SASDFZ3

Escherichia coli YjhC

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2019-12-06T13:07:15.624532+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Escherichia coli YjhC

Concentration— – 8.0 Buffer / pH20 mM Tris, 150 mM NaCl, 0.1 % (w/v) sodium azide, 5 % (v/v) glycerol / 8.0
Experimental temperature12.0 Facility / beamlineAustralian Synchrotron / SAXS/WAXS
Wavelength0.10332 nmExposure1.0 s × 400

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Escherichia coli YjhC
View sequence
>YJHCHHHHHHSSGLVPRGSMINYGVVGVGYFGAELARFMNMHDNAKITCVYDPENGENIARELQCINMSSLDALVSSKLVDCVIVATPNYLHKEPVIKAAKNKKHVFCEKPIALSYEDCVDMVKACKEAGVTFMAGHIMNFFNGVQYARKLIKEGVIGEILSCHTKRNGWENKQERLSWKKMKEQSGGHLYHHIHELDCVQHLLGEIPETVTMIGGNLAHSGPGFGNEDDMLFMTLEFPSGKLATLEWGSAFNWPEHYVIINGTKGSIKIDMQETAGSLRIGGQTKHFLVHETQEEDDDRRKGNMTSEMDGAIAYGHPGKKTPLWLASLIRKETLFLHNILCGAKPEEDYIDLLNGEAAMSAIATADAATLSRSQDRKVKISEIIKHTSVM
proteinEscherichia coli——–—dimerMolecule count 243.048 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1670[3]0.012069–0.50014 1/AHas uncertainty columnMissing 02sasbdb/entries/z3/sasdfz3/source/SASDFZ3.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)10.71—Å
i0Guinier0.0490.00011/cm
i0P(r)0.049251.424e-051/cm
mwExperimental84.5—kDa
mwPorod81.0—kDa
porod_volumePorod130.0—ų
rgGuinier3.1140.036Å
rgP(r)3.180.013Å

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, 150 mM NaCl, 0.1 % (w/v) sodium azide, 5 % (v/v) glycerolBuffer concentration—
pH8.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2018-04-12Storage / measurement temperature4.0 / 12.0
Exposure time1.0Frames400
Wavelength0.10332Sample-to-detector distance1.6
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineAustralian Synchrotron / SAXS/WAXS · Melbourne, Australia
q range0.121 – 5.001Sample 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

