SASDXF3

Multi-domain human O-GlcNAcase

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2025-11-26T16:04:08.969516+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Multi-domain human O-GlcNAcase

Concentration— – 2.5 Buffer / pH25 mM Tris buffer, 150 mM NaCl, and 0.5 mM TCEP / 7.5
Experimental temperature20.0 Facility / beamlineDepartment of Chemistry, iNANO building, Aarhus Uinversity / Bruker Nanostar w Excillum source
Wavelength1.34 nmExposure1800.0 s × 1

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Protein O-GlcNAcase
View sequence
RFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDDIDHNMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKNMNGVRKDVVMTDSEDSTVSIQIKLENEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSRGGGGSGGGGSVTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSVVSVNCKGKDSEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRSHSSAQFLIGDQEPWAFRGGLAGEFQRLLPIDGANDLFFQPPPLTPTSKVYTIRPYFPKDEASVYKICREMYDDGVGLPFQSQPDLIGDKLVGGLLSLSLDYCFVLEDEDGICGYALGTVDVTPFIKKCKISWIPFMQEKYTKPNGDKELSEAEKIMLSFHEEQEVLPETFLANFPSLIKMDIHKKVTDPSVAKSMMACLLSSLKANGSRGAFCEVRPDDKRILEFYSKLGCFEIAKMEGFPKDVVILGRSL
proteinHomo sapiensO6050211–766dimerMolecule count 281.457 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1105[4]0.00981300045–0.415697008 1/AHas uncertainty columnMissing 00sasbdb/entries/f3/sasdxf3/source/SASDXF3.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)18.91—Å
i0Guinier0.527208—1/cm
i0P(r)0.5284—1/cm
mwExperimental278.0—kDa
mwPorod278.0—kDa
porod_volumePorod443.0—ų
rgGuinier5.4350.301Å
rgP(r)5.52—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

Fit 1 · Other wlsq_symxv7XXLd

χ²: 0.8276CorMap p: 0.0Unit: 1/A
ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—atomicAlphaFold P1169.9—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 buffer, 150 mM NaCl, and 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 date2023-06-22Storage / measurement temperature5.0 / 20.0
Exposure time1800.0Frames1
Wavelength1.34Sample-to-detector distance0.9
SourceX-ray in houseDetectorVÅNTEC-2000
Facility / beamlineDepartment of Chemistry, iNANO building, Aarhus Uinversity / Bruker Nanostar w Excillum source · Aarhus C, Denmark
q range0.098 – 4.157Sample 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

