SASDAX8

Ribokinase ThiM

Data type: SASBDB experimental data Status: Published Curve type: Merged Last updated: 2023-05-25T11:21:52.654103+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Ribokinase ThiM

Concentration1.33 – 9.85 mg/mlBuffer / pH50 mM Potassium phosphate 10 mM MgCl2 / 7.5
Experimental temperature12.0 Facility / beamlineDORIS III, DESY / EMBL X33
Wavelength0.15 nmExposure15.0 s × 8

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Ribokinase ThiM
View sequence
MNYLNNIRIENPLTICYTNDVVKNFTANGLLSIGASPAMSEAPEEAEEFYKVAQALLINIGTLTAQNEQDIIAIAQTANEAGLPIVFDPVAVGASTYRKQFCKLLLKSAKVSVIKGNASEILALIDDTATMKGTDSDANLDAVTIAKKAYAIYKTAIVITGKEDVIVQGDKAIVLANGSPLLARVTGAGCLLGGIIAGFLFRETEPDIEALIEAVSVFNIAAEVAAENENCGGPGTFSPLLLDTLYHLNETTYQQRIRIQEVEENLYFQSGHHHHHH
proteinStaphylococcus aureus——–—trimerMolecule count 329.8 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
12135[3]0.182063–6.01554 1/nmHas uncertainty columnMissing 02sasbdb/entries/x8/sasdax8/source/SASDAX8.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)9.0—nm
i0Guinier47.26——
mwExperimental77.0—kDa
mwPorod90.66—kDa
porod_volumePorod145.06—nm³
rgGuinier2.9720.198nm
rgP(r)2.866—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 name50 mM Potassium phosphate 10 mM MgCl2Buffer concentration50.0 mM
pH7.5Additives10 mM MgCl2
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuterationFalse / —

Acquisition Conditions and Instrument

Measurement date2010-11-19Storage / measurement temperature— / 12.0
Exposure time15.0Frames8
Wavelength0.15Sample-to-detector distance2.7
SourceX-ray synchrotronDetectorPilatus 1M-W
Facility / beamlineDORIS III, DESY / EMBL X33 · Hamburg, Germany
q range0.182 – 6.016Sample 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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All source fields (unfiltered)

Every source field is expanded here, including empty values, list members and fields already shown above.

summary.json:182 field values
Field pathRaw value
codeSASDAX8
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleStructure of ThiM from Vitamin B1 biosynthetic pathway of Staphylococcus aureus - Insights into a novel pro-drug approach addressing MRSA infections.
project.publication.titleStructure of ThiM from Vitamin B1 biosynthetic pathway of Staphylococcus aureus - Insights into a novel pro-drug approach addressing MRSA infections.
project.publication.author_listDrebes J, Künz M, Windshügel B, Kikhney AG, Müller IB, Eberle RJ, Oberthür D, Cang H, Svergun DI, Perbandt M, Betzel C, Wrenger C
project.publication.journalSci Rep
project.publication.doi10.1038/srep22871
project.publication.pmid26960569
project.publication.published_date2016 Mar 10
project.statusreleased
project.submitted_date2015-07-09
project.released_date2016-03-10
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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_nameRibokinase ThiM
experiment.sample.molecule[0].short_nameThiM
experiment.sample.molecule[0].sequenceMNYLNNIRIENPLTICYTNDVVKNFTANGLLSIGASPAMSEAPEEAEEFYKVAQALLINIGTLTAQNEQDIIAIAQTANE AGLPIVFDPVAVGASTYRKQFCKLLLKSAKVSVIKGNASEILALIDDTATMKGTDSDANLDAVTIAKKAYAIYKTAIVIT GKEDVIVQGDKAIVLANGSPLLARVTGAGCLLGGIIAGFLFRETEPDIEALIEAVSVFNIAAEVAAENENCGGPGTFSPL LLDTLYHLNETTYQQRIRIQEVEenlyfqsghhhhhh
experiment.sample.molecule[0].organismStaphylococcus aureus
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationtrimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw29.8
experiment.sample.molecule[0].total_mw89.4
experiment.sample.molecule[0].number_molecules3
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.name50 mM Potassium phosphate 10 mM MgCl2
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive10 mM MgCl2
experiment.sample.buffer.concentration50.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
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experiment.sample.contrastnull
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experiment.sample.dry_volnull
experiment.sample.absorbptionnull
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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.date2010-11-19
experiment.storage_temperaturenull
experiment.cell_temperature12.0
experiment.exposure_time15.0
experiment.number_of_frames8
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i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[0]X33
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pddf_point_first40
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last_modified2023-05-25T11:21:52.654103+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDAX8
statussuccess
started_at2026-08-11T16:02:39.881272+00:00
finished_at2026-08-11T16:02:50.224710+00:00
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View the complete summary.json source
{
  "code": "SASDAX8",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structure of ThiM from Vitamin B1 biosynthetic pathway of Staphylococcus aureus - Insights into a novel pro-drug approach addressing MRSA infections.",
    "publication": {
      "title": "Structure of ThiM from Vitamin B1 biosynthetic pathway of Staphylococcus aureus - Insights into a novel pro-drug approach addressing MRSA infections.",
      "author_list": "Drebes J, Künz M, Windshügel B, Kikhney AG, Müller IB, Eberle RJ, Oberthür D, Cang H, Svergun DI, Perbandt M, Betzel C, Wrenger C",
      "journal": "Sci Rep",
      "doi": "10.1038/srep22871",
      "pmid": "26960569",
      "published_date": "2016 Mar 10"
    },
    "status": "released",
    "submitted_date": "2015-07-09",
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          "long_name": "Ribokinase ThiM",
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