SASDBQ4

Neisseria meningitidis iron-regulated FrpD-FrpC lipoprotein/protein complex

Data type: SASBDB experimental data Status: Published Curve type: Merged Last updated: 2023-05-25T11:21:52.654103+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Neisseria meningitidis iron-regulated FrpD-FrpC lipoprotein/protein complex

Concentration0.75 – 4.9 Buffer / pH50 mM Tris-HCl 150 mM NaCl 0.01% NaN3 / 7.4
Experimental temperature— Facility / beamlineDORIS III, DESY / EMBL X33
Wavelength0.15 nmExposure15.0 s × 8

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Iron-regulated outer membrane lipoprotein FrpD
View sequence
KEQTSFNNPEPMTGFEHTVTFDFQGTKMVIPYGYLARYTQDNATKWLSDTPGQDAYSINLIEISVYYKKTDQGWVLEPYNQQNKAHFIQFLRDGLDSVDDIVIRKDACSLSTTMGERLLTYGVKKMPSAYPEYEAYEDKRHIPENPYFHEFYYIKKGENPAIITHRNNRINQTEEDSYSTSVGSCINGFTVQYYPFIREKQQLTQQELVGYHQQVEQLVQSFVNNSNKK
proteinNeisseria meningitidisQ0884043–271monomerMolecule count 126.756 kDa
Iron-regulated protein FrpC
View sequence
MNEGEVVLTPEQIQTLRGYASRGDTYGGWRYLANLGDRYADDAAAIVGKDANLNGLNLWMKKGVENLWDDTVGKKTRLEKFDRVALQHFRQYARLINQNNGRLPNTSEIERSYYKAVTDNGVSSSAAIDLVINRSLPDMADGYWALGLGIEAERIHNEQAVNNPNGSERDNRKQLISALDKGFDGSFKEKHFTFLQSVMMDVTKLGVEYTIDGWQKIGGWGNGIINDLYKSVVKREWTGIFEIVNNNIKQGNEAFKNEINSLVHDMKAAGKEFGDDLNTQWNNLTQAAEIIYNDIVDNTSQGIEKGVKAIKELSEKMKNAASDLADGSAEKAKQVVEDLAQAAKEAYENAKSTAEKAAQAAREFFKGLPSFKDLAEKFRDLFPNPEGWIDDGHQCLAPWVKETKKRNGKYHVYD
proteinNeisseria meningitidisQ9JYV51–414monomerMolecule count 146.402 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
12170[3]0.0854979–6.03197 1/nmHas uncertainty columnMissing 055sasbdb/entries/q4/sasdbq4/source/SASDBQ4.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)13.5—nm
i0Guinier50.30.4—
i0P(r)50.70.15—
mwExperimental40.0—kDa
mwPorod74.0—kDa
porod_volumePorod123.0—nm³
rgGuinier3.720.4nm
rgP(r)3.860.01nm

