SASDFB8

Delta subunit of RNA polymerase, RNAP (B. subtilis): Lysine to glutamate mutant, 400mM NaCl

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2023-06-21T07:56:39.492710+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Delta subunit of RNA polymerase, RNAP (B. subtilis): Lysine to glutamate mutant, 400mM NaCl

Concentration— – 2.6 Buffer / pH20 mM Phosphate buffer, 400 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 - mutant
View sequence
MGIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWYPYDQLDEETQPTVEAEEEEAEEAVEEDLDLDEFEEIDEDDLDLDEVEEELDLEADDFDEEDLDEDDDDLEIEEDIIDEDDEDYDDEEEEIK
proteinBacillus subtilisP124641–173monomerMolecule count 120.405 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11809[3]0.0133796–3.7925 1/nmHas uncertainty columnMissing 046sasbdb/entries/b8/sasdfb8/source/SASDFB8.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)24.0—nm
i0Guinier4417.022.0arbitrary
mwExperimental28.9—kDa
mwPorod49.0—kDa
porod_volumePorod78.0—nm³
rgGuinier4.490.82nm

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

This entry has no source fit record.

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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 name20 mM Phosphate buffer, 400 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 – 3.792Sample 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
codeSASDFB8
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
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experiment.instrument.namePETRA III
experiment.instrument.cityDESY; Hamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL P12
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experiment.sample.molecule[0].long_nameDNA-directed RNA polymerase subunit delta - mutant
experiment.sample.molecule[0].short_namerpoE KE mutant
experiment.sample.molecule[0].sequenceMGIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWYPYDQLDEETQPTVEAEEEEAEEAVEEDLDLDEFEEIDEDDLDLDEVEEELDLEADDFDEEDLDEDDDDLEIEEDIIDEDDEDYDDEEEEIK
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].mw20.405
experiment.sample.molecule[0].total_mw20.405
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, 400 mM NaCl, 0.05% NaN3
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
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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): Lysine to glutamate mutant, 400mM 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
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experiment.concentration_unitnull
experiment.date2016-10-03
experiment.storage_temperature20.0
experiment.cell_temperature20.0
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experiment.sample_detector_distance3.0
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experiment.flow_ratenull
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experiment_descriptionSynchrotron SAXS data from solutions of Lys-Glu mutant RNAP in 20 mM phosphate buffer, 400 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 2.60 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_mw28.9
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guinier_i0_error22.0
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guinier_rg_error0.82
pddf_dmax24.0
pddf_dmax_errornull
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porod_volume_errornull
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guinier_point_last133
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pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDFB8_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
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View the complete summary.json source
{
  "code": "SASDFB8",
  "status": "Published",
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  "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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