SASDCH6

GGDEF domain from Marinobacter aquaeolei diguanylate cyclase complexed with c-di-GMP - Northeast Structural Genomics Consortium Target MqR89a

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

Sample 1 · GGDEF domain from Marinobacter aquaeolei diguanylate cyclase complexed with c-di-GMP - Northeast Structural Genomics Consortium Target MqR89a

Concentration1.92 – 6.1 Buffer / pH5 mM DTT 100 mM NaCl 10 mM Tris-HCl 0.02 % NaN3 / 7.5
Experimental temperature20.0 Facility / beamlineStanford Synchrotron Radiation Lightsource (SSRL) / BL4-2
Wavelength0.13 nmExposure1.0 s × 20

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Diguanylate cyclase
View sequence
MEQLAKLSMTDRLTGLLNRGTWENLVDAEYERFRRYGQATSLVMFDIDHFKPVNDTYGHLAGDEVIRHTADVTRNNIRQSDSAGRYGGEEFGIILPETDAESARVICERIREAIEKSTVSTSAGDIQYTVSMGIAQLTETPENYMQWMQKADEALYKAKESGRNKVVVSLEHHHHHH
proteinMarinobacter hydrocarbonoclasticusA1U3W3—–—monomerMolecule count 120.153 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1348[3]0.026173–0.349599 1/AHas uncertainty columnMissing 00sasbdb/entries/h6/sasdch6/source/SASDCH6.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)6.58—Å
i0Guinier1014.83——
i0P(r)1018.0——
mwExperimental19.07—kDa
mwPorod19.07—kDa
porod_volumePorod31.65—ų
rgGuinier1.88—Å
rgP(r)1.91—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 name5 mM DTT 100 mM NaCl 10 mM Tris-HCl 0.02 % NaN3Buffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2010-02-12Storage / measurement temperature-80.0 / 20.0
Exposure time1.0Frames20
Wavelength0.13Sample-to-detector distance1.5
SourceX-ray synchrotronDetectorRayonix MX225-HE
Facility / beamlineStanford Synchrotron Radiation Lightsource (SSRL) / BL4-2 · Menlo Park, CA, USA
q range0.262 – 3.496Sample 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 (6 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:182 field values
Field pathRaw value
codeSASDCH6
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleSmall angle X-ray scattering as a complementary tool for high-throughput structural studies.
project.publication.titleSmall angle X-ray scattering as a complementary tool for high-throughput structural studies.
project.publication.author_listGrant TD, Luft JR, Wolfley JR, Tsuruta H, Martel A, Montelione GT, Snell EH
project.publication.journalBiopolymers
project.publication.doi10.1002/bip.21630
project.publication.pmid21462184
project.publication.published_date2011 Aug
project.statusreleased
project.submitted_date2017-07-12
project.released_date2017-07-17
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experiment.instrument.detector.typenull
experiment.instrument.detector.nameRayonix MX225-HE
experiment.instrument.detector.resolutionnull
experiment.instrument.nameStanford Synchrotron Radiation Lightsource (SSRL)
experiment.instrument.cityMenlo Park, CA
experiment.instrument.countryUSA
experiment.instrument.beamline_nameBL4-2
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_nameDiguanylate cyclase
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMEQLAKLSMTDRLTGLLNRGTWENLVDAEYERFRRYGQATSLVMFDIDHFK PVNDTYGHLAGDEVIRHTADVTRNNIRQSDSAGRYGGEEFGIILPETDAES ARVICERIREAIEKSTVSTSAGDIQYTVSMGIAQLTETPENYMQWMQKADE ALYKAKESGRNKVVVSLEHHHHHH
experiment.sample.molecule[0].organismMarinobacter hydrocarbonoclasticus
experiment.sample.molecule[0].uniprot_codeA1U3W3
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_sequenceMAFNQDANEFHWLMDMLESVEVGLVVLDLDFHVQAWNGFMEHHSGITARQIRDKVLFEVF PDIPEAWLTRKVDAVAMLNTRAFTSWEQRPYLFKFRNTRPITGTEEYMFQNLTISPITAP NGEVEKVCLLVYDVTEFASSKRALERANEQLAKLSMTDRLTGLLNRGTWENLVDAEYERF RRYGQATSLVMFDIDHFKPVNDTYGHLAGDEVIRHTADVTRNNIRQSDSAGRYGGEEFGI ILPETDAESARVICERIREAIEKSTVSTSAGDIQYTVSMGIAQLTETPENYMQWMQKADE ALYKAKESGRNKVVVS
experiment.sample.molecule[0].mw20.153
experiment.sample.molecule[0].total_mw20.153
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.name5 mM DTT 100 mM NaCl 10 mM Tris-HCl 0.02 % NaN3
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.nameGGDEF domain from Marinobacter aquaeolei diguanylate cyclase complexed with c-di-GMP - Northeast Structural Genomics Consortium Target MqR89a
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_nameUniversity at Buffalo
experiment.contributor[0].affiliation[0].webpagenull
experiment.contributor[0].contributor_nameTom
experiment.contributor[0].contributor_surnameGrant
experiment.contributor[0].orcidhttps://orcid.org/0000-0002-8583-3700
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2010-02-12
experiment.storage_temperature-80.0
experiment.cell_temperature20.0
experiment.exposure_time1.0
experiment.number_of_frames20
experiment.wavelength0.13
experiment.sample_detector_distance1.5
experiment.concentration_min1.92
experiment.concentration_max6.1
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.262
experiment.s_max3.496
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwarePDB (Protein Data Bank)
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fits[0].models[0].bead_radius1.9
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fits[0].softwareCRYSOL
fits[0].chi_square_value4.18
fits[0].p_value0.0
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fits[1].softwareDAMMIF
fits[1].chi_square_value1.39
fits[1].p_value0.000151
fits[1].fit_residual_plotSASDCH6_fit2_fitresiduals_img.png
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fits[1].software_version
fits[1].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version4.5a
i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[]
intensity_unitnull
experimental_mw19.07
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw19.07
porod_mw_errornull
pddf_i01018.0
pddf_i0_errornull
guinier_i01014.83
guinier_i0_errornull
pddf_rg1.91
pddf_rg_errornull
guinier_rg1.88
guinier_rg_errornull
pddf_dmax6.58
pddf_dmax_errornull
porod_volume31.65
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_firstnull
guinier_point_lastnull
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDCH6_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDCH6
statussuccess
started_at2026-08-11T15:10:12.519784+00:00
finished_at2026-08-11T15:10:21.029527+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDCH6",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Small angle X-ray scattering as a complementary tool for high-throughput structural studies.",
    "publication": {
      "title": "Small angle X-ray scattering as a complementary tool for high-throughput structural studies.",
      "author_list": "Grant TD, Luft JR, Wolfley JR, Tsuruta H, Martel A, Montelione GT, Snell EH",
      "journal": "Biopolymers",
      "doi": "10.1002/bip.21630",
      "pmid": "21462184",
      "published_date": "2011 Aug"
    },
    "status": "released",
    "submitted_date": "2017-07-12",
    "released_date": "2017-07-17"
  },
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    "sample": {
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          "long_name": "Diguanylate cyclase",
          "short_name": null,
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          "uniprot_code": "A1U3W3",
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          "oligomerization": "monomer",
          "molecular_type": "protein",
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          "complex_state": false,
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