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 name50 mM Tris-HCl 150 mM NaCl 0.01% NaN3Buffer concentration50.0 mM
pH7.4Additives150 mM NaCl, 0.01% NaN3
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2011-10-19Storage / measurement temperature10.0 / —
Exposure time15.0Frames8
Wavelength0.15Sample-to-detector distance2.7
SourceX-ray synchrotronDetectorPilatus 1M-W
Facility / beamlineDORIS III, DESY / EMBL X33 · Hamburg, Germany
q range0.085 – 6.032Sample 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:173 field values
Field pathRaw value
codeSASDBQ4
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleStructural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis.
project.publication.titleStructural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis.
project.publication.author_listSviridova E, Rezacova P, Bondar A, Veverka V, Novak P, Schenk G, Svergun DI, Kuta Smatanova I, Bumba L
project.publication.journalSci Rep
project.publication.doi10.1038/srep40408
project.publication.pmid28084396
project.publication.published_date2017 Jan 13
project.statusreleased
project.submitted_date2016-04-05
project.released_date2017-01-26
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDBQ4.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDBQ4.dat
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pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBQ4_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBQ4_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDBQ4.sascif
experiment.instrument.detector.typeCustom-built
experiment.instrument.detector.namePilatus 1M-W
experiment.instrument.detector.resolution0.172
experiment.instrument.nameDORIS III, DESY
experiment.instrument.cityHamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL X33
experiment.instrument.beam_geometry0.60
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_nameIron-regulated outer membrane lipoprotein FrpD
experiment.sample.molecule[0].short_nameFrpD
experiment.sample.molecule[0].sequencekeqtsfnnpepmtgfehtvtfdfqgtkmvipygylarytqdnatkwlsdtpgqdaysinlieisvyykktdqgwvlepynqqnkahfiqflrdgldsvddivirkdacslsttmgerlltygvkkmpsaypeyeayedkrhipenpyfhefyyikkgenpaiithrnnrinqteedsystsvgscingftvqyypfirekqqltqqelvgyhqqveqlvqsfvnnsnkk
experiment.sample.molecule[0].organismNeisseria meningitidis
experiment.sample.molecule[0].uniprot_codeQ08840
experiment.sample.molecule[0].uniprot_range_first43
experiment.sample.molecule[0].uniprot_range_last271
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMRPYATTIYQLFILFIGSVFTMTSCEPVNEKTDQKAVSAQQAKEQTSFNNPEPMTGFEHT VTFDFQGTKMVIPYGYLARYTQDNATKWLSDTPGQDAYSINLIEISVYYKKTDQGWVLEP YNQQNKAHFIQFLRDGLDSVDDIVIRKDACSLSTTMGERLLTYGVKKMPSAYPEYEAYED KRHIPENPYFHEFYYIKKGENPAIITHRNNRINQTEEDSYSTSVGSCINGFTVQYYPFIR EKQQLTQQELVGYHQQVEQLVQSFVNNSNKK
experiment.sample.molecule[0].mw26.756
experiment.sample.molecule[0].total_mw26.756
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.molecule[1].long_nameIron-regulated protein FrpC
experiment.sample.molecule[1].short_nameFrpC
experiment.sample.molecule[1].sequencemnegevvltpeqiqtlrgyasrgdtyggwrylanlgdryaddaaaivgkdanlnglnlwmkkgvenlwddtvgkktrlekfdrvalqhfrqyarlinqnngrlpntseiersyykavtdngvsssaaidlvinrslpdmadgywalglgieaerihneqavnnpngserdnrkqlisaldkgfdgsfkekhftflqsvmmdvtklgveytidgwqkiggwgngiindlyksvvkrewtgifeivnnnikqgneafkneinslvhdmkaagkefgddlntqwnnltqaaeiiyndivdntsqgiekgvkaikelsekmknaasdladgsaekakqvvedlaqaakeayenakstaekaaqaareffkglpsfkdlaekfrdlfpnpegwiddghqclapwvketkkrngkyhvyd
experiment.sample.molecule[1].organismNeisseria meningitidis
experiment.sample.molecule[1].uniprot_codeQ9JYV5
experiment.sample.molecule[1].uniprot_range_first1
experiment.sample.molecule[1].uniprot_range_last414
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequenceMNEGEVVLTPEQIQTLRGYASRGDTYGGWRYLANLGDRYADDAAAIVGKDANLNGLNLWM KKGVENLWDDTVGKKTRLEKFDRVALQHFRQYARLINQNNGRLPNTSEIERSYYKAVTDN GVSSSAAIDLVINRSLPDMADGYWALGLGIEAERIHNEQAVNNPNGSERDNRKQLISALD KGFDGSFKEKHFTFLQSVMMDVTKLGVEYTIDGWQKIGGWGNGIINDLYKSVVKREWTGI FEIVNNNIKQGNEAFKNEINSLVHDMKAAGKEFGDDLNTQWNNLTQAAEIIYNDIVDNTS QGIEKGVKAIKELSEKMKNAASDLADGSAEKAKQVVEDLAQAAKEAYENAKSTAEKAAQA AREFFKGLPSFKDLAEKFRDLFPNPEGWIDDGHQCLAPWVKETKKRNGKYHVYDPLALDL DGDGIETVATKGFAGSLFDHTNNGIRTATGWVSADDGLLVRDLNGNGIIDNGAELFGDNT KLADGSFAKHGYAALAELDSNGDNIINAADAAFQTLRVWQDLNQDGISQANELRTLEELG IQSLDLAYKDVNKNLGNGNTLAQQGSYTKTDGTTAKMGDLLLAADNLHSRFKDKVELTAE QAKAANLAGIGRLRDLREAAALSGDLANMLKAYSAAETKEAQLALLDNLIHKWAETDSNW GKKSPMRLSTDWTQTANEGIALTPSQVAQLKKNALVSLSDKAKAAIDAARDRIAVLDAYT GQDSNTLYYMSEEDALNIVKVTNDTYDHLAKNIYQNLLFQTRLQPYLNQISFKMENDTFT LDFSGLVQAFNHVKETNPQKAFVDLAEMLAYGELRSWYEGRRLMTDYVEEAKKAGKFEDY QKVLGQETVALLAKTSGTQADDILQNVGFGHNKNVSLYGNDGNDTLIGGAGNDYLEGGSG SDTYVFGEGFGQDTVYNYDYATGRKDIIRFTDGITADMLTFTREGNHLLIKAKDGSGQVT VQSYFQNDGSGAYRIDEIHFDNGKVLDVATVKELVQQSTDGSDRLYAYQSGNTLNGGLGD DYLYGADGDDLLNGDAGNDSIYSGNGNDTLDGGEGNDALYGYNGNDALNGGEGNDHLNGE DGNDTLIGGAGNDYLEGGSGSDTYVFGKGFGQDTVYNYDYATGRKDIIRFTDGITADMLT FTREGNHLLIKAKDGSGQVTVQYYFQNDGSGAYRIDEIHFDNGKVLDVATVKELVQQSTD GSDRLYAYQSGNTLNGGLGDDYLYGADGDDLLNGDAGNDSIYSGNGNDTLDGGEGNDALY GYNGNDALNGGEGNDHLNGEDGNDTLIGGAGNDYLEGGSGSDTYVFGKGFGQDAVYNYDY ATGRKDIIRFTDGITADMLTFTREGNHLLIKAKDGSGQVTVQSYFQNDGSGAYRIDEIHF DNGKVLDVATVKELVQQSTDGSDRLYAYQSGNTLNGGLGDDYLYGADGDDLLNGDAGNDS IYSGNGNDTLNGGEGNDALYGYNGNDALNGGEGNDHLNGEDGNDTLIGGAGNDYLEGGSG SDTYVFGKGFGQDAVYNYDYATGRKDIIRFTDGITADMLTFTREGNHLLIKAKDGSGQVT VQSYFQNDGSGAYRIDEIHFDNGKVLDVATVKELVQQSTDGSDRLYAYQSGSTLNGGLGD DYLYGADGDDLLNGDAGNDSIYSGNGNDTLDGGEGNDALYGYNGNDALNGGEGNDHLNGE DGNDTLIGGAGNDYLEGGSGSDTYVFGEGFGQDTVYNYHVDKNSDTMHFKGFKAADVHFI RSGSDLVLSASEQDNVRISGFFYGENHRVDTFVFDDAAISNPDFAKYINAGNNLVQSMSV FGSNTAATGGNVDANIQSVQQPLLVTPSA
