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SASDFG7

Pseudomonas putida CBB5 NdmB hexamer

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS 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 NdmB hexamer

Concentration— – 9.7 Buffer / pH20 mM HEPES 150 mM NaCl 2 mM TCEP / 7.5
Experimental temperature18.0 Facility / beamlinePhoton Factory (PF), High Energy Accelerator Research Organization (KEK) / BL-10C
Wavelength0.15 nmExposure10.0 s × 36

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Methylxanthine N3-demethylase NdmB
View sequence
MGSSHHHHHHENLYFQGSMKEQLKPLLEDKTYLRHFWHPVCTLNEFERANASGHGPMGVTLLGEKLVLARLNSKIIAAADRCAHRSAQLSIGRVCSNAGKDYLECPYHGWRYDEAGACQLIPACPDKSISPRAKISSFDCEVKYDIVWVRLDNSFDCTQIPYLSDFDNPDMQVIVADSYIWETVAERRWENFTDFSHFAFVHPGTLYDPFFASHPTVYVNRVDGELQFKLAPPREMKGIPPEAPMGDFTYRCTMPYSVNLEIKLWKDDSRFVLWTTASPVDNKSCRNFMIIVREKDNQPDHMHLAFQKRVLDEDQPVIESQWPLEIQTSEVSVATDKISVQFRKWHKELSLSAVEGREAFRDSVLTNVIEEEQ
proteinPseudomonas putidaH9N290—–—hexamerMolecule count 643.012 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11170[3]0.003329395–0.2808594 1/AHas uncertainty columnMissing 0227sasbdb/entries/g7/sasdfg7/source/SASDFG7.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)12.23—Å
i0Guinier0.61—1/cm
i0P(r)0.6081—1/cm
mwExperimental275.0—kDa
rgGuinier4.325—Å
rgP(r)4.24—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 TCEPBuffer concentration—
pH7.5Additives—
Buffer descriptiongel filtration buffer
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2018-05-21Storage / measurement temperature4.0 / 18.0
Exposure time10.0Frames36
Wavelength0.15Sample-to-detector distance3.0
SourceX-ray synchrotronDetectorPilatus3 2M
Facility / beamlinePhoton Factory (PF), High Energy Accelerator Research Organization (KEK) / BL-10C · Tsukuba, Japan
q range0.033 – 2.809Sample volume / flow rate140.0 / 0.05

