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SASDZ78

Octameric Assembly of the Phospholipase D–Like (PLD-Fold) Nuclease K4 Domain in the Vaccinia Virion Nicking-Joining Enzyme

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2026-08-03T09:48:39.841183+02:00

Molecular mass calculated from the Porod volume using 0.83 Da∙Å-3 obtained from the protein specific mass of 1,37 g∙cm-3. The sequence of the construct after tag-cleavage is provided.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Octameric Assembly of the Phospholipase D–Like (PLD-Fold) Nuclease K4 Domain in the Vaccinia Virion Nicking-Joining Enzyme

Concentration— – 1.0 Buffer / pH20 mM Tris pH 7.5, 150 mM NaCl, 0.5mM TCEP / 7.5
Experimental temperature20.0 Facility / beamlineSOLEIL / SWING
Wavelength0.1033 nmExposure1.0 s × 630

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Virion nicking-joining enzyme (octamer)
View sequence
GAMANPDNTIAVITETIPIGMQFDKVYLSTFNMWREILSNTTKTLDISSFYWSLSDEVGTNFGTIILNEIVQLPKRGVRVRVAVNKSNKPLKDVERLQMAGVEVRYIDITNILGGVLHTKFWISDNTHIYLGSANMDWRSLTQVKELGIAIFNNRNLAADLTQIFEVYWYLGVNNLPYNWKNFYPSYYNTDHPLSINVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIRNASKFVYVSVMNFIPIIYSKAGKILFWPYIEDELRRSAIDRQVSVKLLISCWQRSSFIMRNFLRSIAMLKSKNIDIEVKLFIVPDADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGASINITPDDGLGLRQQLEDIFMRDWNSKYSYELYDTSPTKRCKLLKNMKQCTNDIYCDEIQPEKEIPEYSLE
proteinVaccinia virus (strain Copenhagen)P205372–424octamerMolecule count 849.076 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1321[3]0.003648765–0.1495655 1/AHas uncertainty columnMissing 03sasbdb/entries/78/sasdz78/source/SASDZ78.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)18.01.7Å
i0Guinier0.0129007——
i0P(r)0.01297——
mwExperimental407.0—kDa
mwPorod407.0—kDa
porod_volumePorod491.0—ų
rgGuinier5.030.094Å
rgP(r)5.070.01Å

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 name20 mM Tris pH 7.5, 150 mM NaCl, 0.5mM 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 date2024-10-14Storage / measurement temperature20.0 / 20.0
Exposure time1.0Frames630
Wavelength0.1033Sample-to-detector distance2.0
SourceX-ray synchrotronDetectorEiger 4M
Facility / beamlineSOLEIL / SWING · Saint-Aubin, France
q range0.036 – 1.496Sample volume / flow rate45.0 / 0.3

