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SASDD85

PDZK1 Domain 1-4

Data type: SASBDB experimental data Status: Published Curve type: Merged Last updated: 2023-06-21T07:56:39.492710+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · PDZK1 Domain 1-4

Concentration0.8 – 6.4 Buffer / pH20mM Hepes 150 NaCl 0.5 mM TCEP / 7.5
Experimental temperature15.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.124 nmExposure0.045 s × 30

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Uncharacterized protein C1orf159
View sequence
MHHHHHHSSGVDLGTENLYFQSMMTSTFNPRECKLSKQEGQNYGFFLRIEKDTEGHLVRVVEKCSPAEKAGLQDGDRVLRINGVFVDKEEHMQVVDLVRKSGNSVTLLVLDGDSYEKAVKTRVDLKELGQSQKEQGLSDNILSPVMNGGVQTWTQPRLCYLVKEGGSYGFSLKTVQGKKGVYMTDITPQGVAMRAGVLADDHLIEVNGENVEDASHEEVVEKVKKSGSRVMFLLVDKETDKRHVEQKIQFKRETASLKLLPHQPRIVEMKKGSNGYGFYLRAGSEQKGQIIKDIDSGSPAEEAGLKNNDLVVAVNGESVETLDHDSVVEMIRKGGDQTSLLVVDKETDNMYRLAHFSPFLYYQSQELPNGSVKEAPAPTPTSLEVSSPPDTTEEVDHKPKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCGKKAY
proteinHomo sapiensQ5T2W77–460monomerMolecule count 153.405 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11799[3]0.0279412–3.77706 1/nmHas uncertainty columnMissing 075sasbdb/entries/85/sasdd85/source/SASDD85.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)14.98—nm
i0Guinier0.043—1/cm
i0P(r)0.0435—1/cm
mwExperimental50.2—kDa
mwGuinier I(0)50.2—kDa
mwPorod75.0—kDa
porod_volumePorod120.03—nm³
rgGuinier3.940.02nm
rgP(r)4.056—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 name20mM Hepes 150 NaCl 0.5 mM TCEPBuffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2016-10-28Storage / measurement temperature11.0 / 15.0
Exposure time0.045Frames30
Wavelength0.124Sample-to-detector distance4.0
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.028 – 3.777Sample 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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pddfsasbdb/entries/85/sasdd85/source/SASDD85.outdownloaded86315f4fd6e93ce73b8f1e9cfd51bc2d48feedbd55c2ffbd4679b61e3a67083ecd4c9DownloadView source fileSource site
sascifsasbdb/entries/85/sasdd85/source/SASDD85.sascifdownloaded8050150c06db3868dab1938f403de9299ffc601ac5ad6b73d886f5616b29e6e8b6c327DownloadView source fileSource site
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curve：source record
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full_entry_zip：source record and ZIP contents (15 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：202 field values
Field pathRaw value
codeSASDD85
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleProbing the Architecture of a Multi-PDZ Domain Protein: Structure of PDZK1 in Solution.
project.publication.titleProbing the Architecture of a Multi-PDZ Domain Protein: Structure of PDZK1 in Solution.
project.publication.author_listHajizadeh NR, Pieprzyk J, Skopintsev P, Flayhan A, Svergun DI, Löw C
project.publication.journalStructure
project.publication.doi10.1016/j.str.2018.07.016
project.publication.pmid30220543
project.publication.published_date2018 Nov 6
project.statusreleased
project.submitted_date2018-03-18
project.released_date2018-08-29
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intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDD85.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD85_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD85_kratky_img.png
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intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD85_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDD85.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_nameUncharacterized protein C1orf159
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMHHHHHHSSGVDLGTENLYFQSMMTSTFNPRECKLSKQEGQNYGFFLRIEKDTEGHLVRVVEKCSPAEKAGLQDGDRVLRINGVFVDKEEHMQVVDLVRKSGNSVTLLVLDGDSYEKAVKTRVDLKELGQSQKEQGLSDNILSPVMNGGVQTWTQPRLCYLVKEGGSYGFSLKTVQGKKGVYMTDITPQGVAMRAGVLADDHLIEVNGENVEDASHEEVVEKVKKSGSRVMFLLVDKETDKRHVEQKIQFKRETASLKLLPHQPRIVEMKKGSNGYGFYLRAGSEQKGQIIKDIDSGSPAEEAGLKNNDLVVAVNGESVETLDHDSVVEMIRKGGDQTSLLVVDKETDNMYRLAHFSPFLYYQSQELPNGSVKEAPAPTPTSLEVSSPPDTTEEVDHKPKLCRLAKGENGYGFHLNAIRGLPGSFIKEVQKGGPADLAGLEDEDVIIEVNGVNVLDEPYEKVVDRIQSSGKNVTLLVCGKKAY
