SASDF68

Delta subunit of RNA polymerase, RNAP (B. subtilis), 200 mM NaCl

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2023-06-21T07:56:39.492710+02:00

No concentration effect was observed in higher salt concentration buffers.

▼

1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Delta subunit of RNA polymerase, RNAP (B. subtilis), 200 mM NaCl

Concentration— – 3.6 Buffer / pH20 mM Phosphate buffer, 200 mM NaCl, 0.05% NaN3 / 6.6
Experimental temperature20.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.124 nmExposure0.05 s × 20

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
DNA-directed RNA polymerase subunit delta
View sequence
MGIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWYPYDQLDEETQPTVKAKKKKAKKAVEEDLDLDEFEEIDEDDLDLDEVEEELDLEADDFDEEDLDEDDDDLEIEEDIIDEDDEDYDDEEEEIK
proteinBacillus subtilisP124641–173monomerMolecule count 120.399 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11808[3]0.0133796–3.79041 1/nmHas uncertainty columnMissing 029sasbdb/entries/68/sasdf68/source/SASDF68.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)20.0—nm
i0Guinier7618.027.0arbitrary
mwExperimental33.8—kDa
mwPorod35.0—kDa
porod_volumePorod56.0—nm³
rgGuinier3.930.35nm

These values are reported by SASBDB; SAXSdb did not recalculate them from the experimental curve.

▼

3. Source Fits and Models Source Fits & Models

This entry has no source fit record.

▶

4. Source File Index Source Files

▶

5. Experiment Description and Publication Experiment & Publication

▼

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 name20 mM Phosphate buffer, 200 mM NaCl, 0.05% NaN3Buffer concentration—
pH6.6Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2016-10-03Storage / measurement temperature20.0 / 20.0
Exposure time0.05Frames20
Wavelength0.124Sample-to-detector distance3.0
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.013 – 3.79Sample 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

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:134 field values
Field pathRaw value
codeSASDF68
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleQuantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase.
project.publication.titleQuantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase.
project.publication.author_listKuban V, Srb P, Stegnerova H, Padrta P, Zachrdla M, Jasenakova Z, Šanderová H, Vítovská D, Krasny L, Koval T, Dohnalek J, Ziemska-Legi Cka J, Grynberg M, Jarnot P, Gruca A, Jensen MR, Blackledge M, Zidek L
project.publication.journalJ Am Chem Soc
project.publication.doi10.1021/jacs.9b07837
project.publication.pmid31550880
project.publication.published_date2019 Sep 24
project.statusreleased
project.submitted_date2019-06-22
project.released_date2019-09-30
pddf_datanull
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experiment.instrument.detector.resolutionnull
experiment.instrument.namePETRA III
experiment.instrument.cityDESY; Hamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL P12
experiment.instrument.beam_geometrynull
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
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experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameDNA-directed RNA polymerase subunit delta
experiment.sample.molecule[0].short_nameRpoE
experiment.sample.molecule[0].sequenceMGIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWYPYDQLDEETQPTVKAKKKKAKKAVEEDLDLDEFEEIDEDDLDLDEVEEELDLEADDFDEEDLDEDDDDLEIEEDIIDEDDEDYDDEEEEIK
experiment.sample.molecule[0].organismBacillus subtilis
experiment.sample.molecule[0].uniprot_codeP12464
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last173
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMGIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYT DLNIDGRFLALSDQTWGLRSWYPYDQLDEETQPTVKAKKKKAKKAVEEDLDLDEFEEIDE DDLDLDEVEEELDLEADDFDEEDLDEDDDDLEIEEDIIDEDDEDYDDEEEEIK
experiment.sample.molecule[0].mw20.399
experiment.sample.molecule[0].total_mw20.399
experiment.sample.molecule[0].number_molecules1
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.name20 mM Phosphate buffer, 200 mM NaCl, 0.05% NaN3
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph6.6
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameDelta subunit of RNA polymerase, RNAP (B. subtilis), 200 mM NaCl
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_nameMUNI
experiment.contributor[0].affiliation[0].addressBrno, Czech Republic
experiment.contributor[0].affiliation[0].full_nameMasaryk University; Research group Structure and Dynamics of Proteins.
experiment.contributor[0].affiliation[0].webpagehttps://www.muni.cz/
experiment.contributor[0].contributor_nameVojtěch
experiment.contributor[0].contributor_surnameKubáň
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-10-03
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time0.05
experiment.number_of_frames20
experiment.wavelength0.124
experiment.sample_detector_distance3.0
experiment.concentration_minnull
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experiment.flow_ratenull
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experiment.seccolumnnull
fits[]
estimated_volume_methodnull
pddf_softwarenull
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i0_calibration_standardnull
descriptionNo concentration effect was observed in higher salt concentration buffers.
experiment_descriptionSynchrotron SAXS data from solutions of RNAP in 20 mM phosphate buffer, 200 mM NaCl, 0.05% NaN3, pH 6.6 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.60 mg/ml was measured at 20°C. 20 successive 0.050 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.
tags[]
intensity_unitarbitrary
experimental_mw33.8
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw35.0
porod_mw_errornull
pddf_i0null
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guinier_i07618.0
guinier_i0_error27.0
pddf_rgnull
pddf_rg_errornull
guinier_rg3.93
guinier_rg_error0.35
pddf_dmax20.0
pddf_dmax_errornull
porod_volume56.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first39
guinier_point_last150
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDF68_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:33 field values
Field pathRaw value
codeSASDF68
statussuccess
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View the complete summary.json source
{
  "code": "SASDF68",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase.",
    "publication": {
      "title": "Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase.",
      "author_list": "Kuban V, Srb P, Stegnerova H, Padrta P, Zachrdla M, Jasenakova Z, Šanderová H, Vítovská D, Krasny L, Koval T, Dohnalek J, Ziemska-Legi Cka J, Grynberg M, Jarnot P, Gruca A, Jensen MR, Blackledge M, Zidek L",
      "journal": "J Am Chem Soc",
      "doi": "10.1021/jacs.9b07837",
      "pmid": "31550880",
      "published_date": "2019 Sep 24"
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}
View the complete manifest.json source
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