SASDCD7

Thermotoga maritima phosphodiesterase TM1595 (wildtype, TmPde)

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2023-06-21T07:56:39.492710+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Thermotoga maritima phosphodiesterase TM1595 (wildtype, TmPde)

Concentration— – 7.0 Buffer / pH20mM Tris, 200 mM NaCl, 5%(v/v) glycerol / 7.5
Experimental temperature20.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.123987 nmExposure0.045 s × 34

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Thermotoga maritima phosphodiesterase (wildtype, TmPDE, TM1595)
View sequence
GSGSGMDEIVKVLSQHDRILVVGHIMPDGDCVSSVLSLTLGLEKLGKEVKAAVDYKIPYVFEKFPYIDKIEENPNFDPELLVVVDASSPDRIGKFQDLLDKVPSVVIDHHSTNTNFGNWNWVDPSFAATAQMIFRINKALGVEYDSNLATLNYLGIATDTGFFRHSNADVRVFEDAYKLVKMGADAHFVAKEILENKRFEQFKLFAEVLERLQLLENGKIAYSYIDYDTYLRHNCTDEDSAGFVGELRSIRGVEVAVLFMEFPRGKIHVSMRSKDWFNVNEVAFELGGGGHPRAAGVTFEGKKIEEVIPRVINHLLKKFKEGVESESEKIPEGDVLGG
proteinThermotoga maritimaQ9X1T1—–—dimerMolecule count 237.823 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11187[3]0.0610767–3.19229 1/nmHas uncertainty columnMissing 00sasbdb/entries/d7/sasdcd7/source/SASDCD7.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)7.76—nm
i0Guinier19766.020.06arbitrary
i0P(r)20030.016.4arbitrary
mwExperimental67.0—kDa
mwPorod64.0—kDa
porod_volumePorod105.9—nm³
rgGuinier2.670.01nm
rgP(r)2.730.002nm

