SASDBB7

Human NEI like DNA glycosylase 1 (NEIL1) bound to DNA

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2019-12-06T13:07:15.624532+01:00

The theoretical MW for this NEIL1/DNA complex is 55.8kDa.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Human NEI like DNA glycosylase 1 (NEIL1) bound to DNA

Concentration1.3 – 2.1 Buffer / pH25mM HEPES 100mM NaCl 1mM DTT / 7.5
Experimental temperature10.0 Facility / beamlineAdvanced Light Source (ALS) / 12.3.1 (SIBYLS)
Wavelength1.127 nmExposure0.2 s × 24

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Endonuclease 8-like 1
View sequence
MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRESVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGKGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKSRKKKSKATQLSPEDRVEDALPPSKAPSRTRRAKRDLPKRTATQRPEGTSLQQDPEAPTVPKKGRRKGRQAASGHCRPRKVKADIPSLEPEGTSASLEHHHHHH
proteinHomo sapiensQ96FI4—–—monomerMolecule count 144.722 kDa
dsDNA
View sequence
GCGTCCAGTCTACCCGCAGGTCCAGATGG
DNA———–—monomerMolecule count 12.424 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1920[3]0.016445–0.528544 1/AHas uncertainty columnMissing 00sasbdb/entries/b7/sasdbb7/source/SASDBB7.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)17.51.6Å
i0Guinier309.02.09—
i0P(r)337.06.402—
mwExperimental61.5—kDa
mwGuinier I(0)56.90.385kDa
mwPorod54.142—kDa
porod_volumePorod92.04—ų
rgGuinier3.30.178Å
rgP(r)4.10.123Å

