SASDFA6

Proteolytic fragment of phage flagella binding tail protein YSD1_29 (amino acids 373-1296)

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2020-07-03T15:26:52.401701+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Proteolytic fragment of phage flagella binding tail protein YSD1_29 (amino acids 373-1296)

Concentration— – 10.0 Buffer / pH20 mM Tris, 150 mM NaCl, 0.03 % NaN3, 5.0 % glycerol / 7.8
Experimental temperature23.0 Facility / beamlineAustralian Synchrotron / SAXS/WAXS
Wavelength0.10322 nmExposure1.0 s × 10

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Flagella binding tail protein
View sequence
IRVGTVEDGTLPDGKIKVVALQDQFAFQLNTFNQVEPPAGYEPNLTPAIARRIVYEMPYVDLVQQLPDGELNAVGPNDAFINSQAEKPTDMSAAYDMGIMAEGESGFDVRGNGDFGAFGSLASDIDYLSTQIVLSEMTDMWDDVQPGFVARIAKPVLDGQRTQMEIAEEFVRIDAINGNVITVARGVLDTIPFRHQKSEMLWVTTYDGGTDWQKYAGNESIDIKILPWTLGGGRFPIEDAPIDHLDMDFRQIRPYPPGNVQHYLASTSTLQRWYVPSALTYTANAGETPDTYTLTWAHRDRVLQGDKPVPHIDGDIGPEPGTTYTIRVYNQEGTLVRTESGINGTTWNWPYATAAADMNVEASLFDPVLATLRLTSVRNGRESWEYYEMKVSVYKKPPQFVYDASLMQFAAQPYNATIDPNPPTPPMDGPYVSALMQFAAQPDGSEDFGPAESMNGPNVALLPHQVTQTSSIITPLDTLLYETPYIQLSRDGRDLNTSKVSAYVARSSDRTVDSYTLFTKHETDANYTSAGTQPWTPWGMSTVGLGFFTDEVTIDPTSDKDGVPVAPAKVGDLLLIDQELVSITAINGRTYKIGRGVADTIPAQHYSSRPVWLISVGFGYSDMAFGDNEKAMVIIRPDTYGTDIPLSKLYPLQLQMQYRPKRPYPPGLMMIGGQPFFNTASGLADDFNPYDNLKAKDVVCTYAHRNRVSQSTTARDHFAVGINPEPGVKYRVRIGYAYWSQSGSGFSLLSQFETEDAGFIMRAADLERWGRQAGYAQDAGGYSTLNVTVNAIRDGMLNWQGYTMTVRVPSFPLPPGQKPGGGDGPWNPPGGGNTGGTTPPTEPPDRPDPSEPGTTDPSEPTKPDEPEEPQPPVDPEDPDTDPPEPPEPPVDPTNVPGWSLSWDHGWAMTLPDFRYVPPADEEPELEHHHHHH
proteinSalmonella virus ChiM9NVD3373–1296monomerMolecule count 1102.637 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1800[3]0.005655–0.316942 1/AHas uncertainty columnMissing 02sasbdb/entries/a6/sasdfa6/source/SASDFA6.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)27.38—Å
i0Guinier0.27—arbitrary
i0P(r)0.279—arbitrary
mwExperimental94.26—kDa
mwPorod97.0—kDa
porod_volumePorod155.0—ų
rgGuinier5.610.06Å
rgP(r)6.13—Å

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, 0.03 % NaN3, 5.0 % glycerolBuffer concentration—
pH7.8Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2017-04-04Storage / measurement temperature4.0 / 23.0
Exposure time1.0Frames10
Wavelength0.10322Sample-to-detector distance1.426
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineAustralian Synchrotron / SAXS/WAXS · Melbourne, Australia
q range0.057 – 3.169Sample volume / flow rate100.0 / 0.4