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 name20mM Tris, 200 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 date2015-06-23Storage / measurement temperature— / 20.0
Exposure time0.045Frames34
Wavelength0.123987Sample-to-detector distance3.0
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.061 – 3.192Sample 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:159 field values
Field pathRaw value
codeSASDCD7
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleStructural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.
project.publication.titleStructural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.
project.publication.author_listDrexler DJ, Müller M, Rojas-Cordova CA, Bandera AM, Witte G
project.publication.journalStructure
project.publication.doi10.1016/j.str.2017.10.001
project.publication.pmid29107484
project.publication.published_date2017 Dec 5
project.statusreleased
project.submitted_date2017-09-01
project.released_date2017-10-31
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDCD7.out
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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_nameThermotoga maritima phosphodiesterase (wildtype, TmPDE, TM1595)
experiment.sample.molecule[0].short_nameTmPde
experiment.sample.molecule[0].sequenceGSGSGMDEIVKVLSQHDRILVVGHIMPDGDCVSSVLSLTLGLEKLGKEVKAAVDYKIPYVFEKFPYIDKIEENPNFDPELLVVVDASSPDRIGKFQDLLDKVPSVVIDHHSTNTNFGNWNWVDPSFAATAQMIFRINKALGVEYDSNLATLNYLGIATDTGFFRHSNADVRVFEDAYKLVKMGADAHFVAKEILENKRFEQFKLFAEVLERLQLLENGKIAYSYIDYDTYLRHNCTDEDSAGFVGELRSIRGVEVAVLFMEFPRGKIHVSMRSKDWFNVNEVAFELGGGGHPRAAGVTFEGKKIEEVIPRVINHLLKKFKEGVESESEKIPEGDVLGG
experiment.sample.molecule[0].organismThermotoga maritima
experiment.sample.molecule[0].uniprot_codeQ9X1T1
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMDEIVKVLSQHDRILVVGHIMPDGDCVSSVLSLTLGLEKLGKEVKAAVDYKIPYVFEKFP YIDKIEENPNFDPELLVVVDASSPDRIGKFQDLLDKVPSVVIDHHSTNTNFGNWNWVDPS FAATAQMIFRINKALGVEYDSNLATLNYLGIATDTGFFRHSNADVRVFEDAYKLVKMGAD AHFVAKEILENKRFEQFKLFAEVLERLQLLENGKIAYSYIDYDTYLRHNCTDEDSAGFVG ELRSIRGVEVAVLFMEFPRGKIHVSMRSKDWFNVNEVAFELGGGGHPRAAGVTFEGKKIE EVIPRVINHLLKKFKEGVESESEKIPEGDVLGG
experiment.sample.molecule[0].mw37.823
experiment.sample.molecule[0].total_mw75.646
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.name20mM Tris, 200 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.nameThermotoga maritima phosphodiesterase TM1595 (wildtype, TmPde)
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].addressMunich, Germany
experiment.contributor[0].affiliation[0].full_nameLudwig-Maximilians-Universität München
experiment.contributor[0].affiliation[0].webpagehttps://www.en.uni-muenchen.de
experiment.contributor[0].contributor_nameGregor
experiment.contributor[0].contributor_surnameWitte
experiment.contributor[0].orcidhttps://orcid.org/0000-0003-0313-0962
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2015-06-23
experiment.storage_temperaturenull
experiment.cell_temperature20.0
experiment.exposure_time0.045
experiment.number_of_frames34
experiment.wavelength0.123987
experiment.sample_detector_distance3.0
experiment.concentration_minnull
experiment.concentration_max7.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.061
experiment.s_max3.192
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_code5o25
fits[0].models[0].pdb_link[0].ext_code5O25
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fits[0].models[0].bead_radius1.9
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fits[0].models[0].user229
fits[0].fit_unit1/A
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fits[0].softwareCRYSOL
fits[0].chi_square_value2.3
fits[0].p_value0.0
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fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0 (r6345)
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Thermotoga maritima phosphodiesterase TM1595 (wildtype, TmPde) in 20mM Tris, 200 mM NaCl, 5%(v/v) glycerol, pH 7.5, were collected on the EMBL-P12 beam line on the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123987 nm (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). One solute concentration of 7.00 mg/ml was measured at 20°C. 34 successive 0.045 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 and the different curves were scaled for protein concentration.
tags[]
intensity_unitarbitrary
experimental_mw67.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw64.0
porod_mw_errornull
pddf_i020030.0
pddf_i0_error16.4
guinier_i019766.0
guinier_i0_error20.06
pddf_rg2.73
pddf_rg_error0.002
guinier_rg2.67
guinier_rg_error0.01
pddf_dmax7.76
pddf_dmax_errornull
porod_volume105.9
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last130
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDCD7_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDCD7
statussuccess
started_at2026-08-11T15:27:13.891920+00:00
finished_at2026-08-11T15:27:24.124014+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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View the complete summary.json source
{
  "code": "SASDCD7",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.",
    "publication": {
      "title": "Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.",
      "author_list": "Drexler DJ, Müller M, Rojas-Cordova CA, Bandera AM, Witte G",
      "journal": "Structure",
      "doi": "10.1016/j.str.2017.10.001",
      "pmid": "29107484",
      "published_date": "2017 Dec 5"
    },
    "status": "released",
    "submitted_date": "2017-09-01",
    "released_date": "2017-10-31"
  },
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      "country": "Germany",
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    "sample": {
      "molecule": [
        {
          "long_name": "Thermotoga maritima phosphodiesterase (wildtype, TmPDE, TM1595)",
          "short_name": "TmPde",
          "sequence": "GSGSGMDEIVKVLSQHDRILVVGHIMPDGDCVSSVLSLTLGLEKLGKEVKAAVDYKIPYVFEKFPYIDKIEENPNFDPELLVVVDASSPDRIGKFQDLLDKVPSVVIDHHSTNTNFGNWNWVDPSFAATAQMIFRINKALGVEYDSNLATLNYLGIATDTGFFRHSNADVRVFEDAYKLVKMGADAHFVAKEILENKRFEQFKLFAEVLERLQLLENGKIAYSYIDYDTYLRHNCTDEDSAGFVGELRSIRGVEVAVLFMEFPRGKIHVSMRSKDWFNVNEVAFELGGGGHPRAAGVTFEGKKIEEVIPRVINHLLKKFKEGVESESEKIPEGDVLGG",
          "organism": "Thermotoga maritima",
          "uniprot_code": "Q9X1T1",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MDEIVKVLSQHDRILVVGHIMPDGDCVSSVLSLTLGLEKLGKEVKAAVDYKIPYVFEKFP\nYIDKIEENPNFDPELLVVVDASSPDRIGKFQDLLDKVPSVVIDHHSTNTNFGNWNWVDPS\nFAATAQMIFRINKALGVEYDSNLATLNYLGIATDTGFFRHSNADVRVFEDAYKLVKMGAD\nAHFVAKEILENKRFEQFKLFAEVLERLQLLENGKIAYSYIDYDTYLRHNCTDEDSAGFVG\nELRSIRGVEVAVLFMEFPRGKIHVSMRSKDWFNVNEVAFELGGGGHPRAAGVTFEGKKIE\nEVIPRVINHLLKKFKEGVESESEKIPEGDVLGG",
          "mw": 37.823,
          "total_mw": 75.646,
          "number_molecules": 2,
          "complex_state": false,
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View the complete manifest.json source
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