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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summarysasbdb/entries/78/sasdz78/source/summary.jsondownloaded7379924c027bc1d65ea1bff3c7ccb3366a923bc2863b84a6e27b9773dc54aa06516dDownloadView source fileSource site
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full_entry_zip：source record and ZIP contents (4 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：156 field values
Field pathRaw value
codeSASDZ78
statusPublished
type_of_curveSEC-SAS
angular_unit1/A
project.titleHigh-resolution structure of the vaccinia virus phospholipase D-fold endonuclease K4.
project.publication.titleHigh-resolution structure of the vaccinia virus phospholipase D-fold endonuclease K4.
project.publication.author_listGröger H, Trouba C, Barbaste J, Lacroix G, Schoehn G, Burmeister WP, Tarbouriech N
project.publication.journalJ Mol Biol
project.publication.doi10.1016/j.jmb.2026.169961
project.publication.pmid42526583
project.publication.published_date2026 Jul 29
project.statusreleased
project.submitted_date2026-05-14
project.released_date2026-08-03
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDZ78.out
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDZ78.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.nameEiger 4M
experiment.instrument.detector.resolution75.0
experiment.instrument.nameSOLEIL
experiment.instrument.citySaint-Aubin
experiment.instrument.countryFrance
experiment.instrument.beamline_nameSWING
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_nameVirion nicking-joining enzyme (octamer)
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceGAMANPDNTIAVITETIPIGMQFDKVYLSTFNMWREILSNTTKTLDISSFYWSLSDEVGTNFGTIILNEIVQLPKRGVRVRVAVNKSNKPLKDVERLQMAGVEVRYIDITNILGGVLHTKFWISDNTHIYLGSANMDWRSLTQVKELGIAIFNNRNLAADLTQIFEVYWYLGVNNLPYNWKNFYPSYYNTDHPLSINVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIRNASKFVYVSVMNFIPIIYSKAGKILFWPYIEDELRRSAIDRQVSVKLLISCWQRSSFIMRNFLRSIAMLKSKNIDIEVKLFIVPDADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGASINITPDDGLGLRQQLEDIFMRDWNSKYSYELYDTSPTKRCKLLKNMKQCTNDIYCDEIQPEKEIPEYSLE
experiment.sample.molecule[0].organismVaccinia virus (strain Copenhagen)
experiment.sample.molecule[0].uniprot_codeP20537
experiment.sample.molecule[0].uniprot_range_first2
experiment.sample.molecule[0].uniprot_range_last424
experiment.sample.molecule[0].oligomerizationoctamer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMNPDNTIAVITETIPIGMQFDKVYLSTFNMWREILSNTTKTLDISSFYWSLSDEVGTNFG TIILNEIVQLPKRGVRVRVAVNKSNKPLKDVERLQMAGVEVRYIDITNILGGVLHTKFWI SDNTHIYLGSANMDWRSLTQVKELGIAIFNNRNLAADLTQIFEVYWYLGVNNLPYNWKNF YPSYYNTDHPLSINVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIRNASKFVYVSVMN FIPIIYSKAGKILFWPYIEDELRRSAIDRQVSVKLLISCWQRSSFIMRNFLRSIAMLKSK NIDIEVKLFIVPDADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGASINITPD DGLGLRQQLEDIFMRDWNSKYSYELYDTSPTKRCKLLKNMKQCTNDIYCDEIQPEKEIPE YSLE
experiment.sample.molecule[0].mw49.076
experiment.sample.molecule[0].total_mw392.608
experiment.sample.molecule[0].number_molecules8
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_description
experiment.sample.buffer.name20 mM Tris pH 7.5, 150 mM NaCl, 0.5mM 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.nameOctameric Assembly of the Phospholipase D–Like (PLD-Fold) Nuclease K4 Domain in the Vaccinia Virion Nicking-Joining Enzyme
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_nameIBS
experiment.contributor[0].affiliation[0].addressGrenoble, France
experiment.contributor[0].affiliation[0].full_nameInstitut de Biologie Structurale
experiment.contributor[0].affiliation[0].webpage
experiment.contributor[0].contributor_nameHenri
experiment.contributor[0].contributor_surnameGröger
experiment.contributor[0].orcidhttps://orcid.org/0009-0003-5147-947X
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2024-10-14
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time1.0
experiment.number_of_frames630
experiment.wavelength0.1033
experiment.sample_detector_distance2.0
experiment.concentration_minnull
experiment.concentration_max1.0
experiment.sample_volume45.0
experiment.flow_rate0.3
experiment.s_min0.036
experiment.s_max1.496
experiment.total_exposure_timenull
experiment.seccolumn2
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDZ78_fit1_model1_img.png
fits[0].models[0].softwarePhenix
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
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fits[0].models[0].model_mw382.4
