SASDEN6

Glucosamine kinase from Streptacidiphilus jiangxiensis in presence of 1 mM ATP

Data type: SASBDB experimental data Status: Published Curve type: Extrapolated to infinite dilution Last updated: 2019-12-06T13:07:15.624532+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Glucosamine kinase from Streptacidiphilus jiangxiensis in presence of 1 mM ATP

Concentration1.25 – 10.0 Buffer / pH20 mM Tris-HCl, 150 mM NaCl, 10 mM MgCl2, 5 mM DTT, 1 mM ATP / 8.0
Experimental temperature10.0 Facility / beamlineESRF / BM29
Wavelength0.09919 nmExposure1.0 s × 10

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Glucosamine kinase
View sequence
MTPNWSELVAAADPALVLPSGERRAEVAVPGPLRLDALLDLGEGHAVGVVRSADAARWTVPLVRDGAGGVRRSRPGDGTAEHLVAALARRGATPDAAFVLEAFTGAAPVTGERGIIVDQTNESVIVGECAVVKWAVRLPAEGEPGSPAAQRIAALARGGFTEMPRPWGLLTLAEGAQPVLLASVVAYLPGALDGWDWAVDDVRRLARGELTMDQALLPAAQLGTLTARMHAALAARGRTPATAADVAAWGVRMREELDEAVASVPGAEGERLKAWAPRIADVYAELDALAGTPLIDVHGDFHVGQILRADGRYAVVDFDGNPVLPADQRAARQPAALDVVGMTASLDHVGRVVVFRTPDVDPAPVRAWIAAAQRSFLDAYRTTLARLDADDLFDDRLLTPLRYAQEVREYLYAVRHLPHWVYVPDLSLTDLLPERLKDKKLAAALEHHHHHH
proteinStreptacidiphilus jiangxiensisA0A1H7TQR5—–—monomerMolecule count 148.377 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11033[3]0.08190677–4.943923 1/nmHas uncertainty columnMissing 00sasbdb/entries/n6/sasden6/source/SASDEN6.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)7.8—nm
i0Guinier44.780.03arbitrary
i0P(r)44.95—arbitrary
mwExperimental50.6—kDa
mwGuinier I(0)50.6—kDa
mwPorod45.6—kDa
porod_volumePorod72.95—nm³
rgGuinier2.520.01nm
rgP(r)2.546—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 name20 mM Tris-HCl, 150 mM NaCl, 10 mM MgCl2, 5 mM DTT, 1 mM ATPBuffer concentration—
pH8.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2016-11-24Storage / measurement temperature10.0 / 10.0
Exposure time1.0Frames10
Wavelength0.09919Sample-to-detector distance2.867
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineESRF / BM29 · Grenoble, France
q range0.082 – 4.944Sample 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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full_entry_zip:source record and ZIP contents (5 items)
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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:172 field values
Field pathRaw value
codeSASDEN6
statusPublished
type_of_curveExtrapolated to infinite dilution
angular_unit1/nm
project.titleMolecular Fingerprints for a Novel Enzyme Family in <i>Actinobacteria</i> with Glucosamine Kinase Activity.
project.publication.titleMolecular Fingerprints for a Novel Enzyme Family in <i>Actinobacteria</i> with Glucosamine Kinase Activity.
project.publication.author_listManso JA, Nunes-Costa D, Macedo-Ribeiro S, Empadinhas N, Pereira PJB
project.publication.journalMBio
project.publication.doi10.1128/mBio.00239-19
project.publication.pmid31088917
project.publication.published_date2019 May 14
project.statusreleased
project.submitted_date2018-10-15
project.released_date2019-05-09
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDEN6.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDEN6.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEN6_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEN6_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEN6_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEN6_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDEN6.sascif
experiment.instrument.detector.typeDectris
experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
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
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameGlucosamine kinase
