SASDAB7

Complex ComE-comcde

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2019-12-06T13:07:15.624532+01:00

Use of SAXS to describe the interaction between the phosphorylated mimetic mutant ComED58E of the response regulator ComE from S. pneumonia and its promoter region comcde. The complex is constituted of one dimer of ComE and one monomer of comcde. The SAXS data were collected directly after elution through an on-line size-exclusion high-performance liquid chromatography (SEC-HPLC) column. The molecular weight is not estimated from I(0) because the concentration of the complex cannot be accurately determined. It is obtained from the macromolecule volume using the method developed by Craievich’s team (the SAXS Mow program).

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Complex ComE-comcde

Concentration— – 0.8 mg/mlBuffer / pH50 mM MES 500 mM NaCl 5% (v/v) Glycerol 5 mM β-mercaptoethanol / 6.2
Experimental temperature18.0 Facility / beamlineSOLEIL / SWING
Wavelength0.1 nmExposure1.2 s × 6

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
comcde
View sequence
5’-AAGTACACTTTGGGAGAAAAAAATGACAGTTGAGAGAA-3’3’-TTCATGTGAAACCCTCTTTTTTTACTGTCAACTCTCTT-5'
DNAStreptococcus pneumoniae——–—otherMolecule count —23.5 kDa
Response regulator
View sequence
MKVLILEDVIEHQVRLERILDEISKESNIPISYKTTGKVREFEEYIENDEVNQLYFLAIDIHGIEKKGFEVAQLIRHYNPYAIIVFITSRSEFATLTYKYQVSALDFVDKDINDEMFKKRIEQNIFYTKSMLLENEDVVDYFDYNYKGNDLKIPYHDILYIETTGVSHKLRIIGKNFAKEFYGTMTDIQEKDKHTQRFYSPHKSFLVNIGNIREIDRKNLEIVFYEDHRCPISRLKIRKLKDILEKKSQKHHHHHH
proteinStreptococcus pneumoniaeQ8DMW51–250dimerMolecule count 230.736 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1700[3]0.111721–4.00983 1/nmHas uncertainty columnMissing 01sasbdb/entries/b7/sasdab7/source/SASDAB7.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)10.7—nm
i0Guinier0.05529——
i0P(r)0.0556——
mwExperimental83.0—kDa
mwPorod83.0—kDa
porod_volumePorod122.0—nm³
rgGuinier3.37—nm
rgP(r)3.41—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 MES 500 mM NaCl 5% (v/v) Glycerol 5 mM β-mercaptoethanolBuffer concentration50.0 mM
pH6.2Additives500 mM NaCl, 5% (vol/vol) glycerol, 5 mM β-mercaptoethanol
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2011-02-11Storage / measurement temperature18.0 / 18.0
Exposure time1.2Frames6
Wavelength0.1Sample-to-detector distance1.82
SourceX-ray synchrotronDetectorAVIEX PCCD170170
Facility / beamlineSOLEIL / SWING · Saint-Aubin, France
q range0.112 – 4.01Sample 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:170 field values
Field pathRaw value
codeSASDAB7
statusPublished
type_of_curveSEC-SAS
angular_unit1/nm
project.titleModeling the ComD/ComE/comcde interaction network using small angle X-ray scattering.
project.publication.titleModeling the ComD/ComE/comcde interaction network using small angle X-ray scattering.
project.publication.author_listSanchez D, Boudes M, van Tilbeurgh H, Durand D, Quevillon-Cheruel S
project.publication.journalFEBS J
project.publication.doi10.1111/febs.13240
project.publication.pmid25702779
project.publication.published_date2015 Apr
project.statusreleased
project.submitted_date2015-01-12
project.released_date2015-07-07
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experiment.instrument.detector.resolutionnull
experiment.instrument.nameSOLEIL
experiment.instrument.citySaint-Aubin
experiment.instrument.countryFrance
experiment.instrument.beamline_nameSWING
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
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experiment.sample.molecule[0].long_namecomcde
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequence5’-AAGTACACTTTGGGAGAAAAAAATGACAGTTGAGAGAA-3’ 3’-TTCATGTGAAACCCTCTTTTTTTACTGTCAACTCTCTT-5'
experiment.sample.molecule[0].organismStreptococcus pneumoniae
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationother
experiment.sample.molecule[0].molecular_typeDNA
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw23.5
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experiment.sample.molecule[0].complex_statenull
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.molecule[1].long_nameResponse regulator
experiment.sample.molecule[1].short_nameComE
experiment.sample.molecule[1].sequenceMKVLILEDVIEHQVRLERILDEISKESNIPISYKTTGKVREFEEYIENDEVNQLYFLAID IHGIEKKGFEVAQLIRHYNPYAIIVFITSRSEFATLTYKYQVSALDFVDKDINDEMFKKR IEQNIFYTKSMLLENEDVVDYFDYNYKGNDLKIPYHDILYIETTGVSHKLRIIGKNFAKE FYGTMTDIQEKDKHTQRFYSPHKSFLVNIGNIREIDRKNLEIVFYEDHRCPISRLKIRKL KDILEKKSQKHHHHHH
experiment.sample.molecule[1].organismStreptococcus pneumoniae
experiment.sample.molecule[1].uniprot_codeQ8DMW5
experiment.sample.molecule[1].uniprot_range_first1
experiment.sample.molecule[1].uniprot_range_last250
experiment.sample.molecule[1].oligomerizationdimer
experiment.sample.molecule[1].molecular_typeprotein
