SASDEN9

HcpR transcriptional regulator of Porphyromonas gingivalis

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2020-08-28T15:28:14.076959+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · HcpR transcriptional regulator of Porphyromonas gingivalis

Concentration— – 2.0 Buffer / pH25 mM Tris 150 mM NaCl 1mM TCEP / 7.5
Experimental temperature21.0 Facility / beamlineAdvanced Light Source (ALS) / 12.3.1 (SIBYLS)
Wavelength0.103 nmExposure60.0 s × —

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Hcp Transcriptional regulator
View sequence
MDPEFDLLLKAWKSSGLSVGMKDDELLALLESCSYRVERLKAEELYAIGGDKLQDLRIVGVGEIRAEMVGPSGKQILIDTLAVGRILAPALLFASENILPVTLFANEDSVLFRIGKEEFKGMMHKYPTLMENFIGMISDISAFLMKKIHQLSLRSLQGKIGDYLFQLYTKDGSNRIVVESSWKELSDRFGVNRQSLARSLSQLEEEGIIRVDGKSIEILQPNRLSRL
proteinPorphyromonas gingivalisQ7MVK41–227dimerMolecule count 225.495 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1513[3]0.014291–0.325614 1/AHas uncertainty columnMissing 00sasbdb/entries/n9/sasden9/source/SASDEN9.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)10.5—Å
i0Guinier282.90.57arbitrary
i0P(r)283.10.9arbitrary
mwExperimental44.03—kDa
mwPorod48.0—kDa
porod_volumePorod76.0—ų
rgGuinier2.890.05Å
rgP(r)2.930.01Å

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 name25 mM Tris 150 mM NaCl 1mM TCEPBuffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2014-01-24Storage / measurement temperature4.0 / 21.0
Exposure time60.0Frames—
Wavelength0.103Sample-to-detector distance3.5
SourceX-ray synchrotronDetectorPilatus3 X 2M
Facility / beamlineAdvanced Light Source (ALS) / 12.3.1 (SIBYLS) · Berkeley, CA, USA
q range0.143 – 3.256Sample 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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full_entry_zip:source record and ZIP contents (7 items)
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pddf:source record
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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
Field pathRaw value
codeSASDEN9
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleNitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR.
project.publication.titleNitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR.
project.publication.author_listBelvin BR, Musayev FN, Burgner J, Scarsdale JN, Escalante CR, Lewis JP
project.publication.journalActa Crystallogr D Struct Biol
project.publication.doi10.1107/S205979831900264X
project.publication.pmid30988260
project.publication.published_date2019 Apr 1
project.statusreleased
project.submitted_date2019-01-03
project.released_date2019-04-17
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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_nameHcp Transcriptional regulator
experiment.sample.molecule[0].short_nameHcpR
experiment.sample.molecule[0].sequenceMDPEFDLLLKAWKSSGLSVGMKDDELLALLESCSYRVERLKAEELYAIGGDKLQDLRIVG VGEIRAEMVGPSGKQILIDTLAVGRILAPALLFASENILPVTLFANEDSVLFRIGKEEFK GMMHKYPTLMENFIGMISDISAFLMKKIHQLSLRSLQGKIGDYLFQLYTKDGSNRIVVESSWKELSDRFG VNRQSLARSLSQLEEEGIIRVDGKSIEILQPNRLSRL
experiment.sample.molecule[0].organismPorphyromonas gingivalis
experiment.sample.molecule[0].uniprot_codeQ7MVK4
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last227
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
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experiment.sample.molecule[0].number_molecules2
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
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experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
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experiment.sample.purity_methodnull
experiment.sample.nameHcpR transcriptional regulator of Porphyromonas gingivalis
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
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experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressRichmond, Virginia, USA
experiment.contributor[0].affiliation[0].full_nameVirginia Commonwealth University
experiment.contributor[0].affiliation[0].webpagehttps://www.vcu.edu/
experiment.contributor[0].contributor_nameBenjamin
experiment.contributor[0].contributor_surnameBelvin
experiment.contributor[0].orcid
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experiment.exposure_time60.0
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fits[0].p_value0.0
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pddf_softwareATSAS GNOM
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i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Porphyromonas gingivalis HcpR in 25 mM Trish 150 mM NaCl, 2mM TCEP pH 7.5 were collected on the SIBYLS beam line at the Lawrence Berkeley National Laboratory (Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 3.5 meters at a wavelength of λ = 0.103 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.0 mg/ml was measured at 21°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
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experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
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estimated_volume_errornull
guinier_point_first15
guinier_point_last51
pddf_point_firstnull
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i0_calibration_standard_datanull
intensities_log_log_plotSASDEN9_datloglog_img.png
symmetrynull
last_modified2020-08-28T15:28:14.076959+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDEN9
statussuccess
started_at2026-08-11T16:18:22.393065+00:00
finished_at2026-08-11T16:18:36.619255+00:00
source_last_modified2020-08-28T15:28:14.076959+02:00
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View the complete summary.json source
{
  "code": "SASDEN9",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Nitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR.",
    "publication": {
      "title": "Nitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR.",
      "author_list": "Belvin BR, Musayev FN, Burgner J, Scarsdale JN, Escalante CR, Lewis JP",
      "journal": "Acta Crystallogr D Struct Biol",
      "doi": "10.1107/S205979831900264X",
      "pmid": "30988260",
      "published_date": "2019 Apr 1"
    },
    "status": "released",
    "submitted_date": "2019-01-03",
    "released_date": "2019-04-17"
  },
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    },
    "sample": {
      "molecule": [
        {
          "long_name": "Hcp Transcriptional regulator",
          "short_name": "HcpR",
          "sequence": "MDPEFDLLLKAWKSSGLSVGMKDDELLALLESCSYRVERLKAEELYAIGGDKLQDLRIVG\r\nVGEIRAEMVGPSGKQILIDTLAVGRILAPALLFASENILPVTLFANEDSVLFRIGKEEFK\r\nGMMHKYPTLMENFIGMISDISAFLMKKIHQLSLRSLQGKIGDYLFQLYTKDGSNRIVVESSWKELSDRFG VNRQSLARSLSQLEEEGIIRVDGKSIEILQPNRLSRL",
          "organism": "Porphyromonas gingivalis",
          "uniprot_code": "Q7MVK4",
          "uniprot_range_first": 1,
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View the complete manifest.json source
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