SASDBZ2

Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2023-06-21T07:56:39.492710+02:00

The models displayed above are, from top to bottom: 1) An individual DAMMIN dummy atom model and; 2) CORAL rigid body model with the associated CRYSOL fit to the data. All of the individual DAMMIN models and associated fits can be found in the zip archive for this entry along with the CORAL modelling results.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli

Concentration1.4 – 10.8 Buffer / pH50 mM Tris 10 mM NaCl / 7.5
Experimental temperature10.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.12 nmExposure0.05 s × 20

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli
View sequence
MTDIAQLLGKDADNLLQHCCMTIPSDQLYLPGHDYVDRVMIDNNRPPAVLRNMQTLYNTGRLAGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGCNCVASTYGVLASVSRRYAHRIPFLVKLNHNETLSYPNTYDQTLYASVEQAFNMGAVAVGATIYFGSEESRRQIEEISAAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQANHLAATIGADIVKQKMAENNGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAGLINSGGAAGGETDLSDAVRTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVYLDSKITIA
proteinEscherichia coliA0A0K4BP99—–—decamerMolecule count 1038.056 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11198[3]0.0846518–3.23367 1/nmHas uncertainty columnMissing 011sasbdb/entries/z2/sasdbz2/source/SASDBZ2.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)12.73—nm
i0Guinier16826.025.0—
i0P(r)16670.018.0—
mwExperimental340.0—kDa
mwGuinier I(0)340.0—kDa
mwPorod302.0—kDa
porod_volumePorod484.0—nm³
rgGuinier4.430.02nm
rgP(r)4.340.04nm

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 Tris 10 mM NaClBuffer concentration50.0 mM
pH7.5Additives10 mM NaCl
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2013-06-30Storage / 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 range0.085 – 3.234Sample 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

