SASDAQ7

PBX1-PREB1-DNA complex

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 · PBX1-PREB1-DNA complex

Concentration— – 3.8 mg/mlBuffer / pH20 mM Tris-HCl 150 mM NaCl 5% glycerol 1 mM DTT / 7.4
Experimental temperature— Facility / beamlinePETRA III / EMBL P12
Wavelength0.12 nmExposure— s × —

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Pre-B-cell leukemia transcription factor 1
View sequence
MDEQPRLMHSHAGVGMAGHPGLSQHLQDGAGGTEGEGGRKQDIGDILQQIMTITDQSLDEAQARKHALNCHRMKPALFNVLCEIKEKTVLSIRGAQEEEPTDPQLMRLDNMLLAEGVAGPEKGGGSAAAAAAAAASGGAGSDNSVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVSIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAK
proteinHomo sapiensP404241–308monomerMolecule count 134.455 kDa
Homeobox protein PKNOX1
View sequence
MMATQTLSIDSYQDGQQMQVVTELKTEQDPNCSEPDAEGVSPPPVESQTPMDVDKQAIYRHPLFPLLALLFEKCEQSTQGSEGTTSASFDVDIENFVRKQEKEGKPFFCEDPETDNLMVKAIQVLRIHLLELEKVNELCKDFCSRYIACLKTEMNSETLLSGEPGSPYSPVQSQQIQSAITGTISPQGIVVPASALQQGNVAMATVAGGTVYQPVTVVTPQGQVVTQTLSPGTIRIQNSQLQLQLNQDLSILHQDDGSSKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQPMLDSSCSETPKTKKKTAQNRPVQRF
proteinHomo sapiensP553471–344monomerMolecule count 138.339 kDa
DNA 22mer
View sequence
5'-GCCTAGTGATTGACAGATTCCT-3'
DNA———–—monomerMolecule count 111.9 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11682[3]0.027543–4.45043 1/nmHas uncertainty columnMissing 031sasbdb/entries/q7/sasdaq7/source/SASDAQ7.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)16.3—nm
i0Guinier1640.0——
i0P(r)1613.0——
mwExperimental80.0—kDa
mwGuinier I(0)80.0—kDa
mwPorod136.0—kDa
porod_volumePorod173.0—nm³
rgGuinier4.8—nm
rgP(r)4.8—nm

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 Tris-HCl 150 mM NaCl 5% glycerol 1 mM DTTBuffer concentration20.0 mM
pH7.4Additives150 mM NaCl, 5% glycerol, 1 mM DTT
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2013-12-06Storage / measurement temperature— / —
Exposure time—Frames—
Wavelength0.12Sample-to-detector distance3.1
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.028 – 4.45Sample 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