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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:159 field values
Field pathRaw value
codeSASDFZ3
statusPublished
type_of_curveSEC-SAS
angular_unit1/A
project.titleOn the structure and function of Escherichia coli YjhC: an oxidoreductase involved in bacterial sialic acid metabolism.
project.publication.titleOn the structure and function of Escherichia coli YjhC: an oxidoreductase involved in bacterial sialic acid metabolism.
project.publication.author_listHorne CR, Kind L, Davies JS, Dobson RCJ
project.publication.journalProteins
project.publication.doi10.1002/prot.25846
project.publication.pmid31697432
project.publication.published_date2019 Nov 7
project.statusreleased
project.submitted_date2019-03-13
project.released_date2019-11-12
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experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameAustralian Synchrotron
experiment.instrument.cityMelbourne
experiment.instrument.countryAustralia
experiment.instrument.beamline_nameSAXS/WAXS
experiment.instrument.beam_geometryPoint
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourceTrue
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experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
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experiment.sample.molecule[0].long_nameEscherichia coli YjhC
experiment.sample.molecule[0].short_nameYjhC
experiment.sample.molecule[0].sequence>YjhC HHHHHHSSGLVPRGSMINYGVVGVGYFGAELARFMNMHDNAKITCVYDPENGENIARELQCINMSSLDALVSSKLVDCVIVATPNYLHKEPVIKAAKNKKHVFCEKPIALSYEDCVDMVKACKEAGVTFMAGHIMNFFNGVQYARKLIKEGVIGEILSCHTKRNGWENKQERLSWKKMKEQSGGHLYHHIHELDCVQHLLGEIPETVTMIGGNLAHSGPGFGNEDDMLFMTLEFPSGKLATLEWGSAFNWPEHYVIINGTKGSIKIDMQETAGSLRIGGQTKHFLVHETQEEDDDRRKGNMTSEMDGAIAYGHPGKKTPLWLASLIRKETLFLHNILCGAKPEEDYIDLLNGEAAMSAIATADAATLSRSQDRKVKISEIIKHTSVM
experiment.sample.molecule[0].organismEscherichia coli
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw43.048
experiment.sample.molecule[0].total_mw86.096
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_descriptionnull
experiment.sample.buffer.name20 mM Tris, 150 mM NaCl, 0.1 % (w/v) sodium azide, 5 % (v/v) glycerol
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experiment.sample.purity_methodnull
experiment.sample.nameEscherichia coli YjhC
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].addressNew Zealand
experiment.contributor[0].affiliation[0].full_nameUniversity of Canterbury
experiment.contributor[0].affiliation[0].webpagehttps://www.canterbury.ac.nz/
experiment.contributor[0].contributor_nameChris
experiment.contributor[0].contributor_surnameHorne
experiment.contributor[0].orcid
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experiment.concentration_unitnull
experiment.date2018-04-12
experiment.storage_temperature4.0
experiment.cell_temperature12.0
experiment.exposure_time1.0
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experiment.wavelength0.10332
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fits[0].models[0].pdb_link[0].pdb_code6o15
fits[0].models[0].pdb_link[0].ext_code6O15
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fits[0].models[0].commentnull
fits[0].models[0].user405
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fits[0].p_value0.0
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fits[0].description
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pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data of the oxidoreductase YjhC from Escherichia coli in 20 mM Tris, 150 mM NaCl, 0.1 % (w/v) sodium azide, 5 % (v/v) glycerol, pH 8 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a PILATUS 1M detector at a sample-detector distance of 1.6 m, providing a q range of 0.06-5 nm-1 and at a wavelength of λ = 0.10332 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Coflow size-exclusion chromatography-SAXS (SEC-SAXS) was used to minimize sample dilution and maximize signal to noise (Kirby et al., 2016). 80 µl of purified YjhC protein at 8 mg/ml was injected onto an Superdex S200 Increase 5/150 GL (GE Healthcare) at a flow rate of 0.45 ml/min. Scattering data was collected in 1 second exposures over a total of 400 frames, using a 1.5 mm glass capillary, at 12 °C. 2D intensity plots were radially averaged, normalised to sample transmission, and background subtracted using the Scatterbrain software package (Australian Synchrotron). Analysis of the scattering data was performed using the ATSAS software package (version 2.8.4). PrimusQT was used to perform the Guinier analysis, Kratky analysis, and to generate the pairwise distribution function P(r), calculated using an indirect Fourier transform using GNOM. The molecular mass of the samples was estimated using the SAXS-MoW2 package (Fischer et al., 2010), while CRYSOL was used to evaluate the experimental solution scattering with the calculated scattering from the atomic coordinates of the high-resolution structure of YjhC.
tags[]
intensity_unit1/cm
experimental_mw84.5
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw81.0
porod_mw_errornull
pddf_i00.04925
pddf_i0_error1.424e-05
guinier_i00.049
guinier_i0_error0.0001
pddf_rg3.18
pddf_rg_error0.013
guinier_rg3.114
guinier_rg_error0.036
pddf_dmax10.71
pddf_dmax_errornull
porod_volume130.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first5
guinier_point_last41
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDFZ3_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDFZ3
statussuccess
started_at2026-08-11T14:11:38.106981+00:00
finished_at2026-08-11T14:11:53.404431+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
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  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
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    "title": "On the structure and function of Escherichia coli YjhC: an oxidoreductase involved in bacterial sialic acid metabolism.",
    "publication": {
      "title": "On the structure and function of Escherichia coli YjhC: an oxidoreductase involved in bacterial sialic acid metabolism.",
      "author_list": "Horne CR, Kind L, Davies JS, Dobson RCJ",
      "journal": "Proteins",
      "doi": "10.1002/prot.25846",
      "pmid": "31697432",
      "published_date": "2019 Nov 7"
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          "long_name": "Escherichia coli YjhC",
          "short_name": "YjhC",
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View the complete manifest.json source
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