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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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：156 field values
Field pathRaw value
codeSASDFG7
statusPublished
type_of_curveSEC-SAS
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/SASDFG7.out
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pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFG7_pofr_img.png
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDFG7.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus3 2M
experiment.instrument.detector.resolution0.172
experiment.instrument.namePhoton Factory (PF), High Energy Accelerator Research Organization (KEK)
experiment.instrument.cityTsukuba
experiment.instrument.countryJapan
experiment.instrument.beamline_nameBL-10C
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 N3-demethylase NdmB
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMGSSHHHHHHENLYFQGSMKEQLKPLLEDKTYLRHFWHPVCTLNEFERANASGHGPMGVTLLGEKLVLARLNSKIIAA ADRCAHRSAQLSIGRVCSNAGKDYLECPYHGWRYDEAGACQLIPACPDKSISPRAKISSF DCEVKYDIVWVRLDNSFDCTQIPYLSDFDNPDMQVIVADSYIWETVAERRWENFTDFSHF AFVHPGTLYDPFFASHPTVYVNRVDGELQFKLAPPREMKGIPPEAPMGDFTYRCTMPYSV NLEIKLWKDDSRFVLWTTASPVDNKSCRNFMIIVREKDNQPDHMHLAFQKRVLDEDQPVI ESQWPLEIQTSEVSVATDKISVQFRKWHKELSLSAVEGREAFRDSVLTNVIEEEQ
experiment.sample.molecule[0].organismPseudomonas putida
experiment.sample.molecule[0].uniprot_codeH9N290
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationhexamer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMKEQLKPLLEDKTYLRHFWHPVCTLNEFERANASGHGPMGVTLLGEKLVLARLNSKIIAA ADRCAHRSAQLSIGRVCSNAGKDYLECPYHGWRYDEAGACQLIPACPDKSISPRAKISSF DCEVKYDIVWVRLDNSFDCTQIPYLSDFDNPDMQVIVADSYIWETVAERRWENFTDFSHF AFVHPGTLYDPFFASHPTVYVNRVDGELQFKLAPPREMKGIPPEAPMGDFTYRCTMPYSV NLEIKLWKDDSRFVLWTTASPVDNKSCRNFMIIVREKDNQPDHMHLAFQKRVLDEDQPVI ESQWPLEIQTSEVSVATDKISVQFRKWHKELSLSAVEGREAFRDSVLTNVIEEEQ
experiment.sample.molecule[0].mw43.012
experiment.sample.molecule[0].total_mw258.072
experiment.sample.molecule[0].number_molecules6
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 HEPES 150 mM NaCl 2 mM TCEP
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentgel filtration buffer
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 NdmB hexamer
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.date2018-05-21
experiment.storage_temperature4.0
experiment.cell_temperature18.0
experiment.exposure_time10.0
experiment.number_of_frames36
experiment.wavelength0.15
experiment.sample_detector_distance3.0
experiment.concentration_minnull
experiment.concentration_max9.7
experiment.sample_volume140.0
experiment.flow_rate0.05
experiment.s_min0.033
experiment.s_max2.809
experiment.total_exposure_timenull
experiment.seccolumn1
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDFG7_fit1_model1_img.png
fits[0].models[0].softwareDAMMIF
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fits[0].models[0].model_titlenull
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fits[0].models[0].model_mw222.98
fits[0].models[0].bead_radius4.0
fits[0].models[0].lognull
fits[0].models[0].symmetryP3
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_value0.959
fits[0].p_value0.294224
fits[0].fit_residual_plotB-P3_home_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDFG7_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_mw275.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i00.6081
pddf_i0_errornull
guinier_i00.61
guinier_i0_errornull
pddf_rg4.24
pddf_rg_errornull
guinier_rg4.325
guinier_rg_errornull
pddf_dmax12.23
pddf_dmax_errornull
porod_volumenull
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first12
guinier_point_last113
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDFG7_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json：36 field values
Field pathRaw value
codeSASDFG7
statussuccess
started_at2026-08-11T15:29:21.285823+00:00
finished_at2026-08-11T15:29:34.354155+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDFG7",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "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/SASDFG7.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFG7.dat",
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  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFG7_pofr_img.png",
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFG7.sascif",
  "experiment": {
    "instrument": {
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        "type": null,
        "name": "Pilatus3 2M",
        "resolution": 0.172
      },
      "name": "Photon Factory (PF), High Energy Accelerator Research Organization (KEK)",
      "city": "Tsukuba",
      "country": "Japan",
      "beamline_name": "BL-10C",
      "beam_geometry": null,
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
      "sample_path_length": null,
      "line_collimation_slitlength": null,
      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Methylxanthine N3-demethylase NdmB",
          "short_name": null,
          "sequence": "MGSSHHHHHHENLYFQGSMKEQLKPLLEDKTYLRHFWHPVCTLNEFERANASGHGPMGVTLLGEKLVLARLNSKIIAA\r\nADRCAHRSAQLSIGRVCSNAGKDYLECPYHGWRYDEAGACQLIPACPDKSISPRAKISSF\r\nDCEVKYDIVWVRLDNSFDCTQIPYLSDFDNPDMQVIVADSYIWETVAERRWENFTDFSHF\r\nAFVHPGTLYDPFFASHPTVYVNRVDGELQFKLAPPREMKGIPPEAPMGDFTYRCTMPYSV\r\nNLEIKLWKDDSRFVLWTTASPVDNKSCRNFMIIVREKDNQPDHMHLAFQKRVLDEDQPVI\r\nESQWPLEIQTSEVSVATDKISVQFRKWHKELSLSAVEGREAFRDSVLTNVIEEEQ",
          "organism": "Pseudomonas putida",
          "uniprot_code": "H9N290",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "hexamer",
          "molecular_type": "protein",
          "uniprot_sequence": "MKEQLKPLLEDKTYLRHFWHPVCTLNEFERANASGHGPMGVTLLGEKLVLARLNSKIIAA\nADRCAHRSAQLSIGRVCSNAGKDYLECPYHGWRYDEAGACQLIPACPDKSISPRAKISSF\nDCEVKYDIVWVRLDNSFDCTQIPYLSDFDNPDMQVIVADSYIWETVAERRWENFTDFSHF\nAFVHPGTLYDPFFASHPTVYVNRVDGELQFKLAPPREMKGIPPEAPMGDFTYRCTMPYSV\nNLEIKLWKDDSRFVLWTTASPVDNKSCRNFMIIVREKDNQPDHMHLAFQKRVLDEDQPVI\nESQWPLEIQTSEVSVATDKISVQFRKWHKELSLSAVEGREAFRDSVLTNVIEEEQ",
          "mw": 43.012,
          "total_mw": 258.072,
          "number_molecules": 6,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM HEPES 150 mM NaCl 2 mM TCEP",
        "concentration_unit": null,
        "comment": "gel filtration buffer",
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Pseudomonas putida CBB5 NdmB hexamer",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "South Korea",
            "full_name": "Korea University",
            "webpage": "https://www.korea.edu/"
          }
        ],
        "contributor_name": "Jun Hoe",
        "contributor_surname": "Kim",
        "orcid": "https://orcid.org/0000-0001-5866-9952"
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