SASDFE5

Tetracycline repressor (class D), TetR(D), in complex with 5a,6-anhydrotetracycline (ATc)

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

Sample 1 · Tetracycline repressor (class D), TetR(D), in complex with 5a,6-anhydrotetracycline (ATc)

Concentration1.35 – 1.35 Buffer / pH50 mM Tris/HCl 150 mM NaCl 10 mM MgCl2 / 8.0
Experimental temperature10.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.124 nmExposure0.05 s × 20

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Tetracycline repressor (class D)
View sequence
SRLNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALTDRPAAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQIV
proteinEscherichia coliP0ACT42–208dimerMolecule count 223.259 kDa
5a,6-anhydrotetracycline
View sequence
C22H22N2O7
other———–—dimerMolecule count 20.426 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11673[3]0.0596259–4.45777 1/nmHas uncertainty columnMissing 072sasbdb/entries/e5/sasdfe5/source/SASDFE5.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)6.76—nm
i0Guinier7682.3215.74arbitrary
i0P(r)7510.0—arbitrary
mwExperimental42.6—kDa
mwGuinier I(0)42.6—kDa
mwPorod48.2—kDa
porod_volumePorod77.16—nm³
rgGuinier2.550.06nm
rgP(r)2.435—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 Tris/HCl 150 mM NaCl 10 mM MgCl2Buffer concentration—
pH8.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2013-09-23Storage / measurement temperature— / 10.0
Exposure time0.05Frames20
Wavelength0.124Sample-to-detector distance3.1
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.06 – 4.458Sample 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:176 field values
Field pathRaw value
codeSASDFE5
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleThermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.
project.publication.titleThermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.
project.publication.author_listPalm GJ, Buchholz I, Werten S, Girbardt B, Berndt L, Delcea M, Hinrichs W
project.publication.journalBiochim Biophys Acta Proteins Proteom
project.publication.doi10.1016/j.bbapap.2020.140404
project.publication.pmid32114262
project.publication.published_date2020 Feb 27
project.statusreleased
project.submitted_date2019-04-11
project.released_date2020-03-05
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experiment.instrument.detector.namePilatus 2M
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
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
experiment.instrument.line_collimation_slitlengthnull
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experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameTetracycline repressor (class D)
experiment.sample.molecule[0].short_nameTetR(D)
experiment.sample.molecule[0].sequenceSRLNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALTDRPAAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQIV
experiment.sample.molecule[0].organismEscherichia coli
experiment.sample.molecule[0].uniprot_codeP0ACT4
experiment.sample.molecule[0].uniprot_range_first2
experiment.sample.molecule[0].uniprot_range_last208
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
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experiment.sample.molecule[0].mw23.259
experiment.sample.molecule[0].total_mw46.518
experiment.sample.molecule[0].number_molecules2
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.molecule[1].long_name5a,6-anhydrotetracycline
experiment.sample.molecule[1].short_nameATc
experiment.sample.molecule[1].sequenceC22H22N2O7
experiment.sample.molecule[1].organismnull
experiment.sample.molecule[1].uniprot_codenull
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experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name50 mM Tris/HCl 150 mM NaCl 10 mM MgCl2
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
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experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameTetracycline repressor (class D), TetR(D), in complex with 5a,6-anhydrotetracycline (ATc)
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_namenull
experiment.contributor[0].affiliation[0].addressInnsbruck, Austria
experiment.contributor[0].affiliation[0].full_nameMedical University of Innsbruck
experiment.contributor[0].affiliation[0].webpagehttps://www.i-med.ac.at/
experiment.contributor[0].contributor_nameSebastiaan
experiment.contributor[0].contributor_surnameWerten
experiment.contributor[0].orcidhttps://orcid.org/0000-0003-2244-9688
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experiment.concentration_unitnull
experiment.date2013-09-23
experiment.storage_temperaturenull
experiment.cell_temperature10.0
experiment.exposure_time0.05
experiment.number_of_frames20
experiment.wavelength0.124
experiment.sample_detector_distance3.1
experiment.concentration_min1.35
experiment.concentration_max1.35
experiment.sample_volumenull
experiment.flow_ratenull
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experiment.s_max4.458
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].description
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pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of TetR(D), in complex with ATc in 50 mM Tris/HCl 150 mM NaCl 10 mM MgCl2, pH 8 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.4 and 1.4 mg/ml were measured at 10°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. 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[]
intensity_unitarbitrary
experimental_mw42.6
experimental_mw_errornull
guinier_i0_mw42.6
guinier_i0_mw_errornull
porod_mw48.2
porod_mw_errornull
pddf_i07510.0
pddf_i0_errornull
guinier_i07682.32
guinier_i0_error15.74
pddf_rg2.435
pddf_rg_errornull
guinier_rg2.55
guinier_rg_error0.06
pddf_dmax6.76
pddf_dmax_errornull
porod_volume77.16
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first14
guinier_point_last172
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDFE5_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDFE5
statussuccess
started_at2026-08-11T14:46:22.131897+00:00
finished_at2026-08-11T14:46:31.944557+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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View the complete summary.json source
{
  "code": "SASDFE5",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.",
    "publication": {
      "title": "Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.",
      "author_list": "Palm GJ, Buchholz I, Werten S, Girbardt B, Berndt L, Delcea M, Hinrichs W",
      "journal": "Biochim Biophys Acta Proteins Proteom",
      "doi": "10.1016/j.bbapap.2020.140404",
      "pmid": "32114262",
      "published_date": "2020 Feb 27"
    },
    "status": "released",
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    "released_date": "2020-03-05"
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View the complete manifest.json source
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