SASDBF4

Wild-type LytA (N-His6) with choline

Data type: SASBDB experimental data Status: Published Curve type: Extrapolated to infinite dilution Last updated: 2023-05-25T11:21:52.654103+02:00

The full-length LytA dimer adopts a rigid V-shaped scaffold with the two amidase domains in the trans configuration.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Wild-type LytA (N-His6) with choline

Concentration1.0 – 5.0 mg/mlBuffer / pH20 mM Tris 150 mM NaCl 5 mM choline chloride 1 µM ZnCl2 / 7.5
Experimental temperature10.0 Facility / beamlineDORIS III, DESY / EMBL X33
Wavelength0.15 nmExposure15.0 s × 8

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Lytic Amidase with cholineproteinStreptococcus pneumoniae——–—dimerMolecule count 237.4 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
12138[3]0.176504–6.02412 1/nmHas uncertainty columnMissing 099sasbdb/entries/f4/sasdbf4/source/SASDBF4.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)15.01.5nm
i0Guinier77.9——
i0P(r)78.720.231—
mwExperimental75.08.0kDa
mwGuinier I(0)66.0—kDa
mwPorod72.07.0kDa
porod_volumePorod115.2—nm³
rgGuinier4.850.5nm
rgP(r)4.953—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 Tris 150 mM NaCl 5 mM choline chloride 1 µM ZnCl2Buffer concentration20.0 mM
pH7.5Additives150 mM NaCl, 5 mM choline chloride, 1 µM ZnCl2
Buffer descriptionwith choline
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuterationFalse / —

Acquisition Conditions and Instrument

Measurement date2011-07-02Storage / measurement temperature— / 10.0
Exposure time15.0Frames8
Wavelength0.15Sample-to-detector distance2.7
SourceX-ray synchrotronDetectorPilatus 1M-W
Facility / beamlineDORIS III, DESY / EMBL X33 · Hamburg, Germany
q range0.177 – 6.024Sample 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:179 field values
Field pathRaw value
codeSASDBF4
statusPublished
type_of_curveExtrapolated to infinite dilution
angular_unit1/nm
project.titleStructural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.
project.publication.titleStructural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.
project.publication.author_listMellroth P, Sandalova T, Kikhney A, Vilaplana F, Hesek D, Lee M, Mobashery S, Normark S, Svergun D, Henriques-Normark B, Achour A
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project.publication.doi10.1128/mBio.01120-13
project.publication.pmid24520066
project.publication.published_date2014 Feb 11
project.statusreleased
project.submitted_date2014-02-11
project.released_date2016-03-16
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experiment.sample.molecule[0].sequencenull
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experiment.sample.molecule[0].uniprot_codenull
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experiment.sample.buffer.concentration_unitmM
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experiment.contributor[0].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[0].contributor_nameAl
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i0_calibration_standardBSA
descriptionThe full-length LytA dimer adopts a rigid V-shaped scaffold with the two amidase domains in the trans configuration.
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last_modified2023-05-25T11:21:52.654103+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDBF4
statussuccess
started_at2026-08-11T14:22:19.444952+00:00
finished_at2026-08-11T14:22:33.428791+00:00
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View the complete summary.json source
{
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  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.",
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