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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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
codeSASDFA6
statusPublished
type_of_curveSEC-SAS
angular_unit1/A
project.titleThe flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre.
project.publication.titleThe flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre.
project.publication.author_listDunstan RA, Pickard D, Dougan S, Goulding D, Cormie C, Hardy J, Li F, Grinter R, Harcourt K, Yu L, Song J, Schreiber F, Choudhary J, Clare S, Coulibaly F, Strugnell RA, Dougan G, Lithgow T
project.publication.journalMol Microbiol
project.publication.doi10.1111/mmi.14396
project.publication.pmid31556164
project.publication.published_date2019 Sep 25
project.statusreleased
project.submitted_date2019-05-08
project.released_date2019-09-24
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDFA6.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDFA6.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFA6_dat_img.png
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pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFA6_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFA6_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDFA6.sascif
experiment.instrument.detector.typeDectris
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
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_nameFlagella binding tail protein
experiment.sample.molecule[0].short_nameYSD1_29
experiment.sample.molecule[0].sequenceIRVGTVEDGTLPDGKIKVVALQDQFAFQLNTFNQVEPPAGYEPNLTPAIARRIVYEMPYVDLVQQLPDGELNAVGPNDAFINSQAEKPTDMSAAYDMGIMAEGESGFDVRGNGDFGAFGSLASDIDYLSTQIVLSEMTDMWDDVQPGFVARIAKPVLDGQRTQMEIAEEFVRIDAINGNVITVARGVLDTIPFRHQKSEMLWVTTYDGGTDWQKYAGNESIDIKILPWTLGGGRFPIEDAPIDHLDMDFRQIRPYPPGNVQHYLASTSTLQRWYVPSALTYTANAGETPDTYTLTWAHRDRVLQGDKPVPHIDGDIGPEPGTTYTIRVYNQEGTLVRTESGINGTTWNWPYATAAADMNVEASLFDPVLATLRLTSVRNGRESWEYYEMKVSVYKKPPQFVYDASLMQFAAQPYNATIDPNPPTPPMDGPYVSALMQFAAQPDGSEDFGPAESMNGPNVALLPHQVTQTSSIITPLDTLLYETPYIQLSRDGRDLNTSKVSAYVARSSDRTVDSYTLFTKHETDANYTSAGTQPWTPWGMSTVGLGFFTDEVTIDPTSDKDGVPVAPAKVGDLLLIDQELVSITAINGRTYKIGRGVADTIPAQHYSSRPVWLISVGFGYSDMAFGDNEKAMVIIRPDTYGTDIPLSKLYPLQLQMQYRPKRPYPPGLMMIGGQPFFNTASGLADDFNPYDNLKAKDVVCTYAHRNRVSQSTTARDHFAVGINPEPGVKYRVRIGYAYWSQSGSGFSLLSQFETEDAGFIMRAADLERWGRQAGYAQDAGGYSTLNVTVNAIRDGMLNWQGYTMTVRVPSFPLPPGQKPGGGDGPWNPPGGGNTGGTTPPTEPPDRPDPSEPGTTDPSEPTKPDEPEEPQPPVDPEDPDTDPPEPPEPPVDPTNVPGWSLSWDHGWAMTLPDFRYVPPADEEPELEHHHHHH
experiment.sample.molecule[0].organismSalmonella virus Chi
experiment.sample.molecule[0].uniprot_codeM9NVD3
experiment.sample.molecule[0].uniprot_range_first373
experiment.sample.molecule[0].uniprot_range_last1296
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMGSKSKKVTVGYKYYMGLFMGLFRGPVNEITEIRVGDRTAWTGSITGNTTIQINKESLFG GTKAEGGIDGPLEVYMGAPTQTVSQKLKNMLGGRQPEFRGVVTAYFDGLICAMNPYPKQW KFKARRSTAGWTGGVWYPEKCLVKMQGYDGQGNQHEIHAMNPAHILYECQSNYEWGRGLS RTLIDDTTFRLAADTLFNENFGLCIRWNRQDTLESFMQLILDHIGGAMYVSKVTGKLSLR LIRKDYDFDTLPIFDTDSGLLSIQEATNASPANLVNEVVVTYHNPVMDEDQQVRSHNLAQ IQNQGCLNSNTIEYLGIPTGKLAMQVAQRDLRAASTNVRRFTVICDRRAWNVQPGDVLKV RDPKQRGLTEVVIRVGTVEDGTLPDGKIKVVALQDQFAFQLNTFNQVEPPAGYEPNLTPA IARRIVYEMPYVDLVQQLPDGELNAVGPNDAFINSQAEKPTDMSAAYDMGIMAEGESGFD VRGNGDFGAFGSLASDIDYLSTQIVLSEMTDMWDDVQPGFVARIAKPVLDGQRTQMEIAE EFVRIDAINGNVITVARGVLDTIPFRHQKSEMLWVTTYDGGTDWQKYAGNESIDIKILPW TLGGGRFPIEDAPIDHLDMDFRQIRPYPPGNVQHYLASTSTLQRWYVPSALTYTANAGET PDTYTLTWAHRDRVLQGDKPVPHIDGDIGPEPGTSYTIRVYNQEGTLVRTESGINGTTWN WPYATAAADMNVEASLFDPVLATLRLTSARNGRESWEYYEMKVSVYKKPPQFVYDASLMQ FAAQPYNATSDPNPPTPPMDGPYVSSLMQFAAQPDGSEDFGPAESMNGPNVALLPHQVTQ TSSIITPLDTLLYETPYIQLSRDGRDLNTSKVSAYVARSSDRTVDSYTLFTKHETDANYT SSGTQPWTPWGMSTVGLGFFTDEVTIDPTSDKDGVPVAPAKVGDLLLIDQELVSITAING RTYKIGRGVADTIPAQHYSSRPVWLISVGFGYSDMAFGDNEKAMVIIRPDTYGTDIPLSK LYPLQLQMQYRPKRPYPPGLMMIGGQPFFNTASGLADDFNPYDNLKAKDVVCTYAHRNRV SQSTTARDHFAVGITPEPGVKYRVRIGYAYWSQSGSGFSLLSQFETEDAGFIMRAADLER WGRQAGYAQDAGGYSTLNVTVNAIRDGMLNWQGYTMTVRVPSFPLPPGQKPGGGDGPWNP PGGGNTGGTTPPTEPPDRPDPSEPGTTDPSEPTKPDEPEEPQPPVDPEDPDTDPPEPPEP PVDPTNVPGWSLSWDHGWAMTLPDFRYVPPADEEPE
experiment.sample.molecule[0].mw102.637
experiment.sample.molecule[0].total_mw102.637
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, 0.03 % NaN3, 5.0 % glycerol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.8