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 name25mM HEPES 100mM NaCl 1mM 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 date2016-01-20Storage / measurement temperature4.0 / 10.0
Exposure time0.2Frames24
Wavelength1.127Sample-to-detector distance1.4
SourceX-ray synchrotronDetectorPilatus3 X 2M
Facility / beamlineAdvanced Light Source (ALS) / 12.3.1 (SIBYLS) · Berkeley, CA, USA
q range0.164 – 5.285Sample 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:173 field values
Field pathRaw value
codeSASDBB7
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleDestabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase.
project.publication.titleDestabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase.
project.publication.author_listPrakash A, Moharana K, Wallace SS, Doublié S
project.publication.journalNucleic Acids Res
project.publication.doi10.1093/nar/gkw1282
project.publication.pmid27994037
project.publication.published_date2017 Mar 17
project.statusreleased
project.submitted_date2016-11-04
project.released_date2017-01-03
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDBB7.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDBB7.dat
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intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBB7_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBB7_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBB7_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDBB7.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus3 X 2M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameAdvanced Light Source (ALS)
experiment.instrument.cityBerkeley, CA
experiment.instrument.countryUSA
experiment.instrument.beamline_name12.3.1 (SIBYLS)
experiment.instrument.beam_geometry
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_nameEndonuclease 8-like 1
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRESVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGKGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKSRKKKSKATQLSPEDRVEDALPPSKAPSRTRRAKRDLPKRTATQRPEGTSLQQDPEAPTVPKKGRRKGRQAASGHCRPRKVKADIPSLEPEGTSASLEHHHHHH
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeQ96FI4
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLIL SPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRF GRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRA EILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLG GKGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKSRKKKS KATQLSPEDRVEDALPPSKAPSRTRRAKRDLPKRTATQRPEGTSLQQDPEAPTVPKKGRR KGRQAASGHCRPRKVKADIPSLEPEGTSAS
experiment.sample.molecule[0].mw44.722
experiment.sample.molecule[0].total_mw44.722
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.molecule[1].long_namedsDNA
experiment.sample.molecule[1].short_namenull
experiment.sample.molecule[1].sequenceGCGTCCAGTCTACC CGCAGGTCCAGATGG
experiment.sample.molecule[1].organismnull
experiment.sample.molecule[1].uniprot_codenull
experiment.sample.molecule[1].uniprot_range_firstnull
experiment.sample.molecule[1].uniprot_range_lastnull
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeDNA
experiment.sample.molecule[1].uniprot_sequencenull
experiment.sample.molecule[1].mw2.424
experiment.sample.molecule[1].total_mw2.424
experiment.sample.molecule[1].number_molecules1
experiment.sample.molecule[1].complex_stateFalse
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name25mM HEPES 100mM NaCl 1mM 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.nameHuman NEI like DNA glycosylase 1 (NEIL1) bound to DNA
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].addressBurlington, VT, USA
experiment.contributor[0].affiliation[0].full_nameUniversity of Vermont
experiment.contributor[0].affiliation[0].webpagehttps://www.uvm.edu/
experiment.contributor[0].contributor_nameKedar
experiment.contributor[0].contributor_surnameMoharana
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-01-20
experiment.storage_temperature4.0
experiment.cell_temperature10.0
experiment.exposure_time0.2
experiment.number_of_frames24
experiment.wavelength1.127
experiment.sample_detector_distance1.4
experiment.concentration_min1.3
experiment.concentration_max2.1
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.164
experiment.s_max5.285
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareDAMMIN
fits[0].models[0].pdb_link[]
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fits[0].models[0].model_mwnull
fits[0].models[0].bead_radius4.5
fits[0].models[0].lognull
fits[0].models[0].symmetry
fits[0].models[0].comment
fits[0].models[0].user177
fits[0].fit_unit1/A
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fits[0].softwarenull
fits[0].chi_square_value0.542
fits[0].p_value0.0
fits[0].fit_residual_plotSASDBB7_fit1_fitresiduals_img.png
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fits[0].fit_lognull
fits[0].software_versionnull
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionATSAS GNOM 5.0
i0_calibration_standardnull
descriptionThe theoretical MW for this NEIL1/DNA complex is 55.8kDa.
experiment_descriptionnull
tags[]
intensity_unitnull
experimental_mw61.5
experimental_mw_errornull
guinier_i0_mw56.9
guinier_i0_mw_error0.385
porod_mw54.142
porod_mw_errornull
pddf_i0337.0
pddf_i0_error6.402
guinier_i0309.0
guinier_i0_error2.09
pddf_rg4.1
pddf_rg_error0.123
guinier_rg3.3
guinier_rg_error0.178
pddf_dmax17.5
pddf_dmax_error1.6
porod_volume92.04
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first11
guinier_point_last42
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDBB7_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDBB7
statussuccess
started_at2026-08-11T16:37:41.140532+00:00
finished_at2026-08-11T16:37:49.873428+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDBB7",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase.",
    "publication": {
      "title": "Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase.",
      "author_list": "Prakash A, Moharana K, Wallace SS, Doublié S",
      "journal": "Nucleic Acids Res",
      "doi": "10.1093/nar/gkw1282",
      "pmid": "27994037",
      "published_date": "2017 Mar 17"
    },
    "status": "released",
    "submitted_date": "2016-11-04",
    "released_date": "2017-01-03"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBB7.out",
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  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBB7_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBB7_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBB7_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBB7.sascif",
  "experiment": {
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        "resolution": 172.0
      },
      "name": "Advanced Light Source (ALS)",
      "city": "Berkeley, CA",
      "country": "USA",
      "beamline_name": "12.3.1 (SIBYLS)",
      "beam_geometry": "",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
      "sample_path_length": null,
      "line_collimation_slitlength": null,
      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Endonuclease 8-like 1",
          "short_name": null,
          "sequence": "MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRESVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGKGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKSRKKKSKATQLSPEDRVEDALPPSKAPSRTRRAKRDLPKRTATQRPEGTSLQQDPEAPTVPKKGRRKGRQAASGHCRPRKVKADIPSLEPEGTSASLEHHHHHH",
          "organism": "Homo sapiens",
          "uniprot_code": "Q96FI4",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "protein",
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View the complete manifest.json source
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