SASDFD7

Pseudomonas putida CBB5 NdmAB complex - static

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 · Pseudomonas putida CBB5 NdmAB complex - static

Concentration4.04 – 10.1 Buffer / pH20 mM HEPES 150 mM NaCl 2 mM TCEP 10% v/v glycerol / 7.5
Experimental temperature4.0 Facility / beamlinePohang Accelerator Laboratory / 4C
Wavelength0.0733 nmExposure5.0 s × 6

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Methylxanthine N1-demethylase NdmA
View sequence
MGSSHHHHHHENLYFQGSMEQAIINDEREYLRHFWHPVCTVTELEKAHPSSLGPLAVKLLNEQLVVAKLGDEYVAMRDRCAHRSAKLSLGTVSGNRLQCPYHGWQYDTHGACQLVPACPNSPIPNKAKVDRFDCEERYGLIWIRLDSSFDCTEIPYFSAANDPRLRIVIQEPYWWDATAERRWENFTDFSHFAFIHPGTLFDPNNAEPPIVPMDRFNGQFRFVYDTPEDMAVPNQAPIGSFSYTCSMPFAINLEVSKYSSSSLHVLFNVSCPVDSHTTKNFLIFAREQSDDSDYLHIAFNDLVFAEDKPVIESQWPKDAPADEVSVVADKVSIQYRKWLRELKEAHKEGSQAFRSALLDPVIESDRSYI
proteinPseudomonas putidaH9N289—–—trimerMolecule count 342.327 kDa
Methylxanthine N3-demethylase NdmB
View sequence
MGSSHHHHHHENLYFQGSMKEQLKPLLEDKTYLRHFWHPVCTLNEFERANASGHGPMGVTLLGEKLVLARLNSKIIAAADRCAHRSAQLSIGRVCSNAGKDYLECPYHGWRYDEAGACQLIPACPDKSISPRAKISSFDCEVKYDIVWVRLDNSFDCTQIPYLSDFDNPDMQVIVADSYIWETVAERRWENFTDFSHFAFVHPGTLYDPFFASHPTVYVNRVDGELQFKLAPPREMKGIPPEAPMGDFTYRCTMPYSVNLEIKLWKDDSRFVLWTTASPVDNKSCRNFMIIVREKDNQPDHMHLAFQKRVLDEDQPVIESQWPLEIQTSEVSVATDKISVQFRKWHKELSLSAVEGREAFRDSVLTNVIEEEQ
proteinPseudomonas putidaH9N290—–—trimerMolecule count 343.012 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11299[3]0.0–0.339897 1/AHas uncertainty columnMissing 00sasbdb/entries/d7/sasdfd7/source/SASDFD7.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)12.26—Å
i0Guinier40.27—1/cm
i0P(r)39.29—1/cm
mwExperimental271.0—kDa
rgGuinier4.498—Å
rgP(r)4.32—Å

