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SASDCM9

Ammonium transporter Ks-Amt5

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

MW estimate from excluded volume (DAMMIN)

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Ammonium transporter Ks-Amt5

Concentration— – 10.0 Buffer / pH20 mM Tris/HCl,100 mM NaCl, 5%(w/v) glycerol, 0.09%(w/v) CYMAL-5 / 8.0
Experimental temperature10.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.124 nmExposure1.0 s × 3600

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
ammonium sensor/transducer
View sequence
MENIQININHLWVIMAACMVFLMQLGFTSYETGFSQSKNAISIALRNLVDTLISSLVFFSVGFGFMFGKSYMGLIGIDLFFANDLALHPNTLSYSFFFFQMVFASTAATILTGAIAERSGFIPNIAGTAFIVAIIYPIFGHWAWGNLFSPDQTGWLKELGFIDFAGATVVHSIGGWFAMAAAIMVGPRIDKYNPDGSSNRIGLHNVPLATLGTFFLWFGWFGFNGGSLLRVSVNIGLVILNTNMAAASAGVSALIFIYATRKRIEAGSLFTAILAGLVAITASSNMVTPVSAVAIGLITGILAIIAEGFIEKTLKIDDPVSAIAVHGVGGVIGTLCVAIFAQKSYLLAENGSRMHQLGIQALGVIVAFSWSFGLGMLFFLCLKKVKRLRVTPEEEKRGLNVAEYEDVASWLDFIRITRLQDINTILEKRVQEKTADLQMANVALEKANRLKSEFLTTMSHELRTPLNAIIGFAEVLRDEIAGSLSKDQKEYVTDIHSSGHHLLDMINNILDLSKIETGKMHLQYEEFCIEDAINDTLTIINASANNKGISVHTNIQDNTPLLSADKTKFRQILYNLLSNAVKFTPENGKITINVFQKDNSLQFEIVDTGIGIKPEDKEKLFEAFHQADASLTREYEGTGLGLHLTKRLVELHGGKIWAESTFGKGSTFFFILPINPVNKLEHHHHHH
proteinCandidatus Kuenenia stuttgartiensisQ1Q357—–—trimerMolecule count 375.514 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11634[3]0.0892931–4.42296 1/nmHas uncertainty columnMissing 0596sasbdb/entries/m9/sasdcm9/source/SASDCM9.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)17.00.5nm
i0Guinier470.02.0arbitrary
i0P(r)473.02.0arbitrary
mwExperimental279.0—kDa
mwPorod300.0—kDa
porod_volumePorod511.0—nm³
rgGuinier4.80.1nm
rgP(r)4.90.1nm

