SASDC78

Surface presentation of antigens protein SpaOc-SpaO(SPOA1,2)

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 · Surface presentation of antigens protein SpaOc-SpaO(SPOA1,2)

Concentration— – 7.4 Buffer / pH20 mM HEPES pH 7.5, 150 mM NaCl / 7.5
Experimental temperature20.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.124 nmExposure1.0 s × 3600

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Surface presentation of antigens protein SpaO SpaO(SPOA2)
View sequence
METLDIQHIEEENNTTETAETLPGLNQLPVKLEFVLYRKNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESGNGESAWSHPQFEK
proteinSalmonella enterica subsp. enterica serovar TyphimuriumP40699203–303dimerMolecule count 212.374 kDa
Surface presentation of antigens protein SpaO(SPOA1,2)
View sequence
MSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRWSAWIKPGDWLEHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSCRRLCVENPVPGSALPEGKLLHIMSDRGGLWFEHLPELPAVGGGRPKMLRWPLRFVIGSSDTQRSLLGRIGIGDVLLIRTSRAEVYCYAKKLGHFNRVEGGIIVETLDIQHIEEENNTTETAETLPGLNQLPVKLEFVLYRKNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESGNGE
proteinSalmonella enterica subsp. enterica serovar TyphimuriumP406991–303monomerMolecule count 133.793 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11777[3]0.146779–5.02537 1/nmHas uncertainty columnMissing 025sasbdb/entries/78/sasdc78/source/SASDC78.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)11.05—nm
i0Guinier4373.615.2arbitrary
i0P(r)4404.011.0arbitrary
mwExperimental55.6—kDa
porod_volumePorod108.0—nm³
rgGuinier3.270.2nm
rgP(r)3.330.009nm

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 HEPES pH 7.5, 150 mM NaClBuffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2017-04-24Storage / measurement temperature20.0 / 20.0
Exposure time1.0Frames3600
Wavelength0.124Sample-to-detector distance—
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.147 – 5.025Sample 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