CategoryFileStatusSizeChecksumDownload and View
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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:224 field values
Field pathRaw value
codeSASDAQ7
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleThe flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding.
project.publication.titleThe flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding.
project.publication.author_listMathiasen L, Valentini E, Boivin S, Cattaneo A, Blasi F, Svergun DI, Bruckmann C
project.publication.journalFEBS J
project.publication.doi10.1111/febs.13801
project.publication.pmid27390177
project.publication.published_date2016 Aug
project.statusreleased
project.submitted_datenull
project.released_date2016-07-25
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDAQ7.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDAQ7.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAQ7_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAQ7_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAQ7_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAQ7_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDAQ7.sascif
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_namePre-B-cell leukemia transcription factor 1
experiment.sample.molecule[0].short_namePBX1
experiment.sample.molecule[0].sequenceMDEQPRLMHSHAGVGMAGHPGLSQHLQDGAGGTEGEGGRKQDIGDILQQIMTITDQSLDE AQARKHALNCHRMKPALFNVLCEIKEKTVLSIRGAQEEEPTDPQLMRLDNMLLAEGVAGP EKGGGSAAAAAAAAASGGAGSDNSVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVM NLLREQSRTRPISPKEIERMVSIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF NKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQE EANIYAAK
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeP40424
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last308
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMDEQPRLMHSHAGVGMAGHPGLSQHLQDGAGGTEGEGGRKQDIGDILQQIMTITDQSLDE AQARKHALNCHRMKPALFNVLCEIKEKTVLSIRGAQEEEPTDPQLMRLDNMLLAEGVAGP EKGGGSAAAAAAAAASGGAGSDNSVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVM NLLREQSRTRPISPKEIERMVSIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNF NKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQE EANIYAAKTAVTATNVSAHGSQANSPSTPNSAGSSSSFNMSNSGDLFMSVQSLNGDSYQG AQVGANVQSQVDTLRHVISQTGGYSDGLAASQMYSPQGISANGGWQDATTPSSVTSPTEG PGSVHSDTSN
experiment.sample.molecule[0].mw34.455
experiment.sample.molecule[0].total_mw34.455
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_nameHomeobox protein PKNOX1
experiment.sample.molecule[1].short_namePREP1
experiment.sample.molecule[1].sequenceMMATQTLSIDSYQDGQQMQVVTELKTEQDPNCSEPDAEGVSPPPVESQTPMDVDKQAIYR HPLFPLLALLFEKCEQSTQGSEGTTSASFDVDIENFVRKQEKEGKPFFCEDPETDNLMVK AIQVLRIHLLELEKVNELCKDFCSRYIACLKTEMNSETLLSGEPGSPYSPVQSQQIQSAI TGTISPQGIVVPASALQQGNVAMATVAGGTVYQPVTVVTPQGQVVTQTLSPGTIRIQNSQ LQLQLNQDLSILHQDDGSSKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTN LTLLQVNNWFINARRRILQPMLDSSCSETPKTKKKTAQNRPVQRF
experiment.sample.molecule[1].organismHomo sapiens
experiment.sample.molecule[1].uniprot_codeP55347
experiment.sample.molecule[1].uniprot_range_first1
experiment.sample.molecule[1].uniprot_range_last344
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequenceMMATQTLSIDSYQDGQQMQVVTELKTEQDPNCSEPDAEGVSPPPVESQTPMDVDKQAIYR HPLFPLLALLFEKCEQSTQGSEGTTSASFDVDIENFVRKQEKEGKPFFCEDPETDNLMVK AIQVLRIHLLELEKVNELCKDFCSRYIACLKTKMNSETLLSGEPGSPYSPVQSQQIQSAI TGTISPQGIVVPASALQQGNVAMATVAGGTVYQPVTVVTPQGQVVTQTLSPGTIRIQNSQ LQLQLNQDLSILHQDDGSSKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTN LTLLQVNNWFINARRRILQPMLDSSCSETPKTKKKTAQNRPVQRFWPDSIASGVAQPPPS ELTMSEGAVVTITTPVNMNVDSLQSLSSDGATLAVQQVMMAGQSEDESVDSTEEDAGALA PAHISGLVLENSDSLQ
experiment.sample.molecule[1].mw38.339
experiment.sample.molecule[1].total_mw38.339
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.molecule[2].long_nameDNA 22mer
experiment.sample.molecule[2].short_namenull
experiment.sample.molecule[2].sequence5'-GCCTAGTGATTGACAGATTCCT-3'
experiment.sample.molecule[2].organismnull
experiment.sample.molecule[2].uniprot_codenull
experiment.sample.molecule[2].uniprot_range_firstnull
experiment.sample.molecule[2].uniprot_range_lastnull
experiment.sample.molecule[2].oligomerizationmonomer
experiment.sample.molecule[2].molecular_typeDNA
experiment.sample.molecule[2].uniprot_sequencenull
experiment.sample.molecule[2].mw11.9
experiment.sample.molecule[2].total_mw11.9
experiment.sample.molecule[2].number_molecules1
experiment.sample.molecule[2].complex_stateFalse
experiment.sample.molecule[2].deuterationnull
experiment.sample.molecule[2].molecule_sourcebiological
experiment.sample.molecule[2].molecule_descriptionnull
experiment.sample.buffer.name20 mM Tris-HCl 150 mM NaCl 5% glycerol 1 mM DTT
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive150 mM NaCl, 5% glycerol, 1 mM DTT
experiment.sample.buffer.concentration20.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.4
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.namePBX1-PREB1-DNA 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_nameEMBL-Hamburg
experiment.contributor[0].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[0].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[0].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[0].contributor_nameErica
experiment.contributor[0].contributor_surnameValentini
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitmg/ml
experiment.date2013-12-06
experiment.storage_temperaturenull
experiment.cell_temperaturenull
experiment.exposure_timenull
experiment.number_of_framesnull
experiment.wavelength0.12
experiment.sample_detector_distance3.1
experiment.concentration_minnull
experiment.concentration_max3.8
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.028
experiment.s_max4.45
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].softwarenull
fits[0].chi_square_value1.138489
fits[0].p_value0.133933
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fits[2].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[]
intensity_unitnull
experimental_mw80.0
experimental_mw_errornull
guinier_i0_mw80.0
guinier_i0_mw_errornull
porod_mw136.0
porod_mw_errornull
pddf_i01613.0
pddf_i0_errornull
guinier_i01640.0
guinier_i0_errornull
pddf_rg4.8
pddf_rg_errornull
guinier_rg4.8
guinier_rg_errornull
pddf_dmax16.3
pddf_dmax_errornull
porod_volume173.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first15
guinier_point_last94
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDAQ7_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDAQ7
statussuccess
started_at2026-08-11T15:36:18.615750+00:00
finished_at2026-08-11T15:36:27.139722+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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View the complete summary.json source
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    "title": "The flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding.",
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      "title": "The flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding.",
      "author_list": "Mathiasen L, Valentini E, Boivin S, Cattaneo A, Blasi F, Svergun DI, Bruckmann C",
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View the complete manifest.json source
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