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/HCl,100 mM NaCl, 5%(w/v) glycerol, 0.09%(w/v) CYMAL-5Buffer concentration—
pH8.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2013-03-01Storage / measurement temperature10.0 / 10.0
Exposure time1.0Frames3600
Wavelength0.124Sample-to-detector distance2.7
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.089 – 4.423Sample 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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curve：source record
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full_entry_zip：source record and ZIP contents (4 items)
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pddf：source record
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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：156 field values
Field pathRaw value
codeSASDCM9
statusPublished
type_of_curveSEC-SAS
angular_unit1/nm
project.titleSignaling ammonium across membranes through an ammonium sensor histidine kinase.
project.publication.titleSignaling ammonium across membranes through an ammonium sensor histidine kinase.
project.publication.author_listPflüger T, Hernández CF, Lewe P, Frank F, Mertens H, Svergun D, Baumstark MW, Lunin VY, Jetten MSM, Andrade SLA
project.publication.journalNat Commun
project.publication.doi10.1038/s41467-017-02637-3
project.publication.pmid29323112
project.publication.published_date2018 Jan 11
project.statusreleased
project.submitted_date2017-11-29
project.released_date2018-01-16
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDCM9.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDCM9.dat
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intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCM9_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCM9_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCM9_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDCM9.sascif
experiment.instrument.detector.typenull
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
experiment.instrument.line_collimation_integrationwidthnull
experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameammonium sensor/transducer
experiment.sample.molecule[0].short_nameKs-Amt5
experiment.sample.molecule[0].sequenceMENIQININHLWVIMAACMVFLMQLGFTSYETGFSQSKNAISIALRNLVDTLISSLVFFS VGFGFMFGKSYMGLIGIDLFFANDLALHPNTLSYSFFFFQMVFASTAATILTGAIAERSG FIPNIAGTAFIVAIIYPIFGHWAWGNLFSPDQTGWLKELGFIDFAGATVVHSIGGWFAMA AAIMVGPRIDKYNPDGSSNRIGLHNVPLATLGTFFLWFGWFGFNGGSLLRVSVNIGLVIL NTNMAAASAGVSALIFIYATRKRIEAGSLFTAILAGLVAITASSNMVTPVSAVAIGLITG ILAIIAEGFIEKTLKIDDPVSAIAVHGVGGVIGTLCVAIFAQKSYLLAENGSRMHQLGIQ ALGVIVAFSWSFGLGMLFFLCLKKVKRLRVTPEEEKRGLNVAEYEDVASWLDFIRITRLQ DINTILEKRVQEKTADLQMANVALEKANRLKSEFLTTMSHELRTPLNAIIGFAEVLRDEI AGSLSKDQKEYVTDIHSSGHHLLDMINNILDLSKIETGKMHLQYEEFCIEDAINDTLTII NASANNKGISVHTNIQDNTPLLSADKTKFRQILYNLLSNAVKFTPENGKITINVFQKDNS LQFEIVDTGIGIKPEDKEKLFEAFHQADASLTREYEGTGLGLHLTKRLVELHGGKIWAES TFGKGSTFFFILPINPVNKLEHHHHHH
experiment.sample.molecule[0].organismCandidatus Kuenenia stuttgartiensis
experiment.sample.molecule[0].uniprot_codeQ1Q357
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationtrimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMENIQININHLWVIMAACMVFLMQLGFTSYETGFSQSKNAISIALRNLVDTLISSLVFFS VGFGFMFGKSYMGLIGIDLFFANDLALHPNTLSYSFFFFQMVFASTAATILTGAIAERSG FIPNIAGTAFIVAIIYPIFGHWAWGNLFSPDQTGWLKELGFIDFAGATVVHSIGGWFAMA AAIMVGPRIDKYNPDGSSNRIGLHNVPLATLGTFFLWFGWFGFNGGSLLRVSVNIGLVIL NTNMAAASAGVSALIFIYATRKRIEAGSLFTAILAGLVAITASSNMVTPVSAVAIGLITG ILAIIAEGFIEKTLKIDDPVSAIAVHGVGGVIGTLCVAIFAQKSYLLAENGSRMHQLGIQ ALGVIVAFSWSFGLGMLFFLCLKKVKRLRVTPEEEKRGLNVAEYEDVASWLDFIRITRLQ DINTILEKRVQEKTADLQMANVALEKANRLKSEFLTTMSHELRTPLNAIIGFAEVLRDEI AGSLSKDQKEYVTDIHSSGHHLLDMINNILDLSKIETGKMHLQYEEFCIEDAINDTLTII NASANNKGISVHTNIQDNTPLLSADKTKFRQILYNLLSNAVKFTPENGKITINVFQKDNS LQFEIVDTGIGIKPEDKEKLFEAFHQADASLTREYEGTGLGLHLTKRLVELHGGKIWAES TFGKGSTFFFILPINPVNK
experiment.sample.molecule[0].mw75.514
experiment.sample.molecule[0].total_mw226.542
experiment.sample.molecule[0].number_molecules3
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 Tris/HCl,100 mM NaCl, 5%(w/v) glycerol, 0.09%(w/v) CYMAL-5
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameAmmonium transporter Ks-Amt5
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_nameEMBL-Hamburg
experiment.contributor[0].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[0].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[0].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[0].contributor_nameHaydyn
experiment.contributor[0].contributor_surnameMertens
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2013-03-01
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time1.0
experiment.number_of_frames3600
experiment.wavelength0.124
experiment.sample_detector_distance2.7
experiment.concentration_minnull
experiment.concentration_max10.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.089
experiment.s_max4.423
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareCORAL
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
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fits[0].models[0].model_mw328.1
fits[0].models[0].bead_radius1.9
fits[0].models[0].lognull
fits[0].models[0].symmetryP3
fits[0].models[0].commentnull
fits[0].models[0].user12
fits[0].fit_unit1/A
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fits[0].softwareCORAL
fits[0].chi_square_value1.649
fits[0].p_value0.000496
fits[0].fit_residual_plotSASDCM9_fit1_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_standardnull
descriptionMW estimate from excluded volume (DAMMIN)
experiment_descriptionnull
tags[]
intensity_unitarbitrary
experimental_mw279.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw300.0
porod_mw_errornull
pddf_i0473.0
pddf_i0_error2.0
guinier_i0470.0
guinier_i0_error2.0
pddf_rg4.9
pddf_rg_error0.1
guinier_rg4.8
guinier_rg_error0.1
pddf_dmax17.0
pddf_dmax_error0.5
porod_volume511.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first6
guinier_point_last75
pddf_point_first6
pddf_point_last1500
i0_calibration_standard_datanull
intensities_log_log_plotSASDCM9_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json：36 field values
Field pathRaw value
codeSASDCM9
statussuccess
started_at2026-08-11T16:17:32.783386+00:00
finished_at2026-08-11T16:17:51.298659+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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View the complete summary.json source
{
  "code": "SASDCM9",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "Signaling ammonium across membranes through an ammonium sensor histidine kinase.",
    "publication": {
      "title": "Signaling ammonium across membranes through an ammonium sensor histidine kinase.",
      "author_list": "Pflüger T, Hernández CF, Lewe P, Frank F, Mertens H, Svergun D, Baumstark MW, Lunin VY, Jetten MSM, Andrade SLA",
      "journal": "Nat Commun",
      "doi": "10.1038/s41467-017-02637-3",
      "pmid": "29323112",
      "published_date": "2018 Jan 11"
    },
    "status": "released",
    "submitted_date": "2017-11-29",
    "released_date": "2018-01-16"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCM9.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCM9.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCM9_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCM9_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCM9_pofr_img.png",
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  "experiment": {
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        "type": null,
        "name": "Pilatus 2M",
        "resolution": null
      },
      "name": "PETRA III",
      "city": "DESY; Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL P12",
      "beam_geometry": null,
      "type_of_source": "X-ray synchrotron",
      "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": "ammonium sensor/transducer",
          "short_name": "Ks-Amt5",
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View the complete manifest.json source
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