SASDB74

CyaA Block I-V

Data type: SASBDB experimental data Status: Published Curve type: Extrapolated to infinite dilution Last updated: 2023-06-21T07:56:39.492710+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · CyaA Block I-V

Concentration1.1 – 4.4 mg/mlBuffer / pH10 mM Tris HCl 150 mM NaCl 10 mM CaCl2 / 8.0
Experimental temperature10.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.12 nmExposure0.05 s × 20

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Adenylate cyclase toxin Block I-V
View sequence
EGDIHMSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSDGSTSGSGHHHHHHSAGLVPRGSTAIGMKETAAAKFERQHMDSPDLGTGGGSGIEGRENLYFQGLEHVQHIIGGAGNDSITGNAHDNFLAGGSGDDRLDGGAGNDTLVGGEGQNTVIGGAGDDVFLQDLGVWSNQLDGGAGVDTVKYNVHQPSEERLERMGDTGIHADLQKGTVEKWPALNLFSVDHVKNIENLHGSRLNDRIAGDDQDNELWGHDGNDTIRGRGGDDILRGGLGLDTLYGEDGNDIFLQDDETVSDDIDGGAGLDTVDYSAMIHPGRIVAPHEYGFGIEADLSREWVRKASALGVDYYDNVRNVENVIGTSMKDVLIGDAQANTLMGQGGDDTVRGGDGDDLLFGGDGNDMLYGDAGNDTLYGGLGDDTLEGGAGNDWFGQTQAREHDVLRGGDGVDTVDYSQTGAHAGIAAGRIGLGILADLGAGRVDKLGEAGSSAYDTVSGIENVVGTELADRITGDAQANVLRGAGGADVLAGGEGDDVLLGGDGDDQLSGDAGRDRLYGEAGDDWFFQDAANAGNLLDGGDGRDTVDFSGPGRGLDAGAKGVFLSLGKGFASLMDEPETSNVLRNIENAVGSARDDVLIGDAGANVLNGLAGNDVLSGGAGDDVLLGDEGSDLLSGDAGNDDLFGGQGDDTYLFGVGYGHDTIYESGGGHDTIRINAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAMAQYPDP
proteinBordetella pertussisP0DKX7—–—monomerMolecule count 170.0 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11694[3]0.0290642–4.48844 1/nmHas uncertainty columnMissing 0109sasbdb/entries/74/sasdb74/source/SASDB74.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)17.15—nm
i0Guinier17551.0——
i0P(r)17070.0——
mwExperimental91.0—kDa
mwGuinier I(0)91.0—kDa
mwPorod162.0—kDa
porod_volumePorod275.0—nm³
rgGuinier5.55—nm
rgP(r)5.49—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 name10 mM Tris HCl 150 mM NaCl 10 mM CaCl2Buffer concentration10.0 mM
pH8.0Additives150 mM NaCl, 10 mM CaCl2
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2013-10-31Storage / measurement temperature10.0 / 10.0
Exposure time0.05Frames20
Wavelength0.12Sample-to-detector distance3.1
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.029 – 4.488Sample 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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full_entry_zip:source record and ZIP contents (4 items)
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pddf:source record
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sascif: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:156 field values
Field pathRaw value
codeSASDB74
statusPublished
type_of_curveExtrapolated to infinite dilution
angular_unit1/nm
project.titleCalcium-Driven Folding of RTX Domain β-Rolls Ratchets Translocation of RTX Proteins through Type I Secretion Ducts.
project.publication.titleCalcium-Driven Folding of RTX Domain β-Rolls Ratchets Translocation of RTX Proteins through Type I Secretion Ducts.
