SASDDW4

Procollagen lysyl hydroxylase LH3 measured using SEC-SAXS

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2019-12-06T13:07:15.624532+01:00

The sample was injected at a load concentration of 3.5 mg/mL. The SEC column used was a Superdex 200 PC 3.2/300 Increase (GE Healthcare) at a flow rate 0.075 mL/min.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Procollagen lysyl hydroxylase LH3 measured using SEC-SAXS

Concentration— – 3.5 Buffer / pH25 mM HEPES, 200 mM NaCl / 8.0
Experimental temperature20.0 Facility / beamlineESRF / BM29
Wavelength0.09919 nmExposure1.0 s × 75

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Procollagen lysyl hydroxylase LH3
View sequence
SSDRPRGRDPVNPEKLLVITVATAETEGYLRFLRSAEFFNYTVRTLGLGEEWRGGDVARTVGGGQKVRWLKKEMEKYADREDMIIMFVDSYDVILAGSPTELLKKFVQSGSRLLFSAESFCWPEWGLAEQYPEVGTGKRFLNSGGFIGFATTIHQIVRQWKYKDDDDDQLFYTRLYLDPGLREKLSLNLDHKSRIFQNLNGALDEVVLKFDRNRVRIRNVAYDTLPIVVHGNGPTKLQLNYLGNYVPNGWTPEGGCGFCNQDRRTLPGGQPPPRVFLAVFVEQPTPFLPRFLQRLLLLDYPPDRVTLFLHNNEVFHEPHIADSWPQLQDHFSAVKLVGPEEALSPGEARDMAMDLCRQDPECEFYFSLDADAVLTNLQTLRILIEENRKVIAPMLSRHGKLWSNFWGALSPDEYYARSEDYVELVQRKRVGVWNVPYISQAYVIRGDTLRMELPQRDVFSGSDTDPDMAFCKSFRDKGIFLHLSNQHEFGRLLATSRYDTEHLHPDLWQIFDNPVDWKEQYIHENYSRALEGEGIVEQPCPDVYWFPLLSEQMCDELVAEMEHYGQWSGGRHEDSRLAGGYENVPTVDIHMKQVGYEDQWLQLLRTYVGPMTESLFPGYHTKARAVMNFVVRYRPDEQPSLRPHHDSSTFTLNVALNHKGLDYEGGGCRFLRYDCVISSPRKGWALLHPGRLTHYHEGLPTTWGTRYIMVSFVDPAAA
proteinHomo sapiensO6056825–738dimerMolecule count 290.0 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11040[3]0.05133567–4.927702 1/nmHas uncertainty columnMissing 0101sasbdb/entries/w4/sasddw4/source/SASDDW4.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)20.96—nm
i0Guinier61.50.12arbitrary
i0P(r)62.40.1arbitrary
mwExperimental180.0—kDa
mwGuinier I(0)184.06.0kDa
mwPorod170.0—kDa
porod_volumePorod268.0—nm³
rgGuinier5.050.07nm
rgP(r)5.3460.02nm

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 name25 mM HEPES, 200 mM NaClBuffer concentration—
pH8.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2018-02-28Storage / measurement temperature20.0 / 20.0
Exposure time1.0Frames75
Wavelength0.09919Sample-to-detector distance2.87
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineESRF / BM29 · Grenoble, France
q range0.051 – 4.928Sample 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
codeSASDDW4
statusPublished
type_of_curveSEC-SAS
angular_unit1/nm
project.titleMolecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3.
project.publication.titleMolecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3.
project.publication.author_listScietti L, Chiapparino A, De Giorgi F, Fumagalli M, Khoriauli L, Nergadze S, Basu S, Olieric V, Cucca L, Banushi B, Profumo A, Giulotto E, Gissen P, Forneris F
project.publication.journalNat Commun
project.publication.doi10.1038/s41467-018-05631-5
project.publication.pmid30089812
project.publication.published_date2018 Aug 8
project.statusreleased
project.submitted_date2018-03-09
project.released_date2018-08-13
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experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
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experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameProcollagen lysyl hydroxylase LH3
experiment.sample.molecule[0].short_nameLH3
experiment.sample.molecule[0].sequenceSSDRPRGRDPVNPEKLLVITVATAETEGYLRFLRSAEFFNYTVRTLGLGEEWRGGDVARTV GGGQKVRWLKKEMEKYADREDMIIMFVDSYDVILAGSPTELLKKFVQSGSRLLFSAESFC WPEWGLAEQYPEVGTGKRFLNSGGFIGFATTIHQIVRQWKYKDDDDDQLFYTRLYLDPGL REKLSLNLDHKSRIFQNLNGALDEVVLKFDRNRVRIRNVAYDTLPIVVHGNGPTKLQLNY LGNYVPNGWTPEGGCGFCNQDRRTLPGGQPPPRVFLAVFVEQPTPFLPRFLQRLLLLDYP PDRVTLFLHNNEVFHEPHIADSWPQLQDHFSAVKLVGPEEALSPGEARDMAMDLCRQDPE CEFYFSLDADAVLTNLQTLRILIEENRKVIAPMLSRHGKLWSNFWGALSPDEYYARSEDY VELVQRKRVGVWNVPYISQAYVIRGDTLRMELPQRDVFSGSDTDPDMAFCKSFRDKGIFL HLSNQHEFGRLLATSRYDTEHLHPDLWQIFDNPVDWKEQYIHENYSRALEGEGIVEQPCP DVYWFPLLSEQMCDELVAEMEHYGQWSGGRHEDSRLAGGYENVPTVDIHMKQVGYEDQWL QLLRTYVGPMTESLFPGYHTKARAVMNFVVRYRPDEQPSLRPHHDSSTFTLNVALNHKGL DYEGGGCRFLRYDCVISSPRKGWALLHPGRLTHYHEGLPTTWGTRYIMVSFVDPAAA
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeO60568
experiment.sample.molecule[0].uniprot_range_first25
experiment.sample.molecule[0].uniprot_range_last738
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMTSSGPGPRFLLLLPLLLPPAASASDRPRGRDPVNPEKLLVITVATAETEGYLRFLRSAE FFNYTVRTLGLGEEWRGGDVARTVGGGQKVRWLKKEMEKYADREDMIIMFVDSYDVILAG SPTELLKKFVQSGSRLLFSAESFCWPEWGLAEQYPEVGTGKRFLNSGGFIGFATTIHQIV RQWKYKDDDDDQLFYTRLYLDPGLREKLSLNLDHKSRIFQNLNGALDEVVLKFDRNRVRI RNVAYDTLPIVVHGNGPTKLQLNYLGNYVPNGWTPEGGCGFCNQDRRTLPGGQPPPRVFL AVFVEQPTPFLPRFLQRLLLLDYPPDRVTLFLHNNEVFHEPHIADSWPQLQDHFSAVKLV GPEEALSPGEARDMAMDLCRQDPECEFYFSLDADAVLTNLQTLRILIEENRKVIAPMLSR HGKLWSNFWGALSPDEYYARSEDYVELVQRKRVGVWNVPYISQAYVIRGDTLRMELPQRD VFSGSDTDPDMAFCKSFRDKGIFLHLSNQHEFGRLLATSRYDTEHLHPDLWQIFDNPVDW KEQYIHENYSRALEGEGIVEQPCPDVYWFPLLSEQMCDELVAEMEHYGQWSGGRHEