SASDWG9

PDZ domain of the segment polarity protein dishevelled homolog DVL-3

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2025-06-17T09:21:01.066938+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · PDZ domain of the segment polarity protein dishevelled homolog DVL-3

Concentration— – 5.0 Buffer / pH50 mM sodium phosphate, 50 mM NaCl, 0.5 mM EDTA / 6.5
Experimental temperature25.0 Facility / beamlineCEITEC / Rigaku BioSAXS-2000
Wavelength0.154 nmExposure600.0 s × 6

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Segment polarity protein dishevelled homolog DVL-3
View sequence
GAMALNIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNEINFENMSNDDAVRVLREIVHKPGPITLTVAKCWDPSPRGCFTLPRSE
proteinHomo sapiensQ92997245–351monomerMolecule count 111.978 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1271[3]0.0123364–0.400155 1/AHas uncertainty columnMissing 00sasbdb/entries/g9/sasdwg9/source/SASDWG9.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)4.31—Å
i0Guinier0.79546—arbitrary
i0P(r)0.7841—arbitrary
mwExperimental10.4—kDa
mwPorod12.6—kDa
porod_volumePorod20.2—ų
rgGuinier1.6090.14Å
rgP(r)1.57—Å

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 sodium phosphate, 50 mM NaCl, 0.5 mM EDTABuffer concentration—
pH6.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2021-01-27Storage / measurement temperature4.0 / 25.0
Exposure time600.0Frames6
Wavelength0.154Sample-to-detector distance0.48
SourceX-ray in houseDetectorRigaku HyPix-3000
Facility / beamlineCEITEC / Rigaku BioSAXS-2000 · Brno, Czech Republic
q range0.123 – 4.002Sample 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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summarysasbdb/entries/g9/sasdwg9/source/summary.jsondownloaded82374c7c244920e8d748f2dbd6e99317fd2ee0aab2fbe3da724b82bc0330b4502840DownloadView source fileSource site
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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:156 field values
Field pathRaw value
codeSASDWG9
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleA class III ligand oscillates between internal and terminal binding modes as it engages with the Dishevelled PDZ domain.
project.publication.titleA class III ligand oscillates between internal and terminal binding modes as it engages with the Dishevelled PDZ domain.
project.publication.author_listKumar J, Micka M, Komárek J, Klumpler T, Bystrý V, Sprangers R, Bařinka C, Bryja V, Tripsianes K
project.publication.journalStructure
project.publication.doi10.1016/j.str.2025.05.012
project.publication.pmid40516532
project.publication.published_date2025 Jun 5
project.statusreleased
project.submitted_date2025-02-25
project.released_date2025-06-17
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDWG9.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDWG9.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWG9_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWG9_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDWG9_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWG9_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDWG9.sascif
experiment.instrument.detector.typeHybrid Photon Counting (HPC) X-ray detector
experiment.instrument.detector.nameRigaku HyPix-3000
experiment.instrument.detector.resolution100.0
experiment.instrument.nameCEITEC
experiment.instrument.cityBrno
experiment.instrument.countryCzech Republic
experiment.instrument.beamline_nameRigaku BioSAXS-2000
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_nameSegment polarity protein dishevelled homolog DVL-3
experiment.sample.molecule[0].short_nameDLV3_PDZ
experiment.sample.molecule[0].sequenceGAMALNIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNEINFENMSNDDAVRVLREIVHKPGPITLTVAKCWDPSPRGCFTLPRSE
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeQ92997
experiment.sample.molecule[0].uniprot_range_first245
experiment.sample.molecule[0].uniprot_range_last351
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMGETKIIYHLDGQETPYLVKLPLPAERVTLADFKGVLQRPSYKFFFKSMDDDFGVVKEEI SDDNAKLPCFNGRVVSWLVSAEGSHPDPAPFCADNPSELPPPMERTGGIGDSRPPSFHPH AGGGSQENLDNDTETDSLVSAQRERPRRRDGPEHATRLNGTAKGERRREPGGYDSSSTLM SSELETTSFFDSDEDDSTSRFSSSTEQSSASRLMRRHKRRRRKQKVSRIERSSSFSSITD STMSLNIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLL QVNEINFENMSNDDAVRVLREIVHKPGPITLTVAKCWDPSPRGCFTLPRSEPIRPIDPAA WVSHTAAMTGTFPAYGMSPSLSTITSTSSSITSSIPDTERLDDFHLSIHSDMAAIVKAMA SPESGLEVRDRMWLKITIPNAFIGSDVVDWLYHNVEGFTDRREARKYASNLLKAGFIRHT VNKITFSEQCYYIFGDLCGNMANLSLHDHDGSSGASDQDTLAPLPHPGAAPWPMAFPYQY PPPPHPYNPHPGFPELGYSYGGGSASSQHSEGSRSSGSNRSGSDRRKEKDPKAGDSKSGG SGSESDHTTRSSLRGPRERAPSERSGPAASEHSHRSHHSLASSLRSHHTHPSYGPPGVPP LYGPPMLMMPPPPAAMGPPGAPPGRDLASVPPELTASRQSFRMAMGNPSEFFVDVM
experiment.sample.molecule[0].mw11.978
experiment.sample.molecule[0].total_mw11.978
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionPDZ domain of the Segment polarity protein dishevelled homolog DVL-3. The protein construct used for SAXS contains an additional four non-native amino acids at the N-terminus (GAMA).
experiment.sample.buffer.name50 mM sodium phosphate, 50 mM NaCl, 0.5 mM EDTA
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph6.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.namePDZ domain of the segment polarity protein dishevelled homolog DVL-3
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_namenull
experiment.contributor[0].affiliation[0].addressnull
experiment.contributor[0].affiliation[0].full_nameCEITEC - Central European Institute of Technology, Masaryk University
experiment.contributor[0].affiliation[0].webpagehttps://www.ceitec.eu/
experiment.contributor[0].contributor_nameTomas
experiment.contributor[0].contributor_surnameKlumpler
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2021-01-27
experiment.storage_temperature4.0
experiment.cell_temperature25.0
experiment.exposure_time600.0
experiment.number_of_frames6
experiment.wavelength0.154
experiment.sample_detector_distance0.48
experiment.concentration_minnull
experiment.concentration_max5.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.123
experiment.s_max4.002
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDWG9_fit1_model1_img.png
fits[0].models[0].softwareREFMAC
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelatomic
fits[0].models[0].software_version5.8.0258
fits[0].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDWG9_fit1_model1.pdb
fits[0].models[0].model_mw11.77
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetrynull
fits[0].models[0].commentnull
fits[0].models[0].user195
fits[0].fit_unit1/A
fits[0].fit_plothttps://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWG9_fit1_fixed_fit_img.png
fits[0].softwareCRYSOL
fits[0].chi_square_value0.989
fits[0].p_value0.0321
fits[0].fit_residual_plotSASDWG9_fit1_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDWG9_fit1.fit
fits[0].fit_loghttps://www.sasbdb.org/media/fitting_files/log_files/DVL3_PDZext_C8_chainA00.log
fits[0].software_versionATSAS 2.8.3
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSAXS data from solutions of PDZ domain of the segment polarity protein dishevelled homolog DVL-3 in 50 mM sodium phosphate, 50 mM NaCl, 0.5 mM EDTA, pH 6.5 were collected using a Rigaku BioSAXS-2000 instrument at CEITEC (Brno, Czech Republic) equipped with a Rigaku HyPix-3000 detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 5.00 mg/ml was measured at 25°C. Six successive 600 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.
tags[]
intensity_unitarbitrary
experimental_mw10.4
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw12.6
porod_mw_errornull
pddf_i00.7841
pddf_i0_errornull
guinier_i00.79546
guinier_i0_errornull
pddf_rg1.57
pddf_rg_errornull
guinier_rg1.609
guinier_rg_error0.14
pddf_dmax4.31
pddf_dmax_errornull
porod_volume20.2
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last48
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDWG9_datloglog_img.png
symmetrynull
last_modified2025-06-17T09:21:01.066938+02:00
bragg_peak[]
manifest.json:34 field values
Field pathRaw value
codeSASDWG9
statussuccess
started_at2026-08-11T16:14:47.242562+00:00
finished_at2026-08-11T16:14:54.185250+00:00
source_last_modified2025-06-17T09:21:01.066938+02:00
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View the complete summary.json source
{
  "code": "SASDWG9",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "A class III ligand oscillates between internal and terminal binding modes as it engages with the Dishevelled PDZ domain.",
    "publication": {
      "title": "A class III ligand oscillates between internal and terminal binding modes as it engages with the Dishevelled PDZ domain.",
      "author_list": "Kumar J, Micka M, Komárek J, Klumpler T, Bystrý V, Sprangers R, Bařinka C, Bryja V, Tripsianes K",
      "journal": "Structure",
      "doi": "10.1016/j.str.2025.05.012",
      "pmid": "40516532",
      "published_date": "2025 Jun 5"
    },
    "status": "released",
    "submitted_date": "2025-02-25",
    "released_date": "2025-06-17"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDWG9.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDWG9.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWG9_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWG9_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDWG9_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWG9_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDWG9.sascif",
  "experiment": {
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        "name": "Rigaku HyPix-3000",
        "resolution": 100.0
      },
      "name": "CEITEC",
      "city": "Brno",
      "country": "Czech Republic",
      "beamline_name": "Rigaku BioSAXS-2000",
      "beam_geometry": null,
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    },
    "sample": {
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        {
          "long_name": "Segment polarity protein dishevelled homolog DVL-3",
          "short_name": "DLV3_PDZ",
          "sequence": "GAMALNIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNEINFENMSNDDAVRVLREIVHKPGPITLTVAKCWDPSPRGCFTLPRSE",
          "organism": "Homo sapiens",
          "uniprot_code": "Q92997",
          "uniprot_range_first": 245,
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          "oligomerization": "monomer",
          "molecular_type": "protein",
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          "mw": 11.978,
          "total_mw": 11.978,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": "PDZ domain of the Segment polarity protein dishevelled homolog DVL-3. The protein construct used for SAXS contains an additional four non-native amino acids at the N-terminus (GAMA)."
        }
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        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 6.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "PDZ domain of the segment polarity protein dishevelled homolog DVL-3",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
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View the complete manifest.json source
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