SASDAE6

PsrP functional binding region

Data type: SASBDB experimental data Status: Published Curve type: Extrapolated to infinite dilution Last updated: 2020-08-28T15:28:15.765732+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · PsrP functional binding region

Concentration0.32 – 3.0 mg/mlBuffer / pHPBS 5 % Glycerol / 7.4
Experimental temperature20.0 Facility / beamlineESRF / BM29
Wavelength0.93 nmExposure1.0 s × 10

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Functional binding region (120-395) of the pneumococcal serine-rich repeat protein
View sequence
HHHHHHSSTVVGSQTAAATEATAKKVEEDRKKPASDYVASVTNVNLQSYAKRRKRSVDSIEQLLASIKNAAVFSGNTIVNGAPAINASLNIAKSETKVYTGEGVDSVYRVPIYYKLKVTNDGSKLTFTYTVTYVNPKTNDLGNISSMRPGYSIYNSGTSTQTMLTLGSDLGKPSGVKNYITDKNGRQVLSYNTSTMTTQGSGYTWGNGAQMNGFFAKKGYGLTSSWTVPITGTDTSFTFTPYAARTDRIGINYFNGGGKVVESSTTSQSLSQSKSLSVSASQ
proteinStreptococcus pneumoniaeA0A0H2URK1120–395monomerMolecule count 130.3 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1976[3]0.0499164–4.28196 1/nmHas uncertainty columnMissing 00sasbdb/entries/e6/sasdae6/source/SASDAE6.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)12.5—nm
estimated_volumeReported57.0—nm³
i0Guinier21.83——
i0P(r)22.08——
mwExperimental28.7—kDa
mwGuinier I(0)20.0—kDa
mwPorod25.7—kDa
porod_volumePorod41.1—nm³
rgGuinier2.935—nm
rgP(r)3.13—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 namePBS 5 % GlycerolBuffer concentration—
pH7.4AdditivesGlycerol 5.000 %
Buffer descriptionPhosphate buffered saline
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2013-02-27Storage / measurement temperature20.0 / 20.0
Exposure time1.0Frames10
Wavelength0.93Sample-to-detector distance2.43
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineESRF / BM29 · Grenoble, France
q range0.05 – 4.282Sample 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_zipsasbdb/entries/e6/sasdae6/source/SASDAE6.zipdownloaded920116eea94a8166eeee68885b105661f0c76ad4db473e5501f87da684da950242d91DownloadView source fileSource site
pddfsasbdb/entries/e6/sasdae6/source/SASDAE6.outdownloaded27193de9bc4f55072ba0d61d9b1a5efe33187db3fa3d3893fcae87e7d6eb01736c8e7DownloadView source fileSource site
sascifsasbdb/entries/e6/sasdae6/source/SASDAE6.sascifdownloaded4140695d5a1ba3fbb2baf0c7f8f5851a69748d622813a7259d7e05a5603c2a45aba4dbDownloadView source fileSource site
summarysasbdb/entries/e6/sasdae6/source/summary.jsondownloaded12425293883e7e2d47c8178881c43489529520ce9867b8a456ea91cf85c3ab2ed7f38DownloadView source fileSource site
curve:source record
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full_entry_zip:source record and ZIP contents (8 items)
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pddf:source record
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sascif: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:169 field values
Field pathRaw value
codeSASDAE6
statusPublished
type_of_curveExtrapolated to infinite dilution
angular_unit1/nm
project.titleThe BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation.
project.publication.titleThe BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation.