project.publication.author_listBumba L, Masin J, Macek P, Wald T, Motlova L, Bibova I, Klimova N, Bednarova L, Veverka V, Kachala M, Svergun DI, Barinka C, Sebo P
project.publication.journalMol Cell
project.publication.doi10.1016/j.molcel.2016.03.018
project.publication.pmid27058787
project.publication.published_date2016 Apr 7
project.statusreleased
project.submitted_date2016-02-21
project.released_date2016-07-07
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDB74.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_nameAdenylate cyclase toxin Block I-V
experiment.sample.molecule[0].short_nameCyaA Block I-V
experiment.sample.molecule[0].sequenceEGDIHMSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNL PYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDF ETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPK LVCFKKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSDGSTSGSGHHHHHHSA GLVPRGSTAIGMKETAAAKFERQHMDSPDLGTGGGSGIEGRenlyfqglehvqhiiggagnd sitgnahdnflaggsgddrldggagndtlvggegqntviggagddvflqdlgvwsnqldg gagvdtvkynvhqpseerlermgdtgihadlqkgtvekwpalnlfsvdhvknienlhgsr lndriagddqdnelwghdgndtirgrggddilrgglgldtlygedgndiflqddetvsdd idggagldtvdysamihpgrivapheygfgieadlsrewvrkasalgvdyydnvrnvenv igtsmkdvligdaqantlmgqggddtvrggdgddllfggdgndmlygdagndtlygglgd dtleggagndwfgqtqarehdvlrggdgvdtvdysqtgahagiaagriglgiladlgagr vdklgeagssaydtvsgienvvgteladritgdaqanvlrgaggadvlaggegddvllgg dgddqlsgdagrdrlygeagddwffqdaanagnlldggdgrdtvdfsgpgrgldagakgv flslgkgfaslmdepetsnvlrnienavgsarddvligdaganvlnglagndvlsggagd dvllgdegsdllsgdagnddlfggqgddtylfgvgyghdtiyesggghdtirinagadql wfarqgndleirilgtddaltvhdwyrdadhrveiihaanqavdqagieklveamaqypd p
experiment.sample.molecule[0].organismBordetella pertussis
experiment.sample.molecule[0].uniprot_codeP0DKX7
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_sequenceMQQSHQAGYANAADRESGIPAAVLDGIKAVAKEKNATLMFRLVNPHSTSLIAEGVATKGL GVHAKSSDWGLQAGYIPVNPNLSKLFGRAPEVIARADNDVNSSLAHGHTAVDLTLSKERL DYLRQAGLVTGMADGVVASNHAGYEQFEFRVKETSDGRYAVQYRRKGGDDFEAVKVIGNA AGIPLTADIDMFAIMPHLSNFRDSARSSVTSGDSVTDYLARTRRAASEATGGLDRERIDL LWKIARAGARSAVGTEARRQFRYDGDMNIGVITDFELEVRNALNRRAHAVGAQDVVQHGT EQNNPFPEADEKIFVVSATGESQMLTRGQLKEYIGQQRGEGYVFYENRAYGVAGKSLFDD GLGAAPGVPSGRSKFSPDVLETVPASPGLRRPSLGAVERQDSGYDSLDGVGSRSFSLGEV SDMAAVEAAELEMTRQVLHAGARQDDAEPGVSGASAHWGQRALQGAQAVAAAQRLVHAIA LMTQFGRAGSTNTPQEAASLSAAVFGLGEASSAVAETVSGFFRGSSRWAGGFGVAGGAMA LGGGIAAAVGAGMSLTDDAPAGQKAAAGAEIALQLTGGTVELASSIALALAAARGVTSGL QVAGASAGAAAGALAAALSPMEIYGLVQQSHYADQLDKLAQESSAYGYEGDALLAQLYRD KTAAEGAVAGVSAVLSTVGAAVSIAAAASVVGAPVAVVTSLLTGALNGILRGVQQPIIEK LANDYARKIDELGGPQAYFEKNLQARHEQLANSDGLRKMLADLQAGWNASSVIGVQTTEI SKSALELAAITGNADNLKSVDVFVDRFVQGERVAGQPVVLDVAAGGIDIASRKGERPALT FITPLAAPGEEQRRRTKTGKSEFTTFVEIVGKQDRWRIRDGAADTTIDLAKVVSQLVDAN GVLKHSIKLDVIGGDGDDVVLANASRIHYDGGAGTNTVSYAALGRQDSITVSADGERFNV RKQLNNANVYREGVATQTTAYGKRTENVQYRHVELARVGQLVEVDTLEHVQHIIGGAGND SITGNAHDNFLAGGSGDDRLDGGAGNDTLVGGEGQNTVIGGAGDDVFLQDLGVWSNQLDG GAGVDTVKYNVHQPSEERLERMGDTGIHADLQKGTVEKWPALNLFSVDHVKNIENLHGSR LNDRIAGDDQDNELWGHDGNDTIRGRGGDDILRGGLGLDTLYGEDGNDIFLQDDETVSDD IDGGAGLDTVDYSAMIHPGRIVAPHEYGFGIEADLSREWVRKASALGVDYYDNVRNVENV IGTSMKDVLIGDAQANTLMGQGGDDTVRGGDGDDLLFGGDGNDMLYGDAGNDTLYGGLGD DTLEGGAGNDWFGQTQAREHDVLRGGDGVDTVDYSQTGAHAGIAAGRIGLGILADLGAGR VDKLGEAGSSAYDTVSGIENVVGTELADRITGDAQANVLRGAGGADVLAGGEGDDVLLGG DGDDQLSGDAGRDRLYGEAGDDWFFQDAANAGNLLDGGDGRDTVDFSGPGRGLDAGAKGV FLSLGKGFASLMDEPETSNVLRNIENAVGSARDDVLIGDAGANVLNGLAGNDVLSGGAGD DVLLGDEGSDLLSGDAGNDDLFGGQGDDTYLFGVGYGHDTIYESGGGHDTIRINAGADQL WFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGIEKLVEAMAQYPD PGAAAAAPPAARVPDTLMQSLAVNWR