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameProteolytic fragment of phage flagella binding tail protein YSD1_29 (amino acids 373-1296)
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].addressMelbourne, Australia
experiment.contributor[0].affiliation[0].full_nameMonash University
experiment.contributor[0].affiliation[0].webpagehttp://www.monash.edu/
experiment.contributor[0].contributor_nameGrinter
experiment.contributor[0].contributor_surnameGrinter
experiment.contributor[0].orcidhttps://orcid.org/0000-0002-8195-5348
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-04-04
experiment.storage_temperature4.0
experiment.cell_temperature23.0
experiment.exposure_time1.0
experiment.number_of_frames10
experiment.wavelength0.10322
experiment.sample_detector_distance1.426
experiment.concentration_minnull
experiment.concentration_max10.0
experiment.sample_volume100.0
experiment.flow_rate0.4
experiment.s_min0.057
experiment.s_max3.169
experiment.total_exposure_timenull
experiment.seccolumn1
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDFA6_fit1_model1_img.png
fits[0].models[0].softwareDAMMIF
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modeldummy
fits[0].models[0].software_versionnull
fits[0].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDFA6_fit1_model1.pdb
fits[0].models[0].model_mw133.022
fits[0].models[0].bead_radius5.0
fits[0].models[0].lognull
fits[0].models[0].symmetrynull
fits[0].models[0].commentnull
fits[0].models[0].user322
fits[0].fit_unit1/A
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fits[0].softwareDAMMIF
fits[0].chi_square_value0.504
fits[0].p_value2e-05
fits[0].fit_residual_plotYSD29_800_4SccVAl_fitresiduals_img.png
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fits[0].fit_lognull
fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Proteolytic fragment of phage flagella binding tail protein YSD1_29 (amino acids 373-1296) in 20 mM Tris, 150 mM NaCl, 0.03 % NaN3, 5.0 % glycerol, pH 7.8 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 1.4 m and at a wavelength of λ = 0.10322 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAXS was employed. The SEC parameters were as follows: A 100 μl sample at 10 mg/ml was injected onto a GE Superdex 200 Increase 10/300 column at 23°C. 10 successive 1 second frames were collected through the SEC-elution peak. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.
tags[]
intensity_unitarbitrary
experimental_mw94.26
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw97.0
porod_mw_errornull
pddf_i00.279
pddf_i0_errornull
guinier_i00.27
guinier_i0_errornull
pddf_rg6.13
pddf_rg_errornull
guinier_rg5.61
guinier_rg_error0.06
pddf_dmax27.38
pddf_dmax_errornull
porod_volume155.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first3
guinier_point_last42
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDFA6_datloglog_img.png
symmetrynull
last_modified2020-07-03T15:26:52.401701+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDFA6
statussuccess
started_at2026-08-11T15:04:59.729912+00:00
finished_at2026-08-11T15:05:07.493015+00:00
source_last_modified2020-07-03T15:26:52.401701+02:00
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View the complete summary.json source
{
  "code": "SASDFA6",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre.",
    "publication": {
      "title": "The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre.",
      "author_list": "Dunstan RA, Pickard D, Dougan S, Goulding D, Cormie C, Hardy J, Li F, Grinter R, Harcourt K, Yu L, Song J, Schreiber F, Choudhary J, Clare S, Coulibaly F, Strugnell RA, Dougan G, Lithgow T",
      "journal": "Mol Microbiol",
      "doi": "10.1111/mmi.14396",
      "pmid": "31556164",
      "published_date": "2019 Sep 25"
    },
    "status": "released",
    "submitted_date": "2019-05-08",
    "released_date": "2019-09-24"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFA6.out",
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            "webpage": "http://www.monash.edu/"
          }
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View the complete manifest.json source
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