SASDC72

Alcohol dehydrogenase from bifunctional alcohol/aldehyde dehydrogenase (P0A9Q8)

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2021-01-04T12:08:43.215101+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Alcohol dehydrogenase from bifunctional alcohol/aldehyde dehydrogenase (P0A9Q8)

Concentration— – 10.0 Buffer / pH20 mM Tris 400 mM NaCl 5% v/v glycerol / 7.5
Experimental temperature4.0 Facility / beamlineDiamond Light Source / B21
Wavelength0.1 nmExposure1.0 s × 131

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Aldehyde-alcohol dehydrogenase
View sequence
MLWHKLPKSIYFRRGSLPIALDEVITDGHKRALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVIIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSGTGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAMEAYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLGVCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIADHLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQCTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKKAKKSA
proteinEscherichia coli O157:H7P0A9Q8451–891dimerMolecule count 248.33 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11446[3]0.004470188–0.401659 1/AHas uncertainty columnMissing 04sasbdb/entries/72/sasdc72/source/SASDC72.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)16.87—Å
estimated_volumeDAMMIN178.0—ų
i0Guinier0.0617e-05—
i0P(r)0.06270.0001—
mwExperimental91.4—kDa
porod_volumePorod146.0—ų
rgGuinier3.240.06Å
rgP(r)3.550.23Å

