SASDCU4

Collagenase ColG s2s3as3b at pCa 5

Data type: SASBDB experimental data Status: Published Curve type: Extrapolated to infinite dilution Last updated: 2023-11-09T11:24:47.632397+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Collagenase ColG s2s3as3b at pCa 5

Concentration3.0 – 5.0 Buffer / pH10mM HEPES 100mM NaCl 0.2mM EGTA / 7.5
Experimental temperature10.0 Facility / beamlineAdvanced Light Source (ALS) / 12.3.1 (SIBYLS)
Wavelength0.1127 nmExposure— s × —

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Collagenase ColG segement s2s3as3b
View sequence
GSPGIPGTDNADISNNKAPIAKVTGPSTGAVGRNIEFSGKDSKDEDGKIVSYDWDFGDGATSRGKNSVHAYKKAGTYNVTLKVTDDKGATATESFTIEIKNEDTTTPITKEMEPNDDIKEANGPIVEGVTVKGDLNGSDDADTFYFDVKEDGDVTIELPYSGSSNFTWLVYKEGDDQNHIASGIDKNNSKVGTFKSTKGRHYVFIYKHDSASNISYSLNIKGLGNEKLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK
proteinHathewaya histolyticaQ9X721787–1118monomerMolecule count 137.2 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1950[3]0.012543–0.54135 1/AHas uncertainty columnMissing 00sasbdb/entries/u4/sasdcu4/source/SASDCU4.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)19.7—Å
estimated_volumeDAMFILT192.0—ų
i0Guinier24.550.36—
i0P(r)27.460.38—
mwExperimental37.2—kDa
porod_volumePorod98.4—ų
rgGuinier4.291.7Å
rgP(r)5.330.08Å

