SASDGD2

Putative mitochondrial transferase CAF17: human IBA57

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2023-06-21T07:55:24.740692+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Putative mitochondrial transferase CAF17: human IBA57

Concentration— – 5.0 Buffer / pH50 mM phosphate, 150 mM NaCl, 5 mM DTT / 7.0
Experimental temperature20.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.124 nmExposure0.995 s × 3000

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Putative transferase CAF17, mitochondrial
View sequence
AGAAWACFRLDGRTLLRVRGPDAAPFLLGLLTNELPLPSPAAAGAPPAARAGYAHFLNVQGRTLYDVILYGLQEHSEVSGFLLECDSSVQGALQKHLALYRIRRKVTVEPHPELRVWAVLPSSPEACGAASLQERAGAAAILIRDPRTARMGWRLLTQDEGPALVPGGRLGDLWDYHQHRYLQGVPEGVRDLPPGVALPLESNLAFMNGVSFTKGCYIGQELTARTHHMGVIRKRLFPVRFLDPLPTSGITPGATVLTASGQTVGKFRAGQGNVGLALLWSEKIKGPLHIRASEGAQVALAASVPDWWP
proteinHomo sapiensQ5T44044–352monomerMolecule count 133.242 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11296[3]0.122607–3.69587 1/nmHas uncertainty columnMissing 014sasbdb/entries/d2/sasdgd2/source/SASDGD2.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)7.14—nm
i0Guinier177.00.39arbitrary
i0P(r)177.3—arbitrary
mwExperimental25.6—kDa
mwPorod31.0—kDa
porod_volumePorod50.0—nm³
rgGuinier2.160.015nm
rgP(r)2.172—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 · CRYSOL 2.8.3

χ²: 1.075CorMap p: 0.0758Unit: 1/A

Putative mitochondrial transferase CAF17: human IBA57

ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—atomicPDB (Protein Data Bank) —33.236QE3Model 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 phosphate, 150 mM NaCl, 5 mM DTTBuffer concentration—
pH7.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2018-07-10Storage / measurement temperature20.0 / 20.0
Exposure time0.995Frames3000
Wavelength0.124Sample-to-detector distance3.0
SourceX-ray synchrotronDetectorPilatus 6M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.123 – 3.696Sample volume / flow rate100.0 / 0.5