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experiment.sample.molecule[1].mw30.736
experiment.sample.molecule[1].total_mw61.472
experiment.sample.molecule[1].number_molecules2
experiment.sample.molecule[1].complex_stateFalse
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name50 mM MES 500 mM NaCl 5% (v/v) Glycerol 5 mM β-mercaptoethanol
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive500 mM NaCl, 5% (vol/vol) glycerol, 5 mM β-mercaptoethanol
experiment.sample.buffer.concentration50.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph6.2
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experiment.sample.contrastnull
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experiment.sample.deuterationnull
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experiment.contributor[0].affiliation[]
experiment.contributor[0].contributor_nameDominique
experiment.contributor[0].contributor_surnameDurand
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experiment.concentration_unitmg/ml
experiment.date2011-02-11
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experiment.cell_temperature18.0
experiment.exposure_time1.2
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descriptionUse of SAXS to describe the interaction between the phosphorylated mimetic mutant ComED58E of the response regulator ComE from S. pneumonia and its promoter region comcde. The complex is constituted of one dimer of ComE and one monomer of comcde. The SAXS data were collected directly after elution through an on-line size-exclusion high-performance liquid chromatography (SEC-HPLC) column. The molecular weight is not estimated from I(0) because the concentration of the complex cannot be accurately determined. It is obtained from the macromolecule volume using the method developed by Craievich’s team (the SAXS Mow program).
experiment_descriptionX-ray synchrotron radiation scattering data from solutions of complex ComE-comcde in 50 mM MES 500 mM NaCl, 5% (vol/vol) glycerol, 5 mM β-mercaptoethanol were collected on the SWING beamline on the storage ring SOLEIL (Saint-Aubin, France) using a CCD AVIEX detector (s = 4π sin θ/λ, where 2θ is the scattering angle). The sample was loaded on a SE-HPLC column on line with the SAXS measuring cell. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The scattered intensities were displayed on an absolute scale (cm-1) using the scattering of water. Frames were examined individually and 6 identical frames were averaged and further processed. The corresponding concentration was 0.8 g/L.
tags[]
intensity_unitnull
experimental_mw83.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw83.0
porod_mw_errornull
pddf_i00.0556
pddf_i0_errornull
guinier_i00.05529
guinier_i0_errornull
pddf_rg3.41
pddf_rg_errornull
guinier_rg3.37
guinier_rg_errornull
pddf_dmax10.7
pddf_dmax_errornull
porod_volume122.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_firstnull
guinier_point_lastnull
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symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDAB7
statussuccess
started_at2026-08-11T15:25:49.060536+00:00
finished_at2026-08-11T15:26:02.008267+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDAB7",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "Modeling the ComD/ComE/comcde interaction network using small angle X-ray scattering.",
    "publication": {
      "title": "Modeling the ComD/ComE/comcde interaction network using small angle X-ray scattering.",
      "author_list": "Sanchez D, Boudes M, van Tilbeurgh H, Durand D, Quevillon-Cheruel S",
      "journal": "FEBS J",
      "doi": "10.1111/febs.13240",
      "pmid": "25702779",
      "published_date": "2015 Apr"
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          "long_name": "comcde",
          "short_name": null,
          "sequence": "5’-AAGTACACTTTGGGAGAAAAAAATGACAGTTGAGAGAA-3’\r\n3’-TTCATGTGAAACCCTCTTTTTTTACTGTCAACTCTCTT-5'",
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          "uniprot_range_last": 250,
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        "comment": null,
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      "name": "Complex ComE-comcde",
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      "absorbption": null,
      "deuteration": null,
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    },
    "contributor": [
      {
        "affiliation": [],
        "contributor_name": "Dominique",
        "contributor_surname": "Durand",
        "orcid": null
      }
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    "concentration_unit": "mg/ml",
    "date": "2011-02-11",
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  "last_modified": "2019-12-06T13:07:15.624532+01:00",
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}
View the complete manifest.json source
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