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 HEPES 150 mM NaCl 2 mM TCEP 10% v/v glycerolBuffer concentration—
pH7.5Additives—
Buffer descriptiongel filtration buffer 2
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2018-07-27Storage / measurement temperature20.0 / 4.0
Exposure time5.0Frames6
Wavelength0.0733Sample-to-detector distance—
SourceX-ray synchrotronDetectorRayonix SX165
Facility / beamlinePohang Accelerator Laboratory / 4C · Pohang, South Korea
q range0.0 – 3.399Sample 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 (4 items)
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pddf:source record
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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:173 field values
Field pathRaw value
codeSASDFD7
statusPublished
type_of_curveExtrapolated to infinite dilution
angular_unit1/A
project.titleStructural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.
project.publication.titleStructural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.
project.publication.author_listKim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK
project.publication.journalJ Mol Biol
project.publication.doi10.1016/j.jmb.2019.08.004
project.publication.pmid31412262
project.publication.published_date2019 Sep 6
project.statusreleased
project.submitted_date2019-06-17
project.released_date2019-09-16
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDFD7.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDFD7.dat
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intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD7_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFD7_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD7_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDFD7.sascif
experiment.instrument.detector.typeCCD
experiment.instrument.detector.nameRayonix SX165
experiment.instrument.detector.resolution15.0
experiment.instrument.namePohang Accelerator Laboratory
experiment.instrument.cityPohang
experiment.instrument.countrySouth Korea
experiment.instrument.beamline_name4C
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_nameMethylxanthine N1-demethylase NdmA
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMGSSHHHHHHENLYFQGSMEQAIINDEREYLRHFWHPVCTVTELEKAHPSSLGPLAVKLLNEQLVVAKLGDEYVAMRD RCAHRSAKLSLGTVSGNRLQCPYHGWQYDTHGACQLVPACPNSPIPNKAKVDRFDCEERY GLIWIRLDSSFDCTEIPYFSAANDPRLRIVIQEPYWWDATAERRWENFTDFSHFAFIHPG TLFDPNNAEPPIVPMDRFNGQFRFVYDTPEDMAVPNQAPIGSFSYTCSMPFAINLEVSKY SSSSLHVLFNVSCPVDSHTTKNFLIFAREQSDDSDYLHIAFNDLVFAEDKPVIESQWPKD APADEVSVVADKVSIQYRKWLRELKEAHKEGSQAFRSALLDPVIESDRSYI
experiment.sample.molecule[0].organismPseudomonas putida
experiment.sample.molecule[0].uniprot_codeH9N289
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationtrimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMEQAIINDEREYLRHFWHPVCTVTELEKAHPSSLGPLAVKLLNEQLVVAKLGDEYVAMRD RCAHRSAKLSLGTVSGNRLQCPYHGWQYDTHGACQLVPACPNSPIPNKAKVDRFDCEERY GLIWIRLDSSFDCTEIPYFSAANDPRLRIVIQEPYWWDATAERRWENFTDFSHFAFIHPG TLFDPNNAEPPIVPMDRFNGQFRFVYDTPEDMAVPNQAPIGSFSYTCSMPFAINLEVSKY SSSSLHVLFNVSCPVDSHTTKNFLIFAREQSDDSDYLHIAFNDLVFAEDKPVIESQWPKD APADEVSVVADKVSIQYRKWLRELKEAHKEGSQAFRSALLDPVIESDRSYI
experiment.sample.molecule[0].mw42.327
experiment.sample.molecule[0].total_mw126.981
experiment.sample.molecule[0].number_molecules3
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.molecule[1].long_nameMethylxanthine N3-demethylase NdmB
experiment.sample.molecule[1].short_namenull
experiment.sample.molecule[1].sequenceMGSSHHHHHHENLYFQGSMKEQLKPLLEDKTYLRHFWHPVCTLNEFERANASGHGPMGVTLLGEKLVLARLNSKIIAA ADRCAHRSAQLSIGRVCSNAGKDYLECPYHGWRYDEAGACQLIPACPDKSISPRAKISSF DCEVKYDIVWVRLDNSFDCTQIPYLSDFDNPDMQVIVADSYIWETVAERRWENFTDFSHF AFVHPGTLYDPFFASHPTVYVNRVDGELQFKLAPPREMKGIPPEAPMGDFTYRCTMPYSV NLEIKLWKDDSRFVLWTTASPVDNKSCRNFMIIVREKDNQPDHMHLAFQKRVLDEDQPVI ESQWPLEIQTSEVSVATDKISVQFRKWHKELSLSAVEGREAFRDSVLTNVIEEEQ
experiment.sample.molecule[1].organismPseudomonas putida
experiment.sample.molecule[1].uniprot_codeH9N290
experiment.sample.molecule[1].uniprot_range_firstnull
experiment.sample.molecule[1].uniprot_range_lastnull
experiment.sample.molecule[1].oligomerizationtrimer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequenceMKEQLKPLLEDKTYLRHFWHPVCTLNEFERANASGHGPMGVTLLGEKLVLARLNSKIIAA ADRCAHRSAQLSIGRVCSNAGKDYLECPYHGWRYDEAGACQLIPACPDKSISPRAKISSF DCEVKYDIVWVRLDNSFDCTQIPYLSDFDNPDMQVIVADSYIWETVAERRWENFTDFSHF AFVHPGTLYDPFFASHPTVYVNRVDGELQFKLAPPREMKGIPPEAPMGDFTYRCTMPYSV NLEIKLWKDDSRFVLWTTASPVDNKSCRNFMIIVREKDNQPDHMHLAFQKRVLDEDQPVI ESQWPLEIQTSEVSVATDKISVQFRKWHKELSLSAVEGREAFRDSVLTNVIEEEQ
