SASDCN6

Small GTPase Rab5 conjugated with ubiquitin at K140

Data type: SASBDB experimental data Status: Published Curve type: Merged Last updated: 2020-08-28T15:28:06.281418+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Small GTPase Rab5 conjugated with ubiquitin at K140

Concentration0.9 – 7.3 Buffer / pH50 mM Tris-HCl, 150 mM NaCl, 10 mM MgCl2 / 7.5
Experimental temperature4.0 Facility / beamlinePohang Accelerator Laboratory / 4C
Wavelength0.124 nmExposure10.0 s × 6

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Monoubiquitinated Rab5 at K165
View sequence
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMASRGATRPNGPNTGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKNEPQNPGANSARGRGVDLTEPTQPTRNQCCSN
proteinHomo sapiens——–—monomerMolecule count 132.205 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1682[3]0.0187158–0.164477 1/AHas uncertainty columnMissing 00sasbdb/entries/n6/sasdcn6/source/SASDCN6.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)8.35—Å
i0Guinier4.290.03—
i0P(r)4.348——
mwExperimental30.0—kDa
rgGuinier2.3380.034Å
rgP(r)2.451—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

Fit 1 · EOM/GAJOE

χ²: 1.3CorMap p: 0.0Unit: 1/A
ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—atomicEOM/RANCH —27.63—Model Image
2—atomicEOM/RANCH —27.63—Model Image
3—atomicEOM/RANCH —27.63—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 name50 mM Tris-HCl, 150 mM NaCl, 10 mM MgCl2Buffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2016-11-21Storage / measurement temperature4.0 / 4.0
Exposure time10.0Frames6
Wavelength0.124Sample-to-detector distance3.0
SourceX-ray synchrotronDetectorADSC Quantum 315
Facility / beamlinePohang Accelerator Laboratory / 4C · Pohang, South Korea
q range0.187 – 1.645Sample 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:205 field values
Field pathRaw value
codeSASDCN6
statusPublished
type_of_curveMerged
angular_unit1/A
project.titleSite-specific monoubiquitination downregulates Rab5 by disrupting effector binding and guanine nucleotide conversion.
project.publication.titleSite-specific monoubiquitination downregulates Rab5 by disrupting effector binding and guanine nucleotide conversion.
project.publication.author_listShin D, Na W, Lee JH, Kim G, Baek J, Park SH, Choi CY, Lee S
project.publication.journalElife
project.publication.doi10.7554/eLife.29154
project.publication.pmid28968219
project.publication.published_date2017 Oct 2
project.statusreleased
project.submitted_date2017-07-18
project.released_date2018-03-19
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experiment.instrument.detector.typeCCD
experiment.instrument.detector.nameADSC Quantum 315
experiment.instrument.detector.resolution315.0
experiment.instrument.namePohang Accelerator Laboratory
experiment.instrument.cityPohang
experiment.instrument.countrySouth Korea
experiment.instrument.beamline_name4C
experiment.instrument.beam_geometry
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
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experiment.sample.molecule[0].long_nameMonoubiquitinated Rab5 at K165
experiment.sample.molecule[0].short_namemUbRab5K165
experiment.sample.molecule[0].sequenceMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG MASRGATRPNGPNTGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQ TVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQR QASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKK LPKNEPQNPGANSARGRGVDLTEPTQPTRNQCCSN
experiment.sample.molecule[0].organismHomo sapiens
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].mw32.205
experiment.sample.molecule[0].total_mw32.205
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.name50 mM Tris-HCl, 150 mM NaCl, 10 mM MgCl2
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
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experiment.sample.purity_methodnull
experiment.sample.nameSmall GTPase Rab5 conjugated with ubiquitin at K140
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].addressSeoul, SK
experiment.contributor[0].affiliation[0].full_nameSungkyunkwan University
experiment.contributor[0].affiliation[0].webpagehttp://www.skku.edu/eng_home/index.jsp
experiment.contributor[0].contributor_nameDonghyuk
experiment.contributor[0].contributor_surnameShin
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experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-11-21
experiment.storage_temperature4.0
experiment.cell_temperature4.0
experiment.exposure_time10.0
experiment.number_of_frames6
experiment.wavelength0.124
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experiment.concentration_min0.9
experiment.concentration_max7.3
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tags[]
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symmetrynull
last_modified2020-08-28T15:28:06.281418+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDCN6
statussuccess
started_at2026-08-11T15:12:53.931806+00:00
finished_at2026-08-11T15:13:03.507829+00:00
source_last_modified2020-08-28T15:28:06.281418+02:00
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View the complete summary.json source
{
  "code": "SASDCN6",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/A",
  "project": {
    "title": "Site-specific monoubiquitination downregulates Rab5 by disrupting effector binding and guanine nucleotide conversion.",
    "publication": {
      "title": "Site-specific monoubiquitination downregulates Rab5 by disrupting effector binding and guanine nucleotide conversion.",
      "author_list": "Shin D, Na W, Lee JH, Kim G, Baek J, Park SH, Choi CY, Lee S",
      "journal": "Elife",
      "doi": "10.7554/eLife.29154",
      "pmid": "28968219",
      "published_date": "2017 Oct 2"
    },
    "status": "released",
    "submitted_date": "2017-07-18",
    "released_date": "2018-03-19"
  },
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      "country": "South Korea",
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    },
    "sample": {
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