SASDAA7

Heterotetramer of histidine protein kinase and response regulator

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

Use of SAXS to describe the interaction between ComD and ComE, the two-component system which regulates the competence in S. pneumoniae. The molecular weight is not estimated from I(0) due to the absence of tryptophan in ComE. It is obtained from the macromolecule volume by 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 · Heterotetramer of histidine protein kinase and response regulator

Concentration0.4 – 1.1 mg/mlBuffer / pH20 mM Tris 200 mM NaCl 5% (v/v) Glycerol 5 mM β-mercaptoethanol / 7.5
Experimental temperature4.0 Facility / beamlineIBBMC / Bruker Nanostar
Wavelength0.154 nmExposure1200.0 s × 32

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Histidine protein kinase
View sequence
MEIALKQKKFEQKHLQNYIDEIVGLYNEIRGFRHDYAGMLVSMQMAIDSGNLQEIDRIYNEVLVKANHKLRSDKYTYFDLNNIEDSALRSLVAQSIVYARNNGVEFTLEVKDTITKLPIELLDLVRIMSVLLNNAVEGSADSYKKQMEVAVIKMETETVIVIQNSCKMTMTPSGDLFALGFSTKGRNRGVGLNNVKELLDKYNNIILETEMEGSTFRQIIRFKREFEHHHHHH
proteinStreptococcus pneumoniaeQ8DMW4216–441dimerMolecule count 226.912 kDa
Response regulator
View sequence
MKVLILEDVIEHQVRLERILDEISKESNIPISYKTTGKVREFEEYIENDEVNQLYFLAIDIHGIEKKGFEVAQLIRHYNPYAIIVFITSRSEFATLTYKYQVSALDFVDKDINDEMFKKRIEQNIFYTKSMLLENEDVVDYFDYNYKGNDLKIPYHDILYIETTGVSHKLRIIGKNFAKEFYGTMTDIQEKDKHTQRFYSPHKSFLVNIGNIREIDRKNLEIVFYEDHRCPISRLKIRKLKDILEKKSQKHHHHHH
proteinStreptococcus pneumoniaeQ8DMW51–250dimerMolecule count 230.736 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1275[3]0.1138–4.00979 1/nmHas uncertainty columnMissing 00sasbdb/entries/a7/sasdaa7/source/SASDAA7.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)16.0—nm
i0Guinier0.07466——
i0P(r)0.07508——
mwExperimental116.0—kDa
mwPorod116.0—kDa
porod_volumePorod175.0—nm³
rgGuinier3.98—nm
rgP(r)4.12—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 name20 mM Tris 200 mM NaCl 5% (v/v) Glycerol 5 mM β-mercaptoethanolBuffer concentration20.0 mM
pH7.5Additives200 mM NaCl, 5% (vol/vol) glycerol and 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 date2012-05-16Storage / measurement temperature4.0 / 4.0
Exposure time1200.0Frames32
Wavelength0.154Sample-to-detector distance0.7
SourceX-ray in houseDetectorVÅNTEC-2000
Facility / beamlineIBBMC / Bruker Nanostar · Orsay, France
q range0.114 – 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
codeSASDAA7
statusPublished
type_of_curveMerged
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
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDAA7.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDAA7.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAA7_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAA7_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAA7_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAA7_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDAA7.sascif
experiment.instrument.detector.typeMikroGap gas detector
experiment.instrument.detector.nameVÅNTEC-2000
experiment.instrument.detector.resolution200.0
experiment.instrument.nameIBBMC
experiment.instrument.cityOrsay
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBruker Nanostar
experiment.instrument.beam_geometrynull
experiment.instrument.type_of_sourceX-ray in house
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_nameHistidine protein kinase
experiment.sample.molecule[0].short_nameComD
experiment.sample.molecule[0].sequenceMEIALKQKKFEQKHLQNYIDEIVGLYNEIRGFRHDYAGMLVSMQMAIDSGNLQEIDRIYNE VLVKANHKLRSDKYTYFDLNNIEDSALRSLVAQSIVYARNNGVEFTLEVKDTITKLPIEL LDLVRIMSVLLNNAVEGSADSYKKQMEVAVIKMETETVIVIQNSCKMTMTPSGDLFALGF STKGRNRGVGLNNVKELLDKYNNIILETEMEGSTFRQIIRFKREFEHHHHHH
experiment.sample.molecule[0].organismStreptococcus pneumoniae
experiment.sample.molecule[0].uniprot_codeQ8DMW4
experiment.sample.molecule[0].uniprot_range_first216
experiment.sample.molecule[0].uniprot_range_last441
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMDLFGFGTVIVHFLIISHSYHFICKGQINRKELFVFGAYTLLTEIVFDFPLYILYLDGLG IERFLFPLGLYSYFRWMKQYERDRGLFLSLLLSLLYESTHNFLSVTFSSITGDNFVLQYH FPFFFVVTVLTYFVTLKIIYYFHLELAYFDEDYLYPFLKKVFFALLLLHIVSFVSDMVST IKHLNSFGSILSSIVFISLLLTFFAMNSHKVQMEKEIALKQKKFEQKHLQNYTDEIVGLY NEIRGFRHDYAGMLVSMQMAIDSGNLQEIDRIYNEVLVKANHKLRSDKYTYFDLNNIEDS ALRSLVAQSIVYARNNGVEFTLEVKDTITKLPIELLDLVRIMSVLLNNAVEGSADSYKKQ MEVAVIKMETETVIVIQNSCKMTMTPSGDLFALGFSTKGRNRGVGLNNVKELLDKYNNII LETEMEGSTFRQIIRFKREFE
experiment.sample.molecule[0].mw26.912
experiment.sample.molecule[0].total_mw53.824
experiment.sample.molecule[0].number_molecules2
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
experiment.sample.molecule[1].uniprot_sequenceMKVLILEDVIEHQVRLERILDEISKESNIPISYKTTGKVREFEEYIENDEVNQLYFLDID IHGIEKKGFEVAQLIRHYNPYAIIVFITSRSEFATLTYKYQVSALDFVDKDINDEMFKKR IEQNIFYTKSMLLENEDVVDYFDYNYKGNDLKIPYHDILYIETTGVSHKLRIIGKNFAKE FYGTMTDIQEKDKHTQRFYSPHKSFLVNIGNIREIDRKNLEIVFYEDHRCPISRLKIRKL KDILEKKSQK
experiment.sample.molecule[1].mw30.736
experiment.sample.molecule[1].total_mw61.472
experiment.sample.molecule[1].number_molecules2
experiment.sample.molecule[1].complex_stateTrue
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name20 mM Tris 200 mM NaCl 5% (v/v) Glycerol 5 mM β-mercaptoethanol
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive200 mM NaCl, 5% (vol/vol) glycerol and 5 mM β-mercaptoethanol
experiment.sample.buffer.concentration20.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameHeterotetramer of histidine protein kinase and response regulator
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[]
experiment.contributor[0].contributor_nameDominique
experiment.contributor[0].contributor_surnameDurand
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitmg/ml
experiment.date2012-05-16
experiment.storage_temperature4.0
experiment.cell_temperature4.0
experiment.exposure_time1200.0
experiment.number_of_frames32
experiment.wavelength0.154
experiment.sample_detector_distance0.7
experiment.concentration_min0.4
experiment.concentration_max1.1
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.114
experiment.s_max4.01
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareBUNCH
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