experiment.sample.molecule[1].mw46.402
experiment.sample.molecule[1].total_mw46.402
experiment.sample.molecule[1].number_molecules1
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.name50 mM Tris-HCl 150 mM NaCl 0.01% NaN3
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive150 mM NaCl, 0.01% NaN3
experiment.sample.buffer.concentration50.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.4
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameNeisseria meningitidis iron-regulated FrpD-FrpC lipoprotein/protein complex
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].addressStanford, California, USA
experiment.contributor[0].affiliation[0].full_nameStanford University
experiment.contributor[0].affiliation[0].webpagehttps://www.stanford.edu/
experiment.contributor[0].contributor_nameGundolf
experiment.contributor[0].contributor_surnameSchenk
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2011-10-19
experiment.storage_temperature10.0
experiment.cell_temperaturenull
experiment.exposure_time15.0
experiment.number_of_frames8
experiment.wavelength0.15
experiment.sample_detector_distance2.7
experiment.concentration_min0.75
experiment.concentration_max4.9
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.085
experiment.s_max6.032
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].comment
fits[0].models[0].user122
fits[0].fit_unit1/A
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fits[0].chi_square_value1.15
fits[0].p_value0.029
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fits[0].fit_lognull
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fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionnull
experiment_descriptionX-ray synchrotron radiation scattering data from solutions of the 1:1 FrpD-FrpC complex from Neisseria meningitidis in 50 Tris-HCl, 150 mM NaCl, 0.01% NaN3 were collected on the X33 beam line at the DORIS storage ring (DESY, Hamburg, Germany) using a Pilatus 1M-W detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.15 nm). The data displayed in this entry shows the merged and extrapolated to zero-concentration SAXS profile derived from solute concentrations measured across the range of 0.75-4.90 mg/ml. The SAXS data for each sample were measured using an exposure time of 120 s (collected as 8 x 15 s frames) and were normalized to the intensity of the transmitted beam and radially averaged. The scattering of the solvent-blank was subtracted and the resulting subtracted data were scaled to each respective protein concentration prior to merging.
tags[0]X33
intensity_unitnull
experimental_mw40.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw74.0
porod_mw_errornull
pddf_i050.7
pddf_i0_error0.15
guinier_i050.3
guinier_i0_error0.4
pddf_rg3.86
pddf_rg_error0.01
guinier_rg3.72
guinier_rg_error0.4
pddf_dmax13.5
pddf_dmax_errornull
porod_volume123.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first35
guinier_point_last97
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDBQ4_datloglog_img.png
symmetrynull
last_modified2023-05-25T11:21:52.654103+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDBQ4
statussuccess
started_at2026-08-11T14:28:36.390456+00:00
finished_at2026-08-11T14:28:45.385799+00:00
source_last_modified2023-05-25T11:21:52.654103+02:00
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View the complete summary.json source
{
  "code": "SASDBQ4",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis.",
    "publication": {
      "title": "Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis.",
      "author_list": "Sviridova E, Rezacova P, Bondar A, Veverka V, Novak P, Schenk G, Svergun DI, Kuta Smatanova I, Bumba L",
      "journal": "Sci Rep",
      "doi": "10.1038/srep40408",
      "pmid": "28084396",
      "published_date": "2017 Jan 13"
    },
    "status": "released",
    "submitted_date": "2016-04-05",
    "released_date": "2017-01-26"
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            "address": "Stanford, California, USA",
            "full_name": "Stanford University",
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View the complete manifest.json source
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