SASDUW5

C-terminal domain of Ubiquitinating/deubiquitinating enzyme SdeA (SdeA_CTD)

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2025-11-19T15:45:31.938512+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · C-terminal domain of Ubiquitinating/deubiquitinating enzyme SdeA (SdeA_CTD)

Concentration— – 16.5 Buffer / pH25 mM Tris-HCl, 200 mM NaCl, 5 mM DTT / 7.5
Experimental temperature25.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.124 nmExposure1.0 s × 36

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Ubiquitinating/deubiquitinating enzyme SdeA
View sequence
GSDFSDVEKLEQQIQVIDTKLADAYLLEVTKQISALDNTKPKNQTELKTKIAAFLDRTTDIEMLRNERIKKHGSSKDPLDLSDLDKLSGSLQRINQSLVSDLITTIRVSINQMEAKTFHEQEKEIQQNFELLAKLEKTLDKSKTSEKLREDIPKLNDLLVAKQKAYPQMVQMQLKSEVFVTQLREVCQANHDDLDKTRNARLRELDRLDREAGITRMVGNLIWGLTNKVGLTTDERLDIRTKQQSLARFKNELFNDKIDTDQLISNLARKRPSELQEGLGISTDNAMELHLLLTELAGKTTSPDELEERMKAIDDISTKIGREPEHLKFVMVEEDESNKKTIGF
proteinLegionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)Q5ZTK41158–1499monomerMolecule count 139.388 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11419[3]0.147703–4.10192 1/nmHas uncertainty columnMissing 00sasbdb/entries/w5/sasduw5/source/SASDUW5.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)15.7—nm
i0Guinier20963.4—arbitrary
i0P(r)21430.0—arbitrary
mwExperimental40.0—kDa
mwPorod38.8—kDa
porod_volumePorod62.0—nm³
rgGuinier3.8650.011nm
rgP(r)4.151—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

Fit 1 · MONSA

χ²: 1.246CorMap p: 0.0586Unit: 1/A
ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—dummyMONSA 1.45 (r12592)———Model Image
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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 name25 mM Tris-HCl, 200 mM NaCl, 5 mM DTTBuffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2020-12-04Storage / measurement temperature25.0 / 25.0
Exposure time1.0Frames36
Wavelength0.124Sample-to-detector distance3.0
SourceX-ray synchrotronDetectorPilatus 6M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.148 – 4.102Sample volume / flow rate100.0 / 0.7

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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All source fields (unfiltered)

Every source field is expanded here, including empty values, list members and fields already shown above.