project.publication.author_listSchulte T, Mikaelsson C, Beaussart A, Kikhney A, Deshmukh M, Wolniak S, Pathak A, Ebel C, Löfling J, Fogolari F, Henriques-Normark B, Dufrêne YF, Svergun D, Nygren PÅ, Achour A
project.publication.journalSci Rep
project.publication.doi10.1038/srep32371
project.publication.pmid27582320
project.publication.published_date2016 Sep 1
project.statusreleased
project.submitted_date2015-01-15
project.released_date2016-09-08
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDAE6.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDAE6.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAE6_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAE6_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAE6_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAE6_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDAE6.sascif
experiment.instrument.detector.typeDectris
experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
experiment.instrument.beam_geometry
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_nameFunctional binding region (120-395) of the pneumococcal serine-rich repeat protein
experiment.sample.molecule[0].short_namePsrP BR*(120-395)
experiment.sample.molecule[0].sequenceHHHHHH SSTVVGSQTAAATEATAKKVEEDRKKPASDYVASVTNVNLQSYAKRRKRSVDSIEQLLASIKNAAVFSGNTIVNGAPAINASLNIA KSETKVYTGEGVDSVYRVPIYYKLKVTNDGSKLTFTYTVTYVNPKTNDLGNISSMRPGYSIYNSGTSTQTMLTLGSDLGKPSGVKNYITDKNGRQVLSYNTSTMTTQGSGYTWGNGAQMNGFFAKKGYGLTSSWTVPITGTDTSFTFTPYAARTDRIGINYFNGGGKVVE SSTTSQSLSQSKSLSVSASQ
experiment.sample.molecule[0].organismStreptococcus pneumoniae
experiment.sample.molecule[0].uniprot_codeA0A0H2URK1
experiment.sample.molecule[0].uniprot_range_first120
experiment.sample.molecule[0].uniprot_range_last395
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMTETVEDKVSHSITGLDILKGIVAAGAVISGTVATQTKVFTNESAVLEKTVEKTDALATN DTVVLGTISTSNSASSTSLSASESASTSASESASTSASTSASTSASESASTSASTSISAS STVVGSQTAAATEATAKKVEEDRKKPASDYVASVTNVNLQSYAKRRKRSVDSIEQLLASI KNAAVFSGNTIVNGAPAINASLNIAKSETKVYTGEGVDSVYRVPIYYKLKVTNDGSKLTF TYTVTYVNPKTNDLGNISSMRPGYSIYNSGTSTQTMLTLGSDLGKPSGVKNYITDKNGRQ VLSYNTSTMTTQGSGYTWGNGAQMNGFFAKKGYGLTSSWTVPITGTDTSFTFTPYAARTD RIGINYFNGGGKVVESSTTSQSLSQSKSLSVSASQSASASASTSASASASTSASASASTS ASASASTSASVSASTSASASASTSASASASTSASESASTSASASASTSASASASTSASAS ASTSASESASTSASASASTSASESASTSASASASTSASASASTSASGSASTSTSASASTS ASASASTSASASASISASESASTSASESASTSTSASASTSASESASTSASASASTSASAS ASTSASASASTSASASTSASESASTSASASASTSASASASTSASASASTSASASASTSAS VSASTSASASASTSASASASTSASESASTSASASASTSASASASTSASASASTSASASAS TSASASASTSASESASTSASASASTSASASASTSASASASTSASASASTSASASASISAS ESASTSASASASTSASASASTSASASASTSASESASTSASASASTSASASASTSASASAS TSASASASTSASASASTSASASASTSASESASTSASASASTSASESASTSASASASTSAS ASASTSASASASTSASASASTSASASASTSASASASTSASASTSASESASTSASASASTS ASASASTSASASASTSASESASTSASASASTSASASASTSASASASTSASASASTSASAS ASISASESASTSASASASTSASVSASTSASASASTSASESASTSASASASTSASESASTS ASASASTSASASASISASESASTSASASASTSASASASTSASASASTSASESASTSTSAS ASTSASESASTSASASASTSASASASTSASASASTSASASASTSASASTSASESASTSAS ASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASAS TSASESASTSASASASTSASASASTSASASASTSASASASTSASVSASTSASESASTSAS ASASTSASASASTSASESASTSASASASTSASESASTSASASASTSASASASTSASASAS TSASASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASASTSAS ASASTSASASASTSASASASISASESASTSASASASTSASASASTSASVSASTSASASAS TSASASASISASESASTSASASASTSASASASTSASASASTSASASASISASESASTSAS ASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASAS TSASASASTSASESASTSASASASTSASASASTSASASASTSASVSASTSASESASTSAS ASASTSASASASTSASASASTSASESASTSASASASTSASASASTSASESASTSASASAS