CategoryFileStatusSizeChecksumDownload and View
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full_entry_zip:source record and ZIP contents (2 items)
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pddf:source record
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sascif:source record
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summary: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:151 field values
Field pathRaw value
codeSASDC78
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleMolecular Organization of Soluble Type III Secretion System Sorting Platform Complexes.
project.publication.titleMolecular Organization of Soluble Type III Secretion System Sorting Platform Complexes.
project.publication.author_listBernal I, Börnicke J, Heidemann J, Svergun D, Horstmann JA, Erhardt M, Tuukkanen A, Uetrecht C, Kolbe M
project.publication.journalJ Mol Biol
project.publication.doi10.1016/j.jmb.2019.07.004
project.publication.pmid31288030
project.publication.published_date2019 Sep 6
project.statusreleased
project.submitted_date2018-11-02
project.released_date2019-09-13
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDC78.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDC78.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC78_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC78_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC78_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC78_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDC78.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_nameSurface presentation of antigens protein SpaO SpaO(SPOA2)
experiment.sample.molecule[0].short_nameSpaOc
experiment.sample.molecule[0].sequenceMETLDIQHIEEENNTTET AETLPGLNQLPVKLEFVLYRKNVTLAELEA MGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESGNGESAWSHPQFEK
experiment.sample.molecule[0].organismSalmonella enterica subsp. enterica serovar Typhimurium
experiment.sample.molecule[0].uniprot_codeP40699
experiment.sample.molecule[0].uniprot_range_first203
experiment.sample.molecule[0].uniprot_range_last303
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRWSAWIKPGDWL EHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSCRRLCVENPVPGSALPEGKLL HIMSDRGGLWFEHLPELPAVGGGRPKMLRWPLRFVIGSSDTQRSLLGRIGIGDVLLIRTS RAEVYCYAKKLGHFNRVEGGIIVETLDIQHIEEENNTTETAETLPGLNQLPVKLEFVLYR KNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESG NGE
experiment.sample.molecule[0].mw12.374
experiment.sample.molecule[0].total_mw24.748
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_nameSurface presentation of antigens protein SpaO(SPOA1,2)
experiment.sample.molecule[1].short_nameSpaO
experiment.sample.molecule[1].sequenceMSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRW SAWIKPGDWLEHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSC RRLCVENPVPGSALPEGKLLHIMSDRGGLWFEHLPELPAVGGGRPKMLRW PLRFVIGSSDTQRSLLGRIGIGDVLLIRTSRAEVYCYAKKLGHFNRVEGG IIVETLDIQHIEEENNTTETAETLPGLNQLPVKLEFVLYRKNVTLAELEA MGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESG NGE
experiment.sample.molecule[1].organismSalmonella enterica subsp. enterica serovar Typhimurium
experiment.sample.molecule[1].uniprot_codeP40699
experiment.sample.molecule[1].uniprot_range_first1
experiment.sample.molecule[1].uniprot_range_last303
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequenceMSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRWSAWIKPGDWL EHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSCRRLCVENPVPGSALPEGKLL HIMSDRGGLWFEHLPELPAVGGGRPKMLRWPLRFVIGSSDTQRSLLGRIGIGDVLLIRTS RAEVYCYAKKLGHFNRVEGGIIVETLDIQHIEEENNTTETAETLPGLNQLPVKLEFVLYR KNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESG NGE
experiment.sample.molecule[1].mw33.793
experiment.sample.molecule[1].total_mw33.793
experiment.sample.molecule[1].number_molecules1
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.name20 mM HEPES pH 7.5, 150 mM NaCl
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameSurface presentation of antigens protein SpaOc-SpaO(SPOA1,2)
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_nameAnne
experiment.contributor[0].contributor_surnameTuukkanen
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-04-24
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time1.0
experiment.number_of_frames3600
experiment.wavelength0.124
experiment.sample_detector_distancenull
experiment.concentration_minnull
experiment.concentration_max7.4
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.147
experiment.s_max5.025
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[]
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[]
intensity_unitarbitrary
experimental_mw55.6
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i04404.0
pddf_i0_error11.0
guinier_i04373.6
guinier_i0_error15.2
pddf_rg3.33
pddf_rg_error0.009
guinier_rg3.27
guinier_rg_error0.2
pddf_dmax11.05
pddf_dmax_errornull
porod_volume108.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first15
guinier_point_last92
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDC78_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDC78
statussuccess
started_at2026-08-11T15:47:04.569137+00:00
finished_at2026-08-11T15:47:13.185809+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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View the complete summary.json source
{
  "code": "SASDC78",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Molecular Organization of Soluble Type III Secretion System Sorting Platform Complexes.",
    "publication": {
      "title": "Molecular Organization of Soluble Type III Secretion System Sorting Platform Complexes.",
      "author_list": "Bernal I, Börnicke J, Heidemann J, Svergun D, Horstmann JA, Erhardt M, Tuukkanen A, Uetrecht C, Kolbe M",
      "journal": "J Mol Biol",
      "doi": "10.1016/j.jmb.2019.07.004",
      "pmid": "31288030",
      "published_date": "2019 Sep 6"
    },
    "status": "released",
    "submitted_date": "2018-11-02",
    "released_date": "2019-09-13"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDC78.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDC78.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC78_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC78_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC78_pofr_img.png",
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC78.sascif",
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      "detector": {
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        "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,
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      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
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    },
    "sample": {
      "molecule": [
        {
          "long_name": "Surface presentation of antigens protein SpaO SpaO(SPOA2)",
          "short_name": "SpaOc",
          "sequence": "METLDIQHIEEENNTTET AETLPGLNQLPVKLEFVLYRKNVTLAELEA \r\nMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESGNGESAWSHPQFEK",
          "organism": "Salmonella enterica subsp. enterica serovar Typhimurium",
          "uniprot_code": "P40699",
          "uniprot_range_first": 203,
          "uniprot_range_last": 303,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRWSAWIKPGDWL\nEHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSCRRLCVENPVPGSALPEGKLL\nHIMSDRGGLWFEHLPELPAVGGGRPKMLRWPLRFVIGSSDTQRSLLGRIGIGDVLLIRTS\nRAEVYCYAKKLGHFNRVEGGIIVETLDIQHIEEENNTTETAETLPGLNQLPVKLEFVLYR\nKNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESG\nNGE",
          "mw": 12.374,
          "total_mw": 24.748,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "Surface presentation of antigens protein SpaO(SPOA1,2)",
          "short_name": "SpaO",
          "sequence": "MSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRW \r\nSAWIKPGDWLEHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSC \r\nRRLCVENPVPGSALPEGKLLHIMSDRGGLWFEHLPELPAVGGGRPKMLRW \r\nPLRFVIGSSDTQRSLLGRIGIGDVLLIRTSRAEVYCYAKKLGHFNRVEGG \r\nIIVETLDIQHIEEENNTTETAETLPGLNQLPVKLEFVLYRKNVTLAELEA \r\nMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESG \r\nNGE",
          "organism": "Salmonella enterica subsp. enterica serovar Typhimurium",
          "uniprot_code": "P40699",
          "uniprot_range_first": 1,
          "uniprot_range_last": 303,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MSLRVRQIDRREWLLAQTATECQRHGREATLEYPTRQGMWVRLSDAEKRWSAWIKPGDWL\nEHVSPALAGAAVSAGAEHLVVPWLAATERPFELPVPHLSCRRLCVENPVPGSALPEGKLL\nHIMSDRGGLWFEHLPELPAVGGGRPKMLRWPLRFVIGSSDTQRSLLGRIGIGDVLLIRTS\nRAEVYCYAKKLGHFNRVEGGIIVETLDIQHIEEENNTTETAETLPGLNQLPVKLEFVLYR\nKNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLSESG\nNGE",
          "mw": 33.793,
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View the complete manifest.json source
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