summary.json:174 field values
Field pathRaw value
codeSASDUW5
statusPublished
type_of_curveSEC-SAS
angular_unit1/nm
project.titleStructural Basis for Membrane Targeting and Secretion of Legionella SidE Ubiquitin Ligases
project.publicationnull
project.statusreleased
project.submitted_date2024-03-29
project.released_date2025-11-19
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDUW5.out
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDUW5.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 6M
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_nameUbiquitinating/deubiquitinating enzyme SdeA
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceGSDFSDVEKLEQQIQVIDTKLADAYLLEVTKQISALDNTKPKNQTELKTKIAAFLDRTTDIEMLRNERIKKHGSSKDPLDLSDLDKLSGSLQRINQSLVSDLITTIRVSINQMEAKTFHEQEKEIQQNFELLAKLEKTLDKSKTSEKLREDIPKLNDLLVAKQKAYPQMVQMQLKSEVFVTQLREVCQANHDDLDKTRNARLRELDRLDREAGITRMVGNLIWGLTNKVGLTTDERLDIRTKQQSLARFKNELFNDKIDTDQLISNLARKRPSELQEGLGISTDNAMELHLLLTELAGKTTSPDELEERMKAIDDISTKIGREPEHLKFVMVEEDESNKKTIGF
experiment.sample.molecule[0].organismLegionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
experiment.sample.molecule[0].uniprot_codeQ5ZTK4
experiment.sample.molecule[0].uniprot_range_first1158
experiment.sample.molecule[0].uniprot_range_last1499
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMPKYVEGVELTQEGMHAIFARMGYGDITSGSIYNGVPTIDTGALNRQGFMPVLTGVGPHR DSGHWIMLIKGPGNQYYLFDPLGKTSGEGYQNILAAQLPMGSTLSVIPNGSGLNMGLCGY WVASAGLRAHQALNQHNPPTLLNVGQTITNEMRNELDHDGYRKITGWLRAVADEFPEGDP QLDGKALRENTEKDLKIEIPTLVLPGKDTSPKEMSVKPTAPQDKSVPVWNGFSLYTDDTV KAAAQYAYDNYLGKPYTGSVESAPANFGGRMVYRQHHGLSHTLRTMAYAELIVEEARKAK LRGETLGKFKDGRTIADVTPQELKKIMIAQAFFVAGRDDEASDAKNYQKYHEQSRDAFLK YVKDNESTLIPDVFKDQEDVNFYARVIEDKSHDWESTPAHVLINQGHMVDLVRVKQPPES FLQRYFSSMQRWIGSQATEAVFGIQRQFFHATYEVVAGFDSDNKEPHLVVSGLGRYVIGE DGQPIREAPKKGQKEGDLKVFPQTYKLKENERLMRVDEFLKLPEIQNTFPGSGKHLQGGM PGMNEMDYWNRLNSLNRARCENDVDFCLKQLQTAHDKAKIEPIKQAFQSSKGKERRQPNV DEIAAARIIQQILANPDCIHDDHVLINGQKLEQQFFRDLLAKCEMAVVGSLLNDTDIGNI DTLMRHEKDTEFHSTNPEAVPVKIGEYWINDQRINNSSGNITQKKHDLIFLMQNDAWYFS RVNAIAQNRDKGSTFKEVLITTLMTPLTSKALVDTSQAKPPTRLFRGLNLSEEFTKGLID QANAMIANTTERLFTDHSPEAFKQIKLNDLSKMSGRTNASTTTEIKLVKETWDSNVIFEM LDPDGLLHSKQVGRHGEGTESEFSVYLPEDVALVPVKVTLDGKTQKGENRYVFTFVAVKS PDFTPRHESGYAVEPFLRMQAAKLAEVKSSIEKAQRAPDLETIFNLQNEVEAVQYSHLST GYKNFLKNTVGPVLENSLSGLMESDTDTLSKALAAFPSDTQWSAFNFEEARQAKRQMDAI KQMVGNKVVLDALTQCQDALEKQNIAGALDALKKIPSEKEMGTIRRELREQIQSARQELE SLQRAVVTPVVTDEKKVRERYDALIENTSKKITELETGKLPNLDAVKKGISNLSNLKQEV TVLRNEKIRMHVGTDKVDFSDVEKLEQQIQVIDTKLADAYLLEVTKQISALDNTKPKNQT ELKTKIAAFLDRTTDIEMLRNERIKKHGSSKDPLDLSDLDKLSGSLQRINQSLVSDLITT IRVSINQMEAKTFHEQEKEIQQNFELLAKLEKTLDKSKTSEKLREDIPKLNDLLVAKQKA YPQMVQMQLKSEVFVTQLREVCQANHDDLDKTRNARLRELDRLDREAGITRMVGNLIWGL TNKVGLTTDERLDIRTKQQSLARFKNELFNDKIDTDQLISNLARKRPSELQEGLGISTDN AMELHLLLTELAGKTTSPDELEERMKAIDDISTKIGREPEHLKFVMVEEDESNKKTIGF
experiment.sample.molecule[0].mw39.388
experiment.sample.molecule[0].total_mw39.388
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_descriptionProtein construct used for SAXS contains an additional two non-native amino acids at N-terminus (GS).
experiment.sample.buffer.name25 mM Tris-HCl, 200 mM NaCl, 5 mM DTT
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.nameC-terminal domain of Ubiquitinating/deubiquitinating enzyme SdeA (SdeA_CTD)
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_nameAhmed
experiment.contributor[0].contributor_surnameMohammed
experiment.contributor[0].orcid
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2020-12-04
experiment.storage_temperature25.0
experiment.cell_temperature25.0
experiment.exposure_time1.0
experiment.number_of_frames36
experiment.wavelength0.124
experiment.sample_detector_distance3.0
experiment.concentration_minnull
experiment.concentration_max16.5
experiment.sample_volume100.0
experiment.flow_rate0.7
experiment.s_min0.148
experiment.s_max4.102
experiment.total_exposure_timenull
experiment.seccolumn3
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fits[0].models[0].lognull
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fits[0].models[0].commentnull
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fits[0].softwareMONSA
fits[0].chi_square_value1.246
fits[0].p_value0.0586
fits[0].fit_residual_plotSASDUW5_fit1_fitresiduals_img.png
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fits[0].description
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fits[1].softwareSREFLEX
fits[1].chi_square_value3.984
fits[1].p_value0.0
fits[1].fit_residual_plotSASDUW5_fit2_fitresiduals_img.png
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fits[1].fit_lognull
fits[1].software_versionnull
fits[1].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of SdeA_CTD in 25 mM Tris-HCl, 200 mM NaCl, 5 mM DTT, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 100.00 μl sample at 16.5 mg/ml was injected at a 0.70 ml/min flow rate onto a GE Superdex 75 Increase 10/300 column at 25°C. 36 successive 1 second frames were collected through the main SEC elution peak. 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_mw40.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw38.8
porod_mw_errornull
pddf_i021430.0
pddf_i0_errornull
guinier_i020963.4
guinier_i0_errornull
pddf_rg4.151
pddf_rg_errornull
guinier_rg3.865
guinier_rg_error0.011
pddf_dmax15.7
pddf_dmax_errornull
porod_volume62.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first2
guinier_point_last68
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDUW5_datloglog_img.png
symmetrynull
last_modified2025-11-19T15:45:31.938512+01:00
bragg_peak[]
manifest.json:34 field values
Field pathRaw value
codeSASDUW5
statussuccess
started_at2026-08-11T14:58:05.009307+00:00
finished_at2026-08-11T14:58:13.563216+00:00
source_last_modified2025-11-19T15:45:31.938512+01:00
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View the complete summary.json source
{
  "code": "SASDUW5",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structural Basis for Membrane Targeting and Secretion of Legionella SidE Ubiquitin Ligases",
    "publication": null,
    "status": "released",
    "submitted_date": "2024-03-29",
    "released_date": "2025-11-19"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDUW5.out",
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  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUW5_pofr_img.png",
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUW5.sascif",
  "experiment": {
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        "type": null,
        "name": "Pilatus 6M",
        "resolution": null
      },
      "name": "PETRA III",
      "city": "DESY; Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL P12",
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        "affiliation": [
          {
            "short_name": "EMBL-Hamburg",
            "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
            "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
            "webpage": "http://www.embl-hamburg.de/index.php"
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View the complete manifest.json source
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