVGLEHHHHHH
experiment.sample.molecule[0].organismParacoccus denitrificans
experiment.sample.molecule[0].uniprot_codeA1BCD5
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMPGPRIVAFAGSWSRPSKTRSLVEEAARRAVARFGGSAHVFDIADLGPDFGSLRQPQDGP HTRHLDAFLAADALIVASPVYKGSYTGLFKHFIDLIEPVALVGKPVLLAATGGGDRHALV IEHQLRPVFGFFEAHTLATGLYVSASDFGPDGLASEAASTRLDRAVAQFAAHLSRHDAAP LLAVG
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experiment.sample.purity_methodnull
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experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
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experiment.contributor[0].affiliation[0].webpagehttps://www.ceitec.eu/
experiment.contributor[0].contributor_nameTomas
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i0_calibration_standardnull
descriptionnull
experiment_descriptionSAXS data from solutions of flavin reductase Pden_5119 in 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH 8, were collected on a Rigaku BioSAXS-1000 instrument at the Central European Institute of Technology, CEITEC, (Brno, Czech Republic) using a Pilatus 100K detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.5 and 7.5 mg/ml were measured at 4°C. 30 successive 600 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.
tags[]
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last_modified2023-08-31T11:57:49.604042+02:00
bragg_peak[]
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codeSASDD73
statussuccess
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View the complete summary.json source
{
  "code": "SASDD73",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/A",
  "project": {
    "title": "Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans.",
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      "title": "Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans.",
      "author_list": "Kryl M, Sedláček V, Kučera I",
      "journal": "Int J Mol Sci",
      "doi": "10.3390/ijms24043732",
      "pmid": "36835143",
      "published_date": "2023 Feb 13"
    },
    "status": "released",
    "submitted_date": "2018-01-23",
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View the complete manifest.json source
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