TSASASASTSASASASTSASASASASTSASASASTSASASASTSASASASISASESASTS ASESASTSTSASASTSASESASTSASASASTSASASASTSASASASTSASASTSASESAS TSASASASTSASASASTSASASASTSASASASTSASASASTSASVSASTSASASASTSAS ASASTSASESASTSASASASTSASASASTSASASASTSASASASTSASASASTSASESAS TSASASASTSASASASTSASASASTSASASASTSASASASISASESASTSASASASTSAS ASASTSASASASTSASESASTSASASASTSASASASTSASASASTSASASASTSASASAS TSASASASTSASESASTSASASASTSASESASTSASASASTSASASASTSASASASTSAS ASASTSASASASTSASASASTSASASTSASESASTSASASASTSASASASTSASASASTS ASESASTSASASASTSASASASTSASASASTSASASASTSASASASISASESASTSASAS ASTSASVSASTSASASASTSASESASTSASASASTSASESASTSASASASTSASASASIS ASESASTSASASASTSASASASTSASASASTSASESASTSTSASASTSASESASTSASAS ASTSASASASTSASASASTSASASASTSASASTSASESASTSASASASTSASASASTSAS ASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASAS TSASASASTSASESASTSASASASTSASASASTSASASASTSASVSASTSASESASTSAS ASASTSASASASTSASASASTSASESASTSASASASTSASASASTSASESASTSASASAS TSASASASTSASASASTSASASASASTSASASASTSASASASTSASASASISASESASTS ASASASASTSASASASTSASASASTSASASASISASESASTSASESASTSTSASASTSAS ESASTSASASASTSASASASTSASASASTSASASTSASESASTSASASASTSASASASTS ASASASTSASASASTSASASASTSASVSASTSASASASTSASASASTSASESASTSASAS TSASESASTSASASASTSASASASTSASASASTSASESASTSASASASTSASASASTSAS ESASTSASASASTSASASASTSASASASTSASESASTSASASASTSASESASTSASASAS TSASASASTSASGSASTSTSASASTSASASASTSASASASISASESASTSASESASTSTS ASASTSASESASTSASASASTSASASASTSASASASTSASASTSASESASTSASASASTS ASASASTSASASASTSASASASTSASVSASTSASASASTSASASASTSASESASTSASAS ASTSASASASTSASASASTSASASASTSASASASTSASESASTSASASASTSASASASTS ASASASTSASASASTSASASASISASESASTSASASASTSASASASTSASASASTSASES ASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASESASTS ASASASTSASESASTSASASASTSASASASTSASASASTSASASASTSASASASTSASAS ASTSASASTSASESASTSASASASTSASASASTSASASASTSASESASTSASASASTSAS ASASTSASASASTSASASASTSASASASISASESASTSASASASTSASVSASTSASASAS TSASESASTSASASASTSASESASTSASASASTSASASASISASESASTSASASASTSAS ASASTSASASASTSASESASTSTSASASTSASESASTSASASASTSASASASTSASASAS TSASASASTSASASTSASESASTSASASASTSASASASTSASASASTSASASASTSASAS ASTSASASASTSASASASTSASASASTSASESASTSASASASTSASASASTSASASASTS ASASASTSASVSASTSASESASTSASASASTSASASASTSASESASTSASASASTSASES ASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASASTS ASASASTSASASASTSASASASTSASASASTSASASASTSASASASISASESASTSASAS ASTSASASASTSASVSASTSASASASTSASASASISASESASTSASASASTSASASASTS ASASASTSASASASISASESASTSASASASTSASASASTSASASASTSASASASTSASAS ASTSASASASTSASASASTSASASASTSASASASTSASESASTSASASASTSASASASIS ASESASTSASASASTSASASASTSASASASTSASESASTSTSASASTSASESASTSASAS ASTSASASASTSASASASTSASASASTSASASTSASESASTSASASASTSASASASTSAS ASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASESASTSASASAS TSASASASTSASASASTSASASASTSASVSASTSASESASTSASASASTSASASASTSAS ESASTSASASASTSASESASTSASASASTSASASASTSASASASTSASASASTSASASAS TSASASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASASTSAS ASASISASESASTSASASASTSASASASTSASVSASTSASASASTSASASASISASESAS TSASASASTSASASASTSASASASTSASASASISASESASTSASASASTSASASASTSAS ASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASASTSASASAS TSASASASTSASASASTSASASASTSASASASTSVSNSANHSNSQVGNTSGSTGKSQKEL PNTGTESSIGSVLLGVLAAVTGIGLVAKRRKRDEEE
experiment.sample.molecule[0].mw30.3
experiment.sample.molecule[0].total_mw30.3
experiment.sample.molecule[0].number_molecules1
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.buffer.namePBS 5 % Glycerol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentPhosphate buffered saline
experiment.sample.buffer.additiveGlycerol 5.000 %
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.4
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.namePsrP functional binding region