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full_entry_zip:source record and ZIP contents (4 items)
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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
codeSASDXF3
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleMulti-domain O-GlcNAcase structures reveal allosteric regulatory mechanisms
project.publication.titleMulti-domain O-GlcNAcase structures reveal allosteric regulatory mechanisms
project.publication.author_listHansen S, Bartual S, Yuan H, Raimi O, Gorelik A, Ferenbach A, Lytje K, Pedersen J, Drace T, Boesen T, van Aalten D
project.publication.journalNature Communications
project.publication.doi10.1038/s41467-025-63893-2
project.publication.pmidnull
project.publication.published_date2025 Oct 03
project.statusreleased
project.submitted_date2025-07-14
project.released_date2025-09-11
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDXF3.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDXF3.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXF3_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXF3_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDXF3_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXF3_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDXF3.sascif
experiment.instrument.detector.typeMikroGap gas detector
experiment.instrument.detector.nameVÅNTEC-2000
experiment.instrument.detector.resolution200.0
experiment.instrument.nameDepartment of Chemistry, iNANO building, Aarhus Uinversity
experiment.instrument.cityAarhus C
experiment.instrument.countryDenmark
experiment.instrument.beamline_nameBruker Nanostar w Excillum source
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_nameProtein O-GlcNAcase
experiment.sample.molecule[0].short_nameh-OGA
experiment.sample.molecule[0].sequenceRFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDDIDHNMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKNMNGVRKDVVMTDSEDSTVSIQIKLENEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSRGGGGSGGGGSVTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSVVSVNCKGKDSEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRSHSSAQFLIGDQEPWAFRGGLAGEFQRLLPIDGANDLFFQPPPLTPTSKVYTIRPYFPKDEASVYKICREMYDDGVGLPFQSQPDLIGDKLVGGLLSLSLDYCFVLEDEDGICGYALGTVDVTPFIKKCKISWIPFMQEKYTKPNGDKELSEAEKIMLSFHEEQEVLPETFLANFPSLIKMDIHKKVTDPSVAKSMMACLLSSLKANGSRGAFCEVRPDDKRILEFYSKLGCFEIAKMEGFPKDVVILGRSL
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeO60502
experiment.sample.molecule[0].uniprot_range_first11
experiment.sample.molecule[0].uniprot_range_last766
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMVQKESQATLEERESELSSNPAASAGASLEPPAAPAPGEDNPAGAGGAAVAGAAGGARRF LCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLM TLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDDIDHNM CAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEK LLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRS TELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRKDVVMTDSEDSTVSIQIKLE NEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSRQVAHSGAKASVVDGTPLVAA PSLNATTVVTTVYQEPIMSQGAALSGEPTTLTKEEEKKQPDEEPMDMVVEKQEETDHKND NQILSEIVEAKMAEELKPMDTDKESIAESKSPEMSMQEDCISDIAPMQTDEQTNKEQFVP GPNEKPLYTAEPVTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSVVSVNCKGKD SEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQW LGCRSHSSAQFLIGDQEPWAFRGGLAGEFQRLLPIDGANDLFFQPPPLTPTSKVYTIRPY FPKDEASVYKICREMYDDGVGLPFQSQPDLIGDKLVGGLLSLSLDYCFVLEDEDGICGYA LGTVDVTPFIKKCKISWIPFMQEKYTKPNGDKELSEAEKIMLSFHEEQEVLPETFLANFP SLIKMDIHKKVTDPSVAKSMMACLLSSLKANGSRGAFCEVRPDDKRILEFYSKLGCFEIA KMEGFPKDVVILGRSL
experiment.sample.molecule[0].mw81.457
experiment.sample.molecule[0].total_mw162.914
experiment.sample.molecule[0].number_molecules2
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.name25 mM Tris buffer, 150 mM NaCl, and 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.nameMulti-domain human O-GlcNAcase
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].addressAarhus, Denmark
experiment.contributor[0].affiliation[0].full_nameAarhus University
experiment.contributor[0].affiliation[0].webpagehttp://www.au.dk
experiment.contributor[0].contributor_nameJan Skov
experiment.contributor[0].contributor_surnamePedersen
experiment.contributor[0].orcidhttp://orcid.org/0000-0002-7768-0206
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2023-06-22
experiment.storage_temperature5.0
experiment.cell_temperature20.0
experiment.exposure_time1800.0
experiment.number_of_frames1
experiment.wavelength1.34
experiment.sample_detector_distance0.9
experiment.concentration_minnull
experiment.concentration_max2.5
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.098
experiment.s_max4.157
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDXF3_fit1_model1_img.png
fits[0].models[0].softwareAlphaFold
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelatomic
fits[0].models[0].software_versionnull
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fits[0].models[0].model_mw169.9
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetryP1
fits[0].models[0].commentnull
fits[0].models[0].user560
fits[0].fit_unit1/A
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fits[0].softwareOther
fits[0].chi_square_value0.8276
fits[0].p_value0.0
fits[0].fit_residual_plotSASDXF3_fit1_fitresiduals_img.png
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fits[0].fit_lognull
fits[0].software_versionwlsq_symxv7XXLd
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[]
intensity_unit1/cm
experimental_mw278.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw278.0
porod_mw_errornull
pddf_i00.5284
pddf_i0_errornull
guinier_i00.527208
guinier_i0_errornull
pddf_rg5.52
pddf_rg_errornull
guinier_rg5.435
guinier_rg_error0.301
pddf_dmax18.91
pddf_dmax_errornull
porod_volume443.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first5
guinier_point_last18
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDXF3_datloglog_img.png
symmetrynull
last_modified2025-11-26T16:04:08.969516+01:00
bragg_peak[]
manifest.json:34 field values
Field pathRaw value
codeSASDXF3
statussuccess
started_at2026-08-11T15:09:20.529136+00:00
finished_at2026-08-11T15:09:27.815125+00:00
source_last_modified2025-11-26T16:04:08.969516+01:00
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View the complete summary.json source
{
  "code": "SASDXF3",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Multi-domain O-GlcNAcase structures reveal allosteric regulatory mechanisms",
    "publication": {
      "title": "Multi-domain O-GlcNAcase structures reveal allosteric regulatory mechanisms",
      "author_list": "Hansen S, Bartual S, Yuan H, Raimi O, Gorelik A, Ferenbach A, Lytje K, Pedersen J, Drace T, Boesen T, van Aalten D",
      "journal": "Nature Communications",
      "doi": "10.1038/s41467-025-63893-2",
      "pmid": null,
      "published_date": "2025 Oct 03"
    },
    "status": "released",
    "submitted_date": "2025-07-14",
    "released_date": "2025-09-11"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDXF3.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDXF3.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXF3_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXF3_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDXF3_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXF3_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDXF3.sascif",
  "experiment": {
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      "detector": {
        "type": "MikroGap gas detector",
        "name": "VÅNTEC-2000",
        "resolution": 200.0
      },
      "name": "Department of Chemistry, iNANO building, Aarhus Uinversity",
      "city": "Aarhus C",
      "country": "Denmark",
      "beamline_name": "Bruker Nanostar w Excillum source",
      "beam_geometry": null,
      "type_of_source": "X-ray in house",
      "point_source": null,
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      "xray_energy": null,
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    },
    "sample": {
      "molecule": [
        {
          "long_name": "Protein O-GlcNAcase",
          "short_name": "h-OGA",
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          "uniprot_code": "O60502",
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            "webpage": "http://www.au.dk"
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}
View the complete manifest.json source
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