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMTPNWSELVAAADPALVLPSGERRAEVAVPGPLRLDALLDLGEGHAVGVVRSADAARWTV PLVRDGAGGVRRSRPGDGTAEHLVAALARRGATPDAAFVLEAFTGAAPVTGERGIIVDQT NESVIVGECAVVKWAVRLPAEGEPGSPAAQRIAALARGGFTEMPRPWGLLTLAEGAQPVL LASVVAYLPGALDGWDWAVDDVRRLARGELTMDQALLPAAQLGTLTARMHAALAARGRTP ATAADVAAWGVRMREELDEAVASVPGAEGERLKAWAPRIADVYAELDALAGTPLIDVHGD FHVGQILRADGRYAVVDFDGNPVLPADQRAARQPAALDVVGMTASLDHVGRVVVFRTPDV DPAPVRAWIAAAQRSFLDAYRTTLARLDADDLFDDRLLTPLRYAQEVREYLYAVRHLPHW VYVPDLSLTDLLPERLKDKKLAAALEHHHHHH
experiment.sample.molecule[0].organismStreptacidiphilus jiangxiensis
experiment.sample.molecule[0].uniprot_codeA0A1H7TQR5
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_sequenceMTPNWSELVAAADPALVLPSGERRAEVAVPGPLRLDALLDLGEGHAVGVVRSADAARWTV PLVRDGAGGVRRSRPGDGTAEHLVAALARRGATPDAAFVLEAFTGAAPVTGERGIIVDQT NESVIVGECAVVKWAVRLPAEGEPGSPAAQRIAALARGGFTEMPRPWGLLTLAEGAQPVL LASVVAYLPGALDGWDWAVDDVRRLARGELTMDQALLPAAQLGTLTARMHAALAARGRTP ATAADVAAWGVRMREELDEAVASVPGAEGERLKAWAPRIADVYAELDALAGTPLIDVHGD FHVGQILRADGRYAVVDFDGNPVLPADQRAARQPAALDVVGMTASLDHVGRVVVFRTPDV DPAPVRAWIAAAQRSFLDAYRTTLARLDADDLFDDRLLTPLRYAQEVREYLYAVRHLPHW VYVPDLSLTDLLPERLKD
experiment.sample.molecule[0].mw48.377
experiment.sample.molecule[0].total_mw48.377
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.name20 mM Tris-HCl, 150 mM NaCl, 10 mM MgCl2, 5 mM DTT, 1 mM ATP
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameGlucosamine kinase from Streptacidiphilus jiangxiensis in presence of 1 mM ATP
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].addressnull
experiment.contributor[0].affiliation[0].full_nameInstituto de Biomedicina y Biotecnología de Cantabria (IBBTEC-CSIC-Universidad de Cantabria)
experiment.contributor[0].affiliation[0].webpagenull
experiment.contributor[0].contributor_nameJose A
experiment.contributor[0].contributor_surnameManso
experiment.contributor[0].orcidhttps://orcid.org/0000-0002-2565-6239
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-11-24
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time1.0
experiment.number_of_frames10
experiment.wavelength0.09919
experiment.sample_detector_distance2.867
experiment.concentration_min1.25
experiment.concentration_max10.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.082
experiment.s_max4.944
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwarePDB (Protein Data Bank)
fits[0].models[0].pdb_link[0].pdb_code6hwj
fits[0].models[0].pdb_link[0].ext_code6HWJ
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fits[0].models[0].model_mw45.17
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetrynull
fits[0].models[0].commentVolume fraction for this structure was of 0.75 as determined OLIGOMER
fits[0].models[0].user320
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fits[0].models[1].bead_radiusnull
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fits[0].models[1].symmetrynull
fits[0].models[1].commentVolume fraction for this structure was of 0.25 as determined OLIGOMER
fits[0].models[1].user320
fits[0].fit_unit1/A
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fits[0].softwareOLIGOMER
fits[0].chi_square_value23.31
fits[0].p_value0.0
fits[0].fit_residual_plotgluk01_1mMATP_zero_OLIGOMER_SASBDB_7pcBOZO_fitresiduals_img.png
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fits[0].fit_lognull
fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Streptacidiphilus jiangxiensis glucosamine kinase in presence of 1 mM ATP in 20 mM Tris-HCl (pH 8.0), 150 mM NaCl, 10 mM MgCl2 and 5 mM DTT were collected on the BM29 BIOSAXS beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.867 m and at a wavelength of λ = 0.0992 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle; s-range = 0.035 < s < 4.944 nm-1). Solute concentrations ranging between 1.25 and 10.0 mg/ml were measured at 10°C. 10 successive 1 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. The data were extrapolated to infinite dilution. The volume fractions for the structure above (open conformation) and below (closed conformation) were of 0.75 and 0.25 as determined by OLIGOMER, respectively.