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 name10mM HEPES 100mM NaCl 0.2mM EGTABuffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2016-10-12Storage / measurement temperature4.0 / 10.0
Exposure time—Frames—
Wavelength0.1127Sample-to-detector distance1.5
SourceX-ray synchrotronDetectorPilatus3 X 2M
Facility / beamlineAdvanced Light Source (ALS) / 12.3.1 (SIBYLS) · Berkeley, CA, USA
q range0.125 – 5.413Sample 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:156 field values
Field pathRaw value
codeSASDCU4
statusPublished
type_of_curveExtrapolated to infinite dilution
angular_unit1/A
project.titleCa2+ - Induced Structural Change of Multi-Domain Collagen Binding Segments of Collagenases ColG and ColH from Hathewaya histolytica
project.publication.titleCa2+ - Induced Structural Change of Multi-Domain Collagen Binding Segments of Collagenases ColG and ColH from Hathewaya histolytica
project.publication.author_listChristopher E Ruth
project.publication.journalUniversity of Arkansas Dissertation
project.publication.doinull
project.publication.pmidnull
project.publication.published_date2018 December
project.statusreleased
project.submitted_date2017-06-02
project.released_date2019-08-07
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experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus3 X 2M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameAdvanced Light Source (ALS)
experiment.instrument.cityBerkeley, CA
experiment.instrument.countryUSA
experiment.instrument.beamline_name12.3.1 (SIBYLS)
experiment.instrument.beam_geometry
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_nameCollagenase ColG segement s2s3as3b
experiment.sample.molecule[0].short_names2s3as3b
experiment.sample.molecule[0].sequenceGSPGIPGTDNADISNNKAPIAKVTGPSTGAVGRNIEFSGKDSKDEDGKIVSYDWDFGDGATSRGKNSVHAYKKAGTYNVTLKVTDDKGATATESFTIEIKNEDTTTPITKEMEPNDDIKEANGPIVEGVTVKGDLNGSDDADTFYFDVKEDGDVTIELPYSGSSNFTWLVYKEGDDQNHIASGIDKNNSKVGTFKSTKGRHYVFIYKHDSASNISYSLNIKGLGNEKLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK
experiment.sample.molecule[0].organismHathewaya histolytica
experiment.sample.molecule[0].uniprot_codeQ9X721
experiment.sample.molecule[0].uniprot_range_first787
experiment.sample.molecule[0].uniprot_range_last1118
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMKKNILKILMDSYSKESKIQTVRRVTSVSLLAVYLTMNTSSLVLAKPIENTNDTSIKNVE KLRNAPNEENSKKVEDSKNDKVEHVKNIEEAKVEQVAPEVKSKSTLRSASIANTNSEKYD FEYLNGLSYTELTNLIKNIKWNQINGLFNYSTGSQKFFGDKNRVQAIINALQESGRTYTA NDMKGIETFTEVLRAGFYLGYYNDGLSYLNDRNFQDKCIPAMIAIQKNPNFKLGTAVQDE VITSLGKLIGNASANAEVVNNCVPVLKQFRENLNQYAPDYVKGTAVNELIKGIEFDFSGA AYEKDVKTMPWYGKIDPFINELKALGLYGNITSATEWASDVGIYYLSKFGLYSTNRNDIV QSLEKAVDMYKYGKIAFVAMERITWDYDGIGSNGKKVDHDKFLDDAEKHYLPKTYTFDNG TFIIRAGDKVSEEKIKRLYWASREVKSQFHRVVGNDKALEVGNADDVLTMKIFNSPEEYK FNTNINGVSTDNGGLYIEPRGTFYTYERTPQQSIFSLEELFRHEYTHYLQARYLVDGLWG QGPFYEKNRLTWFDEGTAEFFAGSTRTSGVLPRKSILGYLAKDKVDHRYSLKKTLNSGYD DSDWMFYNYGFAVAHYLYEKDMPTFIKMNKAILNTDVKSYDEIIKKLSDDANKNTEYQNH IQELADKYQGAGIPLVSDDYLKDHGYKKASEVYSEISKAASLTNTSVTAEKSQYFNTFTL RGTYTGETSKGEFKDWDEMSKKLDGTLESLAKNSWSGYKTLTAYFTNYRVTSDNKVQYDV VFHGVLTDNADISNNKAPIAKVTGPSTGAVGRNIEFSGKDSKDEDGKIVSYDWDFGDGAT SRGKNSVHAYKKAGTYNVTLKVTDDKGATATESFTIEIKNEDTTTPITKEMEPNDDIKEA NGPIVEGVTVKGDLNGSDDADTFYFDVKEDGDVTIELPYSGSSNFTWLVYKEGDDQNHIA SGIDKNNSKVGTFKSTKGRHYVFIYKHDSASNISYSLNIKGLGNEKLKEKENNDSSDKAT VIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITY GQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK
experiment.sample.molecule[0].mw37.2
experiment.sample.molecule[0].total_mw37.2
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.name10mM HEPES 100mM NaCl 0.2mM EGTA
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.nameCollagenase ColG s2s3as3b at pCa 5
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].addressFayetteville, AR, USA
experiment.contributor[0].affiliation[0].full_nameUniversity of Arkansas
experiment.contributor[0].affiliation[0].webpagehttps://www.uark.edu/
experiment.contributor[0].contributor_nameChristopher
experiment.contributor[0].contributor_surnameRuth
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-10-12
experiment.storage_temperature4.0
experiment.cell_temperature10.0
experiment.exposure_timenull
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experiment.wavelength0.1127
experiment.sample_detector_distance1.5
experiment.concentration_min3.0
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experiment.sample_volumenull
experiment.flow_ratenull
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experiment.s_max5.413
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].p_value0.357779
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fits[0].descriptionnull
estimated_volume_methodDAMFILT
pddf_softwareATSAS GNOM
pddf_software_version2.6.1
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Collagenase ColG s2s3as3b at pCa 5 in 10mM HEPES 100mM NaCl 0.2mM EGTA, pH 7.5 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS: Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.1127 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 3 and 5 mg/ml were measured at 10°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve. The model represents the averaged spatial representation of the protein (DAMFILT occupancy and volume-corrected bead model).
tags[]
intensity_unitnull
experimental_mw37.2
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i027.46
pddf_i0_error0.38
guinier_i024.55
guinier_i0_error0.36
pddf_rg5.33
pddf_rg_error0.08
guinier_rg4.29
guinier_rg_error1.7
pddf_dmax19.7
pddf_dmax_errornull
porod_volume98.4
porod_volume_errornull
estimated_volume192.0
estimated_volume_errornull
guinier_point_first20
guinier_point_last33
pddf_point_firstnull
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i0_calibration_standard_datanull
intensities_log_log_plotSASDCU4_datloglog_img.png
symmetrynull
last_modified2023-11-09T11:24:47.632397+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDCU4
statussuccess
started_at2026-08-11T16:40:06.520376+00:00
finished_at2026-08-11T16:40:14.433836+00:00
source_last_modified2023-11-09T11:24:47.632397+01:00
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View the complete summary.json source
{
  "code": "SASDCU4",
  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "angular_unit": "1/A",
  "project": {
    "title": "Ca2+ - Induced Structural Change of Multi-Domain Collagen Binding Segments of Collagenases ColG and ColH from Hathewaya histolytica",
    "publication": {
      "title": "Ca2+ - Induced Structural Change of Multi-Domain Collagen Binding Segments of Collagenases ColG and ColH from Hathewaya histolytica",
      "author_list": "Christopher E Ruth",
      "journal": "University of Arkansas Dissertation",
      "doi": null,
      "pmid": null,
      "published_date": "2018 December"
    },
    "status": "released",
    "submitted_date": "2017-06-02",
    "released_date": "2019-08-07"
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    "sample": {
      "molecule": [
        {
          "long_name": "Collagenase ColG segement s2s3as3b",
          "short_name": "s2s3as3b",
          "sequence": "GSPGIPGTDNADISNNKAPIAKVTGPSTGAVGRNIEFSGKDSKDEDGKIVSYDWDFGDGATSRGKNSVHAYKKAGTYNVTLKVTDDKGATATESFTIEIKNEDTTTPITKEMEPNDDIKEANGPIVEGVTVKGDLNGSDDADTFYFDVKEDGDVTIELPYSGSSNFTWLVYKEGDDQNHIASGIDKNNSKVGTFKSTKGRHYVFIYKHDSASNISYSLNIKGLGNEKLKEKENNDSSDKATVIPNFNTTMQGSLLGDDSRDYYSFEVKEEGEVNIELDKKDEFGVTWTLHPESNINDRITYGQVDGNKVSNKVKLRPGKYYLLVYKYSGSGNYELRVNK",
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          "oligomerization": "monomer",
          "molecular_type": "protein",
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          {
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            "address": "Fayetteville, AR, USA",
            "full_name": "University of Arkansas",
            "webpage": "https://www.uark.edu/"
          }
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View the complete manifest.json source
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