experiment.sample.molecule[0].mw70.0
experiment.sample.molecule[0].total_mw70.0
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.name10 mM Tris HCl 150 mM NaCl 10 mM CaCl2
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive150 mM NaCl, 10 mM CaCl2
experiment.sample.buffer.concentration10.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameCyaA Block I-V
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_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_nameMichael
experiment.contributor[0].contributor_surnameKachala
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitmg/ml
experiment.date2013-10-31
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time0.05
experiment.number_of_frames20
experiment.wavelength0.12
experiment.sample_detector_distance3.1
experiment.concentration_min1.1
experiment.concentration_max4.4
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.029
experiment.s_max4.488
experiment.total_exposure_time1.0
experiment.seccolumnnull
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fits[0].models[0].bead_radius4.75
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fits[0].models[0].comment
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fits[0].softwarenull
fits[0].chi_square_value0.84
fits[0].p_value0.386088
fits[0].fit_residual_plotSASDB74_fit1_fitresiduals_img.png
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fits[0].fit_lognull
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fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionGNOM 4.6
i0_calibration_standardBSA
descriptionnull
experiment_descriptionnull
tags[]
intensity_unitnull
experimental_mw91.0
experimental_mw_errornull
guinier_i0_mw91.0
guinier_i0_mw_errornull
porod_mw162.0
porod_mw_errornull
pddf_i017070.0
pddf_i0_errornull
guinier_i017551.0
guinier_i0_errornull
pddf_rg5.49
pddf_rg_errornull
guinier_rg5.55
guinier_rg_errornull
pddf_dmax17.15
pddf_dmax_errornull
porod_volume275.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_firstnull
guinier_point_lastnull
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDB74_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDB74
statussuccess
started_at2026-08-11T14:15:11.348916+00:00
finished_at2026-08-11T14:15:20.613863+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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View the complete summary.json source
{
  "code": "SASDB74",
  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "angular_unit": "1/nm",
  "project": {
    "title": "Calcium-Driven Folding of RTX Domain β-Rolls Ratchets Translocation of RTX Proteins through Type I Secretion Ducts.",
    "publication": {
      "title": "Calcium-Driven Folding of RTX Domain β-Rolls Ratchets Translocation of RTX Proteins through Type I Secretion Ducts.",
      "author_list": "Bumba L, Masin J, Macek P, Wald T, Motlova L, Bibova I, Klimova N, Bednarova L, Veverka V, Kachala M, Svergun DI, Barinka C, Sebo P",
      "journal": "Mol Cell",
      "doi": "10.1016/j.molcel.2016.03.018",
      "pmid": "27058787",
      "published_date": "2016 Apr 7"
    },
    "status": "released",
    "submitted_date": "2016-02-21",
    "released_date": "2016-07-07"
  },
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View the complete manifest.json source
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