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SASDBJ4

Wild-type LytA choline-binding domain

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2023-05-25T11:21:52.654103+02:00

The CBD of wt-LytA forms a dimer in solution, in line with results from the crystal structure.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Wild-type LytA choline-binding domain

Concentration0.7 – 6.92 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 choline-binding domainproteinStreptococcus pneumoniae—173–318dimerMolecule count 217.3 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
12170[3]0.0854979–6.03197 1/nmHas uncertainty columnMissing 047sasbdb/entries/j4/sasdbj4/source/SASDBJ4.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)10.01.0nm
i0Guinier29.84——
i0P(r)27.65——
mwExperimental31.03.0kDa
mwGuinier I(0)31.0—kDa
mwPorod30.81—kDa
porod_volumePorod49.3—nm³
rgGuinier3.340.27nm
rgP(r)3.096—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

Fit 1 · —

χ²: 2.7556CorMap p: 3.1e-05Unit: 1/A

Fit data Fit plot

ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—atomicSASREF 7P234.58—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 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 date2011-12-11Storage / measurement temperature10.0 / 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 range0.085 – 6.032Sample 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：156 field values
Field pathRaw value
codeSASDBJ4
statusPublished
type_of_curveSingle concentration
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
project.publication.journalMBio
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.instrument.detector.namePilatus 1M-W
experiment.instrument.detector.resolution0.172
experiment.instrument.nameDORIS III, DESY
experiment.instrument.cityHamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL X33
experiment.instrument.beam_geometry0.60
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
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experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameLytic Amidase choline-binding domain
experiment.sample.molecule[0].short_nameLytA CBD
experiment.sample.molecule[0].sequencenull
experiment.sample.molecule[0].organismStreptococcus pneumoniae
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_first173
experiment.sample.molecule[0].uniprot_range_last318
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw17.3
experiment.sample.molecule[0].total_mw17.3
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 5 mM choline chloride 1 µM ZnCl2
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentwith choline
experiment.sample.buffer.additive150 mM NaCl, 5 mM choline chloride, 1 µM ZnCl2
experiment.sample.buffer.concentration20.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameWild-type LytA choline-binding domain
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
experiment.sample.deuterationnull
experiment.sample.mixtureFalse
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_nameAl
experiment.contributor[0].contributor_surnameKikhney
experiment.contributor[0].orcidhttps://orcid.org/0000-0003-1321-3956
experiment.concentration_methodnull
experiment.concentration_unitmg/ml
experiment.date2011-12-11
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time15.0
experiment.number_of_frames8
experiment.wavelength0.15
experiment.sample_detector_distance2.7
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pddf_softwareATSAS GNOM
pddf_software_versionGNOM 5
i0_calibration_standardBSA
descriptionThe CBD of wt-LytA forms a dimer in solution, in line with results from the crystal structure.
experiment_descriptionnull
tags[0]X33
intensity_unitnull
experimental_mw31.0
experimental_mw_error3.0
guinier_i0_mw31.0
guinier_i0_mw_errornull
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porod_mw_errornull
pddf_i027.65
pddf_i0_errornull
guinier_i029.84
guinier_i0_errornull
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pddf_rg_errornull
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porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
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guinier_point_last112
pddf_point_first34
pddf_point_last1152
i0_calibration_standard_datanull
intensities_log_log_plotSASDBJ4_datloglog_img.png
symmetrynull
last_modified2023-05-25T11:21:52.654103+02:00
bragg_peak[]
manifest.json：36 field values
Field pathRaw value
codeSASDBJ4
statussuccess
started_at2026-08-11T14:24:29.732050+00:00
finished_at2026-08-11T14:24:39.588962+00:00
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View the complete summary.json source
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  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.",
    "publication": {
      "title": "Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.",
      "author_list": "Mellroth P, Sandalova T, Kikhney A, Vilaplana F, Hesek D, Lee M, Mobashery S, Normark S, Svergun D, Henriques-Normark B, Achour A",
      "journal": "MBio",
      "doi": "10.1128/mBio.01120-13",
      "pmid": "24520066",
      "published_date": "2014 Feb 11"
    },
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    "submitted_date": "2014-02-11",
    "released_date": "2016-03-16"
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View the complete manifest.json source
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