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SASDAB6

Xylose Isomerase

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2023-06-21T07:56:39.492710+02:00

The data displayed at the top of the entry, and the subsequent ab inito and atomic model fit, are data derived from averaging 20 individual frames. The individual 20 data frames used for the averaging are also displayed, with the respective atomic-model fits (CRYSOL; PDB 4E3V).

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Xylose Isomerase

Concentration— – 5.76 Buffer / pH20 mM HEPES 200 mM Na2SO4 50 mM K2SO4 500 % v/v D2O 1 mM MgCl2 / 6.6
Experimental temperature10.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.12 nmExposure— s × 20

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Xylose Isomerase
View sequence
>4E3V|PDBID|COMPLETE|SEQUENCEMNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARGMNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARGMNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARGMNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG
proteinStreptomyces rubiginosus——–—tetramerMolecule count 443.2 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11297[3]0.0906896–3.5006 1/nmHas uncertainty columnMissing 075sasbdb/entries/b6/sasdab6/source/SASDAB6.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)9.1—nm
i0Guinier3733.8——
i0P(r)3770.0——
mwExperimental149.0—kDa
mwGuinier I(0)149.0—kDa
mwPorod137.3—kDa
porod_volumePorod233.5—nm³
rgGuinier3.21—nm
rgP(r)3.24—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 name20 mM HEPES 200 mM Na2SO4 50 mM K2SO4 500 % v/v D2O 1 mM MgCl2Buffer concentration20.0 mM
pH6.6AdditivesNa2SO4 200.000 mM, K2SO4 50.000 mM, D2O 50.000 % v/v, MgCl2 1.000 mM
Buffer descriptionpD = 7.0
Purity measurement methodCrystalline, Hampton ResearchExtinction coefficient1.075
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2013-12-10Storage / measurement temperature10.0 / 10.0
Exposure time—Frames20
Wavelength0.12Sample-to-detector distance3.1
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.091 – 3.501Sample 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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pddf：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：416 field values
Field pathRaw value
codeSASDAB6
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleCorrelation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.
project.publication.titleCorrelation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.
project.publication.author_listFranke D, Jeffries CM, Svergun DI
project.publication.journalNat Methods
project.publication.doi10.1038/nmeth.3358
project.publication.pmid25849637
project.publication.published_date2015 May
project.statusreleased
project.submitted_datenull
project.released_date2015-05-01
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDAB6.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDAB6.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAB6_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAB6_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAB6_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAB6_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDAB6.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_nameXylose Isomerase
experiment.sample.molecule[0].short_nameGI Glucose isomerase
experiment.sample.molecule[0].sequence>4E3V|PDBID|COMPLETE|SEQUENCE MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALD DTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKE AFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK LFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAF RADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALD DTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKE AFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK LFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAF RADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALD DTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKE AFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK LFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAF RADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALD DTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKE AFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK LFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAF RADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG
experiment.sample.molecule[0].organismStreptomyces rubiginosus
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationtetramer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw43.2
experiment.sample.molecule[0].total_mw172.8
experiment.sample.molecule[0].number_molecules4
experiment.sample.molecule[0].complex_statenull
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.buffer.name20 mM HEPES 200 mM Na2SO4 50 mM K2SO4 500 % v/v D2O 1 mM MgCl2
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentpD = 7.0
experiment.sample.buffer.additiveNa2SO4 200.000 mM, K2SO4 50.000 mM, D2O 50.000 % v/v, MgCl2 1.000 mM
experiment.sample.buffer.concentration20.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph6.6
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodCrystalline, Hampton Research
experiment.sample.nameXylose Isomerase
experiment.sample.ext_coefficient1.075
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_nameDaniel
experiment.contributor[0].contributor_surnameFranke
experiment.contributor[0].orcidnull
experiment.contributor[1].affiliation[0].short_nameEMBL-Hamburg
experiment.contributor[1].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[1].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[1].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[1].contributor_nameCy M
experiment.contributor[1].contributor_surnameJeffries
experiment.contributor[1].orcidnull
experiment.contributor[2].affiliation[0].short_nameEMBL-Hamburg
experiment.contributor[2].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[2].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[2].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[2].contributor_nameDmitri
experiment.contributor[2].contributor_surnameSvergun
experiment.contributor[2].orcidnull
experiment.concentration_methodA280 nm
experiment.concentration_unitnull
experiment.date2013-12-10
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_timenull
experiment.number_of_frames20
experiment.wavelength0.12
experiment.sample_detector_distance3.1
experiment.concentration_minnull
experiment.concentration_max5.76
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.091
experiment.s_max3.501
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDAB6_fit1_model1_img.png
fits[0].models[0].softwareDAMMIF
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modeldummy
fits[0].models[0].software_version
fits[0].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDAB6_fit1_model1.pdb
fits[0].models[0].model_mw140.5
fits[0].models[0].bead_radius1.9
fits[0].models[0].loghttps://www.sasbdb.org/media/log_files/6.log
fits[0].models[0].symmetryP4
fits[0].models[0].comment
fits[0].models[0].user9
fits[0].fit_unit1/A
fits[0].fit_plothttps://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAB6_fit1_fixed_fit_img.png
fits[0].softwarenull
fits[0].chi_square_value1.354896
fits[0].p_value0.0
fits[0].fit_residual_plotSASDAB6_fit1_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDAB6_fit1.fir
fits[0].fit_lognull
fits[0].software_versionnull
fits[0].descriptionnull
fits[1].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDAB6_fit2_model1_img.png
fits[1].models[0].softwareCRYSOL
fits[1].models[0].pdb_link[0].pdb_code4e3v
fits[1].models[0].pdb_link[0].ext_code4e3v
fits[1].models[0].pdb_link[0].ext_typepdb
fits[1].models[0].pdb_link[0].difference_with_modelnull
fits[1].models[0].model_titlenull
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i0_calibration_standardBSA
descriptionThe data displayed at the top of the entry, and the subsequent ab inito and atomic model fit, are data derived from averaging 20 individual frames. The individual 20 data frames used for the averaging are also displayed, with the respective atomic-model fits (CRYSOL; PDB 4E3V).
experiment_descriptionX-ray synchrotron radiation scattering data from solutions of Xylose Isomerase in 20 mM HEPES, 200 mM Na2SO4, 50 mM K2SO4, 50% v/v D2O, 1 mM MgCl2 mM, pH 6.6 were collected on the P12 beam line at Petra-III (Hamburg, Germany) using a Pilatus 2M detector (I(s) vs s, where s = 4π sin θ/λ; 2θ is the scattering angle and λ = 0.12 nm). One solute concentration at 5.76 mg/ml was measured using a total exposure time of 1 second (20 x 0.050 second frames). The data were normalized to the intensity of the transmitted beam and radially averaged. Scattering contributions from the matched solvent blank were subtracted and the resulting 1D scattering data were scaled to protein concentration. The data presented in this entry were obtained from a single concentration scattering curve.
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intensities_log_log_plotSASDAB6_datloglog_img.png
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last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json：36 field values
Field pathRaw value
codeSASDAB6
statussuccess
started_at2026-08-11T15:05:27.704952+00:00
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View the complete summary.json source
{
  "code": "SASDAB6",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.",
    "publication": {
      "title": "Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.",
      "author_list": "Franke D, Jeffries CM, Svergun DI",
      "journal": "Nat Methods",
      "doi": "10.1038/nmeth.3358",
      "pmid": "25849637",
      "published_date": "2015 May"
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