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetryC2
fits[0].models[0].commentFull octamer
fits[0].models[0].user1362
fits[0].fit_unit1/A
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fits[0].softwareCRYSOL
fits[0].chi_square_value0.026
fits[0].p_value0.0023
fits[0].fit_residual_plotSASDZ78_fit1_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDZ78_fit1.fit
fits[0].fit_lognull
fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionMolecular mass calculated from the Porod volume using 0.83 Da∙Å-3 obtained from the protein specific mass of 1,37 g∙cm-3. The sequence of the construct after tag-cleavage is provided.
experiment_descriptionnull
tags[]
intensity_unitnull
experimental_mw407.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw407.0
porod_mw_errornull
pddf_i00.01297
pddf_i0_errornull
guinier_i00.0129007
guinier_i0_errornull
pddf_rg5.07
pddf_rg_error0.01
guinier_rg5.03
guinier_rg_error0.094
pddf_dmax18.0
pddf_dmax_error1.7
porod_volume491.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first25
guinier_point_last37
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDZ78_datloglog_img.png
symmetrynull
last_modified2026-08-03T09:48:39.841183+02:00
bragg_peak[]
manifest.json：34 field values
Field pathRaw value
codeSASDZ78
statussuccess
started_at2026-08-11T15:47:31.233649+00:00
finished_at2026-08-11T15:47:39.230476+00:00
source_last_modified2026-08-03T09:48:39.841183+02:00
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View the complete summary.json source
{
  "code": "SASDZ78",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "High-resolution structure of the vaccinia virus phospholipase D-fold endonuclease K4.",
    "publication": {
      "title": "High-resolution structure of the vaccinia virus phospholipase D-fold endonuclease K4.",
      "author_list": "Gröger H, Trouba C, Barbaste J, Lacroix G, Schoehn G, Burmeister WP, Tarbouriech N",
      "journal": "J Mol Biol",
      "doi": "10.1016/j.jmb.2026.169961",
      "pmid": "42526583",
      "published_date": "2026 Jul 29"
    },
    "status": "released",
    "submitted_date": "2026-05-14",
    "released_date": "2026-08-03"
  },
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      },
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      "country": "France",
      "beamline_name": "SWING",
      "beam_geometry": null,
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          "long_name": "Virion nicking-joining enzyme (octamer)",
          "short_name": null,
          "sequence": "GAMANPDNTIAVITETIPIGMQFDKVYLSTFNMWREILSNTTKTLDISSFYWSLSDEVGTNFGTIILNEIVQLPKRGVRVRVAVNKSNKPLKDVERLQMAGVEVRYIDITNILGGVLHTKFWISDNTHIYLGSANMDWRSLTQVKELGIAIFNNRNLAADLTQIFEVYWYLGVNNLPYNWKNFYPSYYNTDHPLSINVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIRNASKFVYVSVMNFIPIIYSKAGKILFWPYIEDELRRSAIDRQVSVKLLISCWQRSSFIMRNFLRSIAMLKSKNIDIEVKLFIVPDADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGASINITPDDGLGLRQQLEDIFMRDWNSKYSYELYDTSPTKRCKLLKNMKQCTNDIYCDEIQPEKEIPEYSLE",
          "organism": "Vaccinia virus (strain Copenhagen)",
          "uniprot_code": "P20537",
          "uniprot_range_first": 2,
          "uniprot_range_last": 424,
          "oligomerization": "octamer",
          "molecular_type": "protein",
          "uniprot_sequence": "MNPDNTIAVITETIPIGMQFDKVYLSTFNMWREILSNTTKTLDISSFYWSLSDEVGTNFG\nTIILNEIVQLPKRGVRVRVAVNKSNKPLKDVERLQMAGVEVRYIDITNILGGVLHTKFWI\nSDNTHIYLGSANMDWRSLTQVKELGIAIFNNRNLAADLTQIFEVYWYLGVNNLPYNWKNF\nYPSYYNTDHPLSINVSGVPHSVFIASAPQQLCTMERTNDLTALLSCIRNASKFVYVSVMN\nFIPIIYSKAGKILFWPYIEDELRRSAIDRQVSVKLLISCWQRSSFIMRNFLRSIAMLKSK\nNIDIEVKLFIVPDADPPIPYSRVNHAKYMVTDKTAYIGTSNWTGNYFTDTCGASINITPD\nDGLGLRQQLEDIFMRDWNSKYSYELYDTSPTKRCKLLKNMKQCTNDIYCDEIQPEKEIPE\nYSLE",
          "mw": 49.076,
          "total_mw": 392.608,
          "number_molecules": 8,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": ""
        }
      ],
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        "concentration_unit": null,
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        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Octameric Assembly of the Phospholipase D–Like (PLD-Fold) Nuclease K4 Domain in the Vaccinia Virion Nicking-Joining Enzyme",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
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View the complete manifest.json source
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