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:159 field values
Field pathRaw value
codeSASDGD2
statusPublished
type_of_curveSEC-SAS
angular_unit1/nm
project.titleStructural properties of [2Fe-2S] ISCA2-IBA57: a complex of the mitochondrial iron-sulfur cluster assembly machinery
project.publication.titleStructural properties of [2Fe-2S] ISCA2-IBA57: a complex of the mitochondrial iron-sulfur cluster assembly machinery
project.publication.author_listNasta V, Da Vela S, Gourdoupis S, Ciofi-Baffoni S, Svergun D, Banci L
project.publication.journalScientific Reports
project.publication.doi10.1038/s41598-019-55313-5
project.publication.pmidnull
project.publication.published_date2019 Dec 12
project.statusreleased
project.submitted_date2019-07-22
project.released_date2019-12-07
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experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 6M
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_namePutative transferase CAF17, mitochondrial
experiment.sample.molecule[0].short_nameIBA57
experiment.sample.molecule[0].sequenceAGAAWACFRLDGRTLLRVRGPDAAPFLLGLLTNELPLPSPAAAGAPPAARAGYAHFLNVQGRTLYDVILYGLQEHSEVSGFLLECDSSVQGALQKHLALYRIRRKVTVEPHPELRVWAVLPSSPEACGAASLQERAGAAAILIRDPRTARMGWRLLTQDEGPALVPGGRLGDLWDYHQHRYLQGVPEGVRDLPPGVALPLESNLAFMNGVSFTKGCYIGQELTARTHHMGVIRKRLFPVRFLDPLPTSGITPGATVLTASGQTVGKFRAGQGNVGLALLWSEKIKGPLHIRASEGAQVALAASVPDWWP
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeQ5T440
experiment.sample.molecule[0].uniprot_range_first44
experiment.sample.molecule[0].uniprot_range_last352
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMATAALLRGATPGRGGPVWRWRLRAAPRCRLAHSSCSPGGDPTAGAAWACFRLDGRTLLR VRGPDAAPFLLGLLTNELPLPSPAAAGAPPAARAGYAHFLNVQGRTLYDVILYGLQEHSE VSGFLLECDSSVQGALQKHLALYRIRRKVTVEPHPELRVWAVLPSSPEACGAASLQERAG AAAILIRDPRTARMGWRLLTQDEGPALVPGGRLGDLWDYHQHRYLQGVPEGVRDLPPGVA LPLESNLAFMNGVSFTKGCYIGQELTARTHHMGVIRKRLFPVRFLDPLPTSGITPGATVL TASGQTVGKFRAGQGNVGLALLWSEKIKGPLHIRASEGAQVALAASVPDWWPTVSK
experiment.sample.molecule[0].mw33.242
experiment.sample.molecule[0].total_mw33.242
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 phosphate, 150 mM NaCl, 5 mM DTT
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.namePutative mitochondrial transferase CAF17: human IBA57
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_nameStefano
experiment.contributor[0].contributor_surnameDa Vela
experiment.contributor[0].orcidhttps://orcid.org/0000-0002-1700-4759
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2018-07-10
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time0.995
experiment.number_of_frames3000
experiment.wavelength0.124
experiment.sample_detector_distance3.0
experiment.concentration_minnull
experiment.concentration_max5.0
experiment.sample_volume100.0
experiment.flow_rate0.5
experiment.s_min0.123
experiment.s_max3.696
experiment.total_exposure_timenull
experiment.seccolumn1
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fits[0].models[0].softwarePDB (Protein Data Bank)
fits[0].models[0].pdb_link[0].pdb_code6qe3
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fits[0].models[0].bead_radius1.9
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fits[0].softwareCRYSOL
fits[0].chi_square_value1.075
fits[0].p_value0.0758
fits[0].fit_residual_plotSASDGD2_fit1_fitresiduals_img.png
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fits[0].fit_lognull
fits[0].software_version2.8.3
fits[0].descriptionPutative mitochondrial transferase CAF17: human IBA57
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of human IBA57 in 50 mM phosphate, 150 mM NaCl, 5 mM DTT, pH 7 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 100.00 μl sample at 5 mg/ml was injected at a 0.50 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 3000 successive 0.995 second frames were collected. 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_mw25.6
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw31.0
porod_mw_errornull
pddf_i0177.3
pddf_i0_errornull
guinier_i0177.0
guinier_i0_error0.39
pddf_rg2.172
pddf_rg_errornull
guinier_rg2.16
guinier_rg_error0.015
pddf_dmax7.14
pddf_dmax_errornull
porod_volume50.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first3
guinier_point_last174
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDGD2_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:55:24.740692+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDGD2
statussuccess
started_at2026-08-11T13:36:03.888862+00:00
finished_at2026-08-11T13:36:18.176516+00:00
source_last_modified2023-06-21T07:55:24.740692+02:00
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View the complete summary.json source
{
  "code": "SASDGD2",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structural properties of [2Fe-2S] ISCA2-IBA57: a complex of the mitochondrial iron-sulfur cluster assembly machinery",
    "publication": {
      "title": "Structural properties of [2Fe-2S] ISCA2-IBA57: a complex of the mitochondrial iron-sulfur cluster assembly machinery",
      "author_list": "Nasta V, Da Vela S, Gourdoupis S, Ciofi-Baffoni S, Svergun D, Banci L",
      "journal": "Scientific Reports",
      "doi": "10.1038/s41598-019-55313-5",
      "pmid": null,
      "published_date": "2019 Dec 12"
    },
    "status": "released",
    "submitted_date": "2019-07-22",
    "released_date": "2019-12-07"
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    "sample": {
      "molecule": [
        {
          "long_name": "Putative transferase CAF17, mitochondrial",
          "short_name": "IBA57",
          "sequence": "AGAAWACFRLDGRTLLRVRGPDAAPFLLGLLTNELPLPSPAAAGAPPAARAGYAHFLNVQGRTLYDVILYGLQEHSEVSGFLLECDSSVQGALQKHLALYRIRRKVTVEPHPELRVWAVLPSSPEACGAASLQERAGAAAILIRDPRTARMGWRLLTQDEGPALVPGGRLGDLWDYHQHRYLQGVPEGVRDLPPGVALPLESNLAFMNGVSFTKGCYIGQELTARTHHMGVIRKRLFPVRFLDPLPTSGITPGATVLTASGQTVGKFRAGQGNVGLALLWSEKIKGPLHIRASEGAQVALAASVPDWWP",
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          "uniprot_range_first": 44,
          "uniprot_range_last": 352,
          "oligomerization": "monomer",
          "molecular_type": "protein",
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          "mw": 33.242,
          "total_mw": 33.242,
          "number_molecules": 1,
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          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
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        "concentration_unit": null,
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View the complete manifest.json source
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