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fits[0].models[0].bead_radius1.9
fits[0].models[0].lognull
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fits[0].models[0].comment
fits[0].models[0].user40
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fits[0].softwarenull
fits[0].chi_square_value1.043758
fits[0].p_value0.001974
fits[0].fit_residual_plotfit4columns208_fitresiduals_img.png
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fits[0].fit_lognull
fits[0].software_versionnull
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardwater
descriptionUse of SAXS to describe the interaction between ComD and ComE, the two-component system which regulates the competence in S. pneumoniae. The molecular weight is not estimated from I(0) due to the absence of tryptophan in ComE. It is obtained from the macromolecule volume by using the method developed by Craievich's team (the SAXS Mow program).
experiment_descriptionX-ray in house radiation scattering data from solutions of the two-componentsystem ComD-ComE in 20 mM Tris 200 mM NaCl, 5% (vol/vol) glycerol and 5 mM β-mercaptoethanol were collected on the Bruker Nanostar camera (Orsay, France) using a VANTEC detector (s = 4π sin θ/λ, where 2θ is the scattering angle). Different solute concentrations in the range 0.40-1.10 mg/ml were measured. 32 successive 1200 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 scattered intensities were displayed on an absolute scale (cm-1) using the scattering by water. The low angle data collected were merged with the highest concentration high angle data to yield the final composite scattering curve.
tags[]
intensity_unitnull
experimental_mw116.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw116.0
porod_mw_errornull
pddf_i00.07508
pddf_i0_errornull
guinier_i00.07466
guinier_i0_errornull
pddf_rg4.12
pddf_rg_errornull
guinier_rg3.98
guinier_rg_errornull
pddf_dmax16.0
pddf_dmax_errornull
porod_volume175.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_firstnull
guinier_point_lastnull
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDAA7_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDAA7
statussuccess
started_at2026-08-11T15:25:04.517825+00:00
finished_at2026-08-11T15:25:17.876311+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDAA7",
  "status": "Published",
  "type_of_curve": "Merged",
  "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"
    },
    "status": "released",
    "submitted_date": "2015-01-12",
    "released_date": "2015-07-07"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDAA7.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDAA7.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAA7_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAA7_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAA7_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAA7_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAA7.sascif",
  "experiment": {
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      "detector": {
        "type": "MikroGap gas detector",
        "name": "VÅNTEC-2000",
        "resolution": 200.0
      },
      "name": "IBBMC",
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      "country": "France",
      "beamline_name": "Bruker Nanostar",
      "beam_geometry": null,
      "type_of_source": "X-ray in house",
      "point_source": null,
      "line_collimation": null,
      "sample_path_length": null,
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      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Histidine protein kinase",
          "short_name": "ComD",
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          "uniprot_range_last": 441,
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          "molecular_type": "protein",
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          "molecule_source": "biological",
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        },
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          "molecular_type": "protein",
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        }
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        "name": "20 mM Tris 200 mM NaCl 5% (v/v) Glycerol 5 mM β-mercaptoethanol",
        "concentration_unit": "mM",
        "comment": null,
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        "deuteration": null
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      "purity_method": null,
      "name": "Heterotetramer of histidine protein kinase and response regulator ",
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      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [],
        "contributor_name": "Dominique",
        "contributor_surname": "Durand",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": "mg/ml",
    "date": "2012-05-16",
    "storage_temperature": 4.0,
    "cell_temperature": 4.0,
    "exposure_time": 1200.0,
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    "wavelength": 0.154,
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          "software": "BUNCH",
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          "type_of_model": "atomic",
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          "user": 40
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      "software": null,
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      "fit_residual_plot": "fit4columns208_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAA7_fit1.fit",
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  "description": "Use of SAXS to describe the interaction between ComD and ComE, the two-component system which regulates the competence in S. pneumoniae.\r\nThe molecular weight is not estimated from I(0) due to the absence of tryptophan in ComE. It is obtained from the macromolecule volume by using the method developed by Craievich's team (the SAXS Mow program).",
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  "intensities_log_log_plot": "SASDAA7_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
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View the complete manifest.json source
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