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeQ5T2W7
experiment.sample.molecule[0].uniprot_range_first7
experiment.sample.molecule[0].uniprot_range_last460
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMALRHLALLAGLLVGVASKSMENTAQLPECCVDVVGVNASCPGASLCGPGCYRRWNADGS ASCVRCGNGTLPAYNGSECRSFAGPGAPFPMNRSSGTPGRPHPGAPRVAASLFLGTFFIS SGLILSVAGFFYLKRSSKLPRACYRRNKAPALQPGEAAAMIPPPQSSAPPEDRRSRPPPG PPEQPSLQWCWVRRTQESARTEAALRQAGAAPGQGHGSRCLPG
experiment.sample.molecule[0].mw53.405
experiment.sample.molecule[0].total_mw53.405
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_descriptionnull
experiment.sample.buffer.name20mM Hepes 150 NaCl 0.5 mM TCEP
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.namePDZK1 Domain 1-4
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_nameNelly
experiment.contributor[0].contributor_surnameHajizadeh
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-10-28
experiment.storage_temperature11.0
experiment.cell_temperature15.0
experiment.exposure_time0.045
experiment.number_of_frames30
experiment.wavelength0.124
experiment.sample_detector_distance4.0
experiment.concentration_min0.8
experiment.concentration_max6.4
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.028
experiment.s_max3.777
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].chi_square_value1.34
fits[0].p_value0.371417
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fits[1].softwareMONSA
fits[1].chi_square_value1.2
fits[1].p_value0.0
fits[1].fit_residual_plotSASDD85_fit2_fitresiduals_img.png
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fits[1].descriptionnull
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fits[2].models[0].model_mw56.71
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fits[2].softwareBUNCH
fits[2].chi_square_value1.15
fits[2].p_value7e-06
fits[2].fit_residual_plotSASDD85_fit3_fitresiduals_img.png
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fits[2].fit_lognull
fits[2].software_versionnull
fits[2].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[]
intensity_unit1/cm
experimental_mw50.2
experimental_mw_errornull
guinier_i0_mw50.2
guinier_i0_mw_errornull
porod_mw75.0
porod_mw_errornull
pddf_i00.0435
pddf_i0_errornull
guinier_i00.043
guinier_i0_errornull
pddf_rg4.056
pddf_rg_errornull
guinier_rg3.94
guinier_rg_error0.02
pddf_dmax14.98
pddf_dmax_errornull
porod_volume120.03
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first16
guinier_point_last147
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDD85_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json：36 field values
Field pathRaw value
codeSASDD85
statussuccess
started_at2026-08-11T14:41:40.857906+00:00
finished_at2026-08-11T14:41:51.464724+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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View the complete summary.json source
{
  "code": "SASDD85",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "Probing the Architecture of a Multi-PDZ Domain Protein: Structure of PDZK1 in Solution.",
    "publication": {
      "title": "Probing the Architecture of a Multi-PDZ Domain Protein: Structure of PDZK1 in Solution.",
      "author_list": "Hajizadeh NR, Pieprzyk J, Skopintsev P, Flayhan A, Svergun DI, Löw C",
      "journal": "Structure",
      "doi": "10.1016/j.str.2018.07.016",
      "pmid": "30220543",
      "published_date": "2018 Nov 6"
    },
    "status": "released",
    "submitted_date": "2018-03-18",
    "released_date": "2018-08-29"
  },
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View the complete manifest.json source
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