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 400 mM NaCl 5% v/v glycerolBuffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2015-11-27Storage / measurement temperature4.0 / 4.0
Exposure time1.0Frames131
Wavelength0.1Sample-to-detector distance4.04
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlineDiamond Light Source / B21 · Didcot, UK
q range0.045 – 4.017Sample 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:169 field values
Field pathRaw value
codeSASDC72
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleHigh-resolution structure of the alcohol dehydrogenase domain of the bifunctional bacterial enzyme AdhE.
project.publication.titleHigh-resolution structure of the alcohol dehydrogenase domain of the bifunctional bacterial enzyme AdhE.
project.publication.author_listAzmi L, Bragginton EC, Cadby IT, Byron O, Roe AJ, Lovering AL, Gabrielsen M
project.publication.journalActa Crystallogr F Struct Biol Commun
project.publication.doi10.1107/S2053230X20010237
project.publication.pmid32880589
project.publication.published_date2020 Sep 1
project.statusreleased
project.submitted_date2017-05-11
project.released_date2017-12-12
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experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 2M
experiment.instrument.detector.resolutionnull
experiment.instrument.nameDiamond Light Source
experiment.instrument.cityDidcot
experiment.instrument.countryUK
experiment.instrument.beamline_nameB21
experiment.instrument.beam_geometry1 x 5 mm
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_nameAldehyde-alcohol dehydrogenase
experiment.sample.molecule[0].short_nameAdhE
experiment.sample.molecule[0].sequenceMLWHKLPKSIYFRRGSLPIALDEVITDGHKRALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVIIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAMEAYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLGVCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIADHLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQCTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKKAKKSA
experiment.sample.molecule[0].organismEscherichia coli O157:H7
experiment.sample.molecule[0].uniprot_codeP0A9Q8
experiment.sample.molecule[0].uniprot_range_first451
experiment.sample.molecule[0].uniprot_range_last891
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ CTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKKAKKSA
experiment.sample.molecule[0].mw48.33
experiment.sample.molecule[0].total_mw96.66
experiment.sample.molecule[0].number_molecules2
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 400 mM NaCl 5% v/v 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.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameAlcohol dehydrogenase from bifunctional alcohol/aldehyde dehydrogenase (P0A9Q8)
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].addressGlasgow, Scotland, UK
experiment.contributor[0].affiliation[0].full_nameUniversity of Glasgow
experiment.contributor[0].affiliation[0].webpagehttp://www.gla.ac.uk/
experiment.contributor[0].contributor_nameLiyana
experiment.contributor[0].contributor_surnameAzmi
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2015-11-27
experiment.storage_temperature4.0
experiment.cell_temperature4.0
experiment.exposure_time1.0
experiment.number_of_frames131
experiment.wavelength0.1
experiment.sample_detector_distance4.04
experiment.concentration_minnull
experiment.concentration_max10.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.045
experiment.s_max4.017
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].softwareDAMMIF
fits[0].chi_square_value1.85
fits[0].p_value0.2137
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fits[0].software_versionr9217
fits[0].descriptionnull
estimated_volume_methodDAMMIN
pddf_softwareATSAS GNOM
pddf_software_versionPRIMUS 2.7.1 GNOM
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data, I(s) vs s (s = 4π sin θ/λ, where 2θ is the scattering angle and λ is the X-ray wavelength) were collected from a sample of alcohol dehydrogenase from a bifunctional alcohol/aldehyde dehydrogenase protein (P0A9Q8) using continuous-flow size-exclusion chromatography SAXS (SEC-SAXS) on the B21 beam line at the Diamond Light Source (Oxfordshire, UK). Data (131 successive 1 second frames) were collected using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm. The SEC mobile phase consisted of 20 mM Tris, 400 mM NaCl, 5% v/v glycerol, pH 7.5 (4°C) with a sample injection concentration of 10 mg/ml. Data obtained from solute-free eluates and SEC-elution peak were normalized to the intensity of the transmitted beam and radially averaged. The scattering of the solvent-blank was subtracted from the SEC-peak frames using ScÅtter and then analysed using Primus to produce the data displayed in this entry.
tags[]
intensity_unitnull
experimental_mw91.4
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i00.0627
pddf_i0_error0.0001
guinier_i00.061
guinier_i0_error7e-05
pddf_rg3.55
pddf_rg_error0.23
guinier_rg3.24
guinier_rg_error0.06
pddf_dmax16.87
pddf_dmax_errornull
porod_volume146.0
porod_volume_errornull
estimated_volume178.0
estimated_volume_errornull
guinier_point_first36
guinier_point_last130
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDC72_datloglog_img.png
symmetrynull
last_modified2021-01-04T12:08:43.215101+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDC72
statussuccess
started_at2026-08-11T16:29:37.846028+00:00
finished_at2026-08-11T16:29:46.854026+00:00
source_last_modified2021-01-04T12:08:43.215101+01:00
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View the complete summary.json source
{
  "code": "SASDC72",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "High-resolution structure of the alcohol dehydrogenase domain of the bifunctional bacterial enzyme AdhE.",
    "publication": {
      "title": "High-resolution structure of the alcohol dehydrogenase domain of the bifunctional bacterial enzyme AdhE.",
      "author_list": "Azmi L, Bragginton EC, Cadby IT, Byron O, Roe AJ, Lovering AL, Gabrielsen M",
      "journal": "Acta Crystallogr F Struct Biol Commun",
      "doi": "10.1107/S2053230X20010237",
      "pmid": "32880589",
      "published_date": "2020 Sep 1"
    },
    "status": "released",
    "submitted_date": "2017-05-11",
    "released_date": "2017-12-12"
  },
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      },
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      "city": "Didcot",
      "country": "UK",
      "beamline_name": "B21",
      "beam_geometry": "1 x 5 mm",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
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      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Aldehyde-alcohol dehydrogenase",
          "short_name": "AdhE",
          "sequence": "MLWHKLPKSIYFRRGSLPIALDEVITDGHKRALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVIIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG\r\nTGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAMEAYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLGVCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIADHLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQCTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKKAKKSA",
          "organism": "Escherichia coli O157:H7",
          "uniprot_code": "P0A9Q8",
          "uniprot_range_first": 451,
          "uniprot_range_last": 891,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG\nIVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA\nIFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA\nLMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF\nDNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP\nAYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV\nAMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG\nCGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK\nRALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI\nIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG\nTGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME\nAYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG\nVCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD\nHLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ\nCTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKKAKKSA",
          "mw": 48.33,
          "total_mw": 96.66,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM Tris 400 mM NaCl 5% v/v glycerol",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Alcohol dehydrogenase from bifunctional alcohol/aldehyde dehydrogenase (P0A9Q8)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Glasgow, Scotland, UK",
            "full_name": "University of Glasgow",
            "webpage": "http://www.gla.ac.uk/"
          }
        ],
        "contributor_name": "Liyana",
        "contributor_surname": "Azmi",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2015-11-27",
    "storage_temperature": 4.0,
    "cell_temperature": 4.0,
    "exposure_time": 1.0,
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    "wavelength": 0.1,
    "sample_detector_distance": 4.04,
    "concentration_min": null,
    "concentration_max": 10.0,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.045,
    "s_max": 4.017,
    "total_exposure_time": null,
    "seccolumn": null
  },
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      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC72_fit1_model1_img.png",
          "software": "DAMMIF",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
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          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDC72_fit1_model1.pdb",
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          "symmetry": "P2",
          "comment": "",
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          "comment": "",
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      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC72_fit1_fixed_fit_img.png",
      "software": "DAMMIF",
      "chi_square_value": 1.85,
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      "fit_residual_plot": "SASDC72_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC72_fit1.fir",
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  "description": null,
  "experiment_description": "Synchrotron SAXS data, I(s) vs s (s = 4π sin θ/λ, where 2θ is the scattering angle and λ is the X-ray wavelength) were collected from a sample of alcohol dehydrogenase from a bifunctional alcohol/aldehyde dehydrogenase protein (P0A9Q8) using continuous-flow size-exclusion chromatography SAXS (SEC-SAXS) on the B21 beam line at the Diamond Light Source (Oxfordshire, UK). Data (131 successive 1 second frames) were collected using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm. The SEC mobile phase consisted of 20 mM Tris, 400 mM NaCl, 5% v/v glycerol, pH 7.5 (4°C) with a sample injection concentration of 10 mg/ml. Data obtained from solute-free eluates and SEC-elution peak were normalized to the intensity of the transmitted beam and radially averaged. The scattering of the solvent-blank was subtracted from the SEC-peak frames using ScÅtter and then analysed using Primus to produce the data displayed in this entry.",
  "tags": [],
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  "guinier_point_last": 130,
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  "intensities_log_log_plot": "SASDC72_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2021-01-04T12:08:43.215101+01:00",
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}
View the complete manifest.json source
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