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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:179 field values
Field pathRaw value
codeSASDBZ2
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleX-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism.
project.publication.titleX-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism.
project.publication.author_listDadinova LA, Shtykova EV, Konarev PV, Rodina EV, Snalina NE, Vorobyeva NN, Kurilova SA, Nazarova TI, Jeffries CM, Svergun DI
project.publication.journalPLoS One
project.publication.doi10.1371/journal.pone.0156105
project.publication.pmid27227414
project.publication.published_date2016
project.statusreleased
project.submitted_date2015-12-14
project.released_date2016-07-01
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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_nameClass I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli
experiment.sample.molecule[0].short_nameFbaB
experiment.sample.molecule[0].sequenceMTDIAQLLGKDADNLLQHCCMTIPSDQLYLPGHDYVDRVMIDNNRPPAVLRNMQTLYNTG RLAGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGCNCVASTYGVLASVS RRYAHRIPFLVKLNHNETLSYPNTYDQTLYASVEQAFNMGAVAVGATIYFGSEESRRQIE EISAAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQANHLAATIGADIVKQKM AENNGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAGLINSGGAAGGETDLS DAVRTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVYLDSKITIA
experiment.sample.molecule[0].organismEscherichia coli
experiment.sample.molecule[0].uniprot_codeA0A0K4BP99
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationdecamer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw38.056
experiment.sample.molecule[0].total_mw380.557
experiment.sample.molecule[0].number_molecules10
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 10 mM NaCl
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive10 mM NaCl
experiment.sample.buffer.concentration50.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameClass I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli
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_nameMSU
experiment.contributor[0].affiliation[0].addressMoscow, Russia
experiment.contributor[0].affiliation[0].full_nameLomonosov Moscow State University
experiment.contributor[0].affiliation[0].webpagehttp://www.msu.ru
experiment.contributor[0].contributor_nameLiubov
experiment.contributor[0].contributor_surnameDadinova
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2013-06-30
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_min1.4
experiment.concentration_max10.8
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.085
experiment.s_max3.234
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareDAMMIN
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fits[0].chi_square_value1.23
fits[0].p_value0.00021
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fits[1].chi_square_value1.81
fits[1].p_value0.0
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fits[1].fit_lognull
fits[1].software_versionnull
fits[1].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionThe models displayed above are, from top to bottom: 1) An individual DAMMIN dummy atom model and; 2) CORAL rigid body model with the associated CRYSOL fit to the data. All of the individual DAMMIN models and associated fits can be found in the zip archive for this entry along with the CORAL modelling results.
experiment_descriptionSynchrotron SAXS data from solutions of Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli in 50 mM Tris pH 7.5 were collected on the P12 beam line of Petra-III (Hamburg, Germany) using a Pilatus 2M detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.124 nm). Different solute concentrations in the range 2.6-13.30 mg/ml were measured using an exposure time of 1 s (recorded as 20 x 0.050 s frames). The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering from the matched solvent-blank was subtracted. The data presented here are from a single concentration scattering curve (9.3 mg/ml).
tags[]
intensity_unitnull
experimental_mw340.0
experimental_mw_errornull
guinier_i0_mw340.0
guinier_i0_mw_errornull
porod_mw302.0
porod_mw_errornull
pddf_i016670.0
pddf_i0_error18.0
guinier_i016826.0
guinier_i0_error25.0
pddf_rg4.34
pddf_rg_error0.04
guinier_rg4.43
guinier_rg_error0.02
pddf_dmax12.73
pddf_dmax_errornull
porod_volume484.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first2
guinier_point_last81
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDBZ2_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDBZ2
statussuccess
started_at2026-08-11T13:49:42.824397+00:00
finished_at2026-08-11T13:50:03.716442+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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View the complete summary.json source
{
  "code": "SASDBZ2",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism.",
    "publication": {
      "title": "X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism.",
      "author_list": "Dadinova LA, Shtykova EV, Konarev PV, Rodina EV, Snalina NE, Vorobyeva NN, Kurilova SA, Nazarova TI, Jeffries CM, Svergun DI",
      "journal": "PLoS One",
      "doi": "10.1371/journal.pone.0156105",
      "pmid": "27227414",
      "published_date": "2016"
    },
    "status": "released",
    "submitted_date": "2015-12-14",
    "released_date": "2016-07-01"
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          "long_name": "Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli",
          "short_name": "FbaB",
          "sequence": "MTDIAQLLGKDADNLLQHCCMTIPSDQLYLPGHDYVDRVMIDNNRPPAVLRNMQTLYNTG\r\nRLAGTGYLSILPVDQGVEHSAGASFAANPLYFDPKNIVELAIEAGCNCVASTYGVLASVS\r\nRRYAHRIPFLVKLNHNETLSYPNTYDQTLYASVEQAFNMGAVAVGATIYFGSEESRRQIE\r\nEISAAFERAHELGMVTVLWAYLRNSAFKKDGVDYHVSADLTGQANHLAATIGADIVKQKM\r\nAENNGGYKAINYGYTDDRVYSKLTSENPIDLVRYQLANCYMGRAGLINSGGAAGGETDLS\r\nDAVRTAVINKRAGGMGLILGRKAFKKSMADGVKLINAVQDVYLDSKITIA",
          "organism": "Escherichia coli",
          "uniprot_code": "A0A0K4BP99",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "decamer",
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          "uniprot_sequence": null,
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          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "50 mM Tris 10 mM NaCl",
        "concentration_unit": "mM",
        "comment": null,
        "additive": "10 mM NaCl",
        "concentration": 50.0,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "MSU",
            "address": "Moscow, Russia",
            "full_name": "Lomonosov Moscow State University",
            "webpage": "http://www.msu.ru"
          }
        ],
        "contributor_name": "Liubov",
        "contributor_surname": "Dadinova",
        "orcid": null
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    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2013-06-30",
    "storage_temperature": 10.0,
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    "wavelength": 0.12,
    "sample_detector_distance": 3.1,
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    "flow_rate": null,
    "s_min": 0.085,
    "s_max": 3.234,
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          "user": 94
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      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBZ2_fit1_fit_img.png",
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      "fit_residual_plot": "SASDBZ2_fit2_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBZ2_fit2.fit",
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  "description": "The models displayed above are, from top to bottom: 1) An individual DAMMIN dummy atom model and; 2) CORAL rigid body model with the associated CRYSOL fit to the data. All of the individual DAMMIN models and associated fits can be found in the zip archive for this entry along with the CORAL modelling results.",
  "experiment_description": "Synchrotron SAXS data from solutions of Class I fructose-1,6-bisphosphate aldolase (FbaB) from E. coli in 50 mM Tris pH 7.5 were collected on the P12 beam line of Petra-III (Hamburg, Germany) using a Pilatus 2M detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.124 nm). Different solute concentrations in the range 2.6-13.30 mg/ml were measured using an exposure time of 1 s (recorded as 20 x 0.050 s frames). The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering from the matched solvent-blank was subtracted. The data presented here are from a single concentration scattering curve (9.3 mg/ml).",
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDBZ2_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2023-06-21T07:56:39.492710+02:00",
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}
View the complete manifest.json source
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