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SASDBH4

Wild-type LytA (N-His6) without choline

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

Without choline LytA is monomeric in solution.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Wild-type LytA (N-His6) without choline

Concentration1.0 – 4.0 mg/mlBuffer / pH20 mM Tris 150 mM NaCl 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 without cholineproteinStreptococcus pneumoniae——–—monomerMolecule count 137.4 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
12138[3]0.176504–6.02412 1/nmHas uncertainty columnMissing 0126sasbdb/entries/h4/sasdbh4/source/SASDBH4.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)12.51.3nm
i0Guinier39.83——
mwExperimental40.04.0kDa
mwGuinier I(0)66.0—kDa
mwPorod35.04.0kDa
porod_volumePorod56.0—nm³
rgGuinier3.36—nm
rgP(r)3.655—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: 2.053489CorMap p: 0.0Unit: 1/A

Fit data Fit plot

ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—atomicSASREF 7—36.98—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 1 µM ZnCl2Buffer concentration20.0 mM
pH7.5Additives150 mM NaCl, 1 µM ZnCl2
Buffer descriptionno choline
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuterationFalse / —

Acquisition Conditions and Instrument

Measurement date2011-07-03Storage / 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：156 field values
Field pathRaw value
codeSASDBH4
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
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.typeCustom-built
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
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_nameLytic Amidase without choline
experiment.sample.molecule[0].short_namewt-LytA-His6
experiment.sample.molecule[0].sequencenull
experiment.sample.molecule[0].organismStreptococcus pneumoniae
experiment.sample.molecule[0].uniprot_codenull
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_sequencenull
experiment.sample.molecule[0].mw37.4
experiment.sample.molecule[0].total_mw37.4
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.buffer.name20 mM Tris 150 mM NaCl 1 µM ZnCl2
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentno choline
experiment.sample.buffer.additive150 mM NaCl, 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 (N-His6) without choline
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.date2011-07-03
experiment.storage_temperaturenull
experiment.cell_temperature10.0
experiment.exposure_time15.0
experiment.number_of_frames8
experiment.wavelength0.15
experiment.sample_detector_distance2.7
experiment.concentration_min1.0
experiment.concentration_max4.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.177
experiment.s_max6.024
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].fit_lognull
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fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionGNOM 5
i0_calibration_standardBSA
descriptionWithout choline LytA is monomeric in solution.
experiment_descriptionnull
tags[0]X33
intensity_unitnull
experimental_mw40.0
experimental_mw_error4.0
guinier_i0_mw66.0
guinier_i0_mw_errornull
porod_mw35.0
porod_mw_error4.0
pddf_i0null
pddf_i0_errornull
guinier_i039.83
guinier_i0_errornull
pddf_rg3.655
pddf_rg_errornull
guinier_rg3.36
guinier_rg_errornull
pddf_dmax12.5
pddf_dmax_error1.3
porod_volume56.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first28
guinier_point_last75
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDBH4_datloglog_img.png
symmetrynull
last_modified2023-05-25T11:21:52.654103+02:00
bragg_peak[]
manifest.json：36 field values
Field pathRaw value
codeSASDBH4
statussuccess
started_at2026-08-11T14:23:50.423804+00:00
finished_at2026-08-11T14:24:00.617603+00:00
source_last_modified2023-05-25T11:21:52.654103+02:00
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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",
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    "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"
    },
    "status": "released",
    "submitted_date": "2014-02-11",
    "released_date": "2016-03-16"
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      "country": "Germany",
      "beamline_name": "EMBL X33",
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      "name": "Wild-type LytA (N-His6) without choline",
      "ext_coefficient": null,
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View the complete manifest.json source
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