experiment.sample.molecule[1].mw43.012
experiment.sample.molecule[1].total_mw129.036
experiment.sample.molecule[1].number_molecules3
experiment.sample.molecule[1].complex_stateFalse
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name20 mM HEPES 150 mM NaCl 2 mM TCEP 10% v/v glycerol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentgel filtration buffer 2
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.namePseudomonas putida CBB5 NdmAB complex - static
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].addressSouth Korea
experiment.contributor[0].affiliation[0].full_nameKorea University
experiment.contributor[0].affiliation[0].webpagehttps://www.korea.edu/
experiment.contributor[0].contributor_nameJun Hoe
experiment.contributor[0].contributor_surnameKim
experiment.contributor[0].orcidhttps://orcid.org/0000-0001-5866-9952
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2018-07-27
experiment.storage_temperature20.0
experiment.cell_temperature4.0
experiment.exposure_time5.0
experiment.number_of_frames6
experiment.wavelength0.0733
experiment.sample_detector_distancenull
experiment.concentration_min4.04
experiment.concentration_max10.1
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.0
experiment.s_max3.399
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDFD7_fit1_model1_img.png
fits[0].models[0].softwareDAMMIF
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modeldummy
fits[0].models[0].software_versionnull
fits[0].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDFD7_fit1_model1.pdb
fits[0].models[0].model_mw239.595
fits[0].models[0].bead_radius4.5
fits[0].models[0].lognull
fits[0].models[0].symmetryP1
fits[0].models[0].commentnull
fits[0].models[0].user458
fits[0].fit_unit1/A
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fits[0].softwareDAMMIN
fits[0].chi_square_value0.774
fits[0].p_value0.0
fits[0].fit_residual_plotmerge_001_AB_4m2m_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDFD7_fit1.fir
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_descriptionnull
tags[]
intensity_unit1/cm
experimental_mw271.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i039.29
pddf_i0_errornull
guinier_i040.27
guinier_i0_errornull
pddf_rg4.32
pddf_rg_errornull
guinier_rg4.498
guinier_rg_errornull
pddf_dmax12.26
pddf_dmax_errornull
porod_volumenull
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first57
guinier_point_last186
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDFD7_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDFD7
statussuccess
started_at2026-08-11T15:27:21.325968+00:00
finished_at2026-08-11T15:27:30.656061+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDFD7",
  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "angular_unit": "1/A",
  "project": {
    "title": "Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.",
    "publication": {
      "title": "Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.",
      "author_list": "Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK",
      "journal": "J Mol Biol",
      "doi": "10.1016/j.jmb.2019.08.004",
      "pmid": "31412262",
      "published_date": "2019 Sep 6"
    },
    "status": "released",
    "submitted_date": "2019-06-17",
    "released_date": "2019-09-16"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFD7.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFD7.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD7_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFD7_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFD7_pofr_img.png",
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        "name": "Rayonix SX165",
        "resolution": 15.0
      },
      "name": "Pohang Accelerator Laboratory",
      "city": "Pohang",
      "country": "South Korea",
      "beamline_name": "4C",
      "beam_geometry": null,
      "type_of_source": "X-ray synchrotron",
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      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Methylxanthine N1-demethylase NdmA",
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View the complete manifest.json source
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