tags[]
intensity_unitarbitrary
experimental_mw50.6
experimental_mw_errornull
guinier_i0_mw50.6
guinier_i0_mw_errornull
porod_mw45.6
porod_mw_errornull
pddf_i044.95
pddf_i0_errornull
guinier_i044.78
guinier_i0_error0.03
pddf_rg2.546
pddf_rg_errornull
guinier_rg2.52
guinier_rg_error0.01
pddf_dmax7.8
pddf_dmax_errornull
porod_volume72.95
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first31
guinier_point_last92
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDEN6_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDEN6
statussuccess
started_at2026-08-11T15:13:02.449727+00:00
finished_at2026-08-11T15:13:12.935329+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDEN6",
  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "angular_unit": "1/nm",
  "project": {
    "title": "Molecular Fingerprints for a Novel Enzyme Family in <i>Actinobacteria</i> with Glucosamine Kinase Activity.",
    "publication": {
      "title": "Molecular Fingerprints for a Novel Enzyme Family in <i>Actinobacteria</i> with Glucosamine Kinase Activity.",
      "author_list": "Manso JA, Nunes-Costa D, Macedo-Ribeiro S, Empadinhas N, Pereira PJB",
      "journal": "MBio",
      "doi": "10.1128/mBio.00239-19",
      "pmid": "31088917",
      "published_date": "2019 May 14"
    },
    "status": "released",
    "submitted_date": "2018-10-15",
    "released_date": "2019-05-09"
  },
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      "country": "France",
      "beamline_name": "BM29",
      "beam_geometry": "",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
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      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Glucosamine kinase",
          "short_name": null,
          "sequence": "MTPNWSELVAAADPALVLPSGERRAEVAVPGPLRLDALLDLGEGHAVGVVRSADAARWTV\r\nPLVRDGAGGVRRSRPGDGTAEHLVAALARRGATPDAAFVLEAFTGAAPVTGERGIIVDQT\r\nNESVIVGECAVVKWAVRLPAEGEPGSPAAQRIAALARGGFTEMPRPWGLLTLAEGAQPVL\r\nLASVVAYLPGALDGWDWAVDDVRRLARGELTMDQALLPAAQLGTLTARMHAALAARGRTP\r\nATAADVAAWGVRMREELDEAVASVPGAEGERLKAWAPRIADVYAELDALAGTPLIDVHGD\r\nFHVGQILRADGRYAVVDFDGNPVLPADQRAARQPAALDVVGMTASLDHVGRVVVFRTPDV\r\nDPAPVRAWIAAAQRSFLDAYRTTLARLDADDLFDDRLLTPLRYAQEVREYLYAVRHLPHW\r\nVYVPDLSLTDLLPERLKDKKLAAALEHHHHHH",
          "organism": "Streptacidiphilus jiangxiensis",
          "uniprot_code": "A0A1H7TQR5",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MTPNWSELVAAADPALVLPSGERRAEVAVPGPLRLDALLDLGEGHAVGVVRSADAARWTV\nPLVRDGAGGVRRSRPGDGTAEHLVAALARRGATPDAAFVLEAFTGAAPVTGERGIIVDQT\nNESVIVGECAVVKWAVRLPAEGEPGSPAAQRIAALARGGFTEMPRPWGLLTLAEGAQPVL\nLASVVAYLPGALDGWDWAVDDVRRLARGELTMDQALLPAAQLGTLTARMHAALAARGRTP\nATAADVAAWGVRMREELDEAVASVPGAEGERLKAWAPRIADVYAELDALAGTPLIDVHGD\nFHVGQILRADGRYAVVDFDGNPVLPADQRAARQPAALDVVGMTASLDHVGRVVVFRTPDV\nDPAPVRAWIAAAQRSFLDAYRTTLARLDADDLFDDRLLTPLRYAQEVREYLYAVRHLPHW\nVYVPDLSLTDLLPERLKD",
          "mw": 48.377,
          "total_mw": 48.377,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM Tris-HCl, 150 mM NaCl, 10 mM MgCl2, 5 mM DTT, 1 mM ATP",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 8.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Glucosamine kinase from Streptacidiphilus jiangxiensis in presence of 1 mM ATP",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": null,
            "full_name": "Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC-CSIC-Universidad de Cantabria)",
            "webpage": null
          }
        ],
        "contributor_name": "Jose A",
        "contributor_surname": "Manso",
        "orcid": "https://orcid.org/0000-0002-2565-6239"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2016-11-24",
    "storage_temperature": 10.0,
    "cell_temperature": 10.0,
    "exposure_time": 1.0,
    "number_of_frames": 10,
    "wavelength": 0.09919,
    "sample_detector_distance": 2.867,
    "concentration_min": 1.25,
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    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.082,
    "s_max": 4.944,
    "total_exposure_time": null,
    "seccolumn": null
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    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEN6_fit1_model1_img.png",
          "software": "PDB (Protein Data Bank)",
          "pdb_link": [
            {
              "pdb_code": "6hwj",
              "ext_code": "6HWJ",
              "ext_type": "pdb",
              "difference_with_model": "identical"
            }
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          "type_of_model": "atomic",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEN6_fit1_model1.pdb",
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          "log": null,
          "symmetry": null,
          "comment": "Volume fraction for this structure was of 0.75 as determined OLIGOMER",
          "user": 320
        },
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEN6_fit1_model2_img.png",
          "software": "PDB (Protein Data Bank)",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "atomic",
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          "comment": "Volume fraction for this structure was of 0.25 as determined OLIGOMER",
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      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/gluk01_1mMATP_zero_OLIGOMER_SASBDB_7pcBOZO_fit_img.png",
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      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEN6_fit1.fit",
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  "description": null,
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDEN6_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
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}
View the complete manifest.json source
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