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_nameAl
experiment.contributor[0].contributor_surnameKikhney
experiment.contributor[0].orcidhttps://orcid.org/0000-0003-1321-3956
experiment.concentration_methodnull
experiment.concentration_unitmg/ml
experiment.date2013-02-27
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time1.0
experiment.number_of_frames10
experiment.wavelength0.93
experiment.sample_detector_distance2.43
experiment.concentration_min0.32
experiment.concentration_max3.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.05
experiment.s_max4.282
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDAE6_fit1_model1_img.png
fits[0].models[0].softwareEOM/RANCH
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelmix
fits[0].models[0].software_version1.3
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fits[0].models[0].model_mw30.82
fits[0].models[0].bead_radius1.9
fits[0].models[0].loghttps://www.sasbdb.org/media/log_files/GA001.log
fits[0].models[0].symmetry
fits[0].models[0].comment
fits[0].models[0].user4
fits[0].models[1].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDAE6_fit1_model2_img.png
fits[0].models[1].softwareEOM/RANCH
fits[0].models[1].pdb_link[]
fits[0].models[1].model_titlenull
fits[0].models[1].type_of_modelmix
fits[0].models[1].software_version1.3
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fits[0].models[1].model_mw30.82
fits[0].models[1].bead_radius1.9
fits[0].models[1].lognull
fits[0].models[1].symmetry
fits[0].models[1].comment
fits[0].models[1].user4
fits[0].fit_unit1/A
fits[0].fit_plothttps://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAE6_fit1_fixed_fit_img.png
fits[0].softwarenull
fits[0].chi_square_value1.663
fits[0].p_value0.0572
fits[0].fit_residual_plotfit4columns471_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDAE6_fit1.fit
fits[0].fit_lognull
fits[0].software_versionnull
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionGNOM
i0_calibration_standardBSA
descriptionnull
experiment_descriptionnull
tags[]
intensity_unitnull
experimental_mw28.7
experimental_mw_errornull
guinier_i0_mw20.0
guinier_i0_mw_errornull
porod_mw25.7
porod_mw_errornull
pddf_i022.08
pddf_i0_errornull
guinier_i021.83
guinier_i0_errornull
pddf_rg3.13
pddf_rg_errornull
guinier_rg2.935
guinier_rg_errornull
pddf_dmax12.5
pddf_dmax_errornull
porod_volume41.1
porod_volume_errornull
estimated_volume57.0
estimated_volume_errornull
guinier_point_first16
guinier_point_last86
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDAE6_datloglog_img.png
symmetrynull
last_modified2020-08-28T15:28:15.765732+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDAE6
statussuccess
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View the complete summary.json source
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  "code": "SASDAE6",
  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "angular_unit": "1/nm",
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    "title": "The BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation.",
    "publication": {
      "title": "The BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation.",
      "author_list": "Schulte T, Mikaelsson C, Beaussart A, Kikhney A, Deshmukh M, Wolniak S, Pathak A, Ebel C, Löfling J, Fogolari F, Henriques-Normark B, Dufrêne YF, Svergun D, Nygren PÅ, Achour A",
      "journal": "Sci Rep",
      "doi": "10.1038/srep32371",
      "pmid": "27582320",
      "published_date": "2016 Sep 1"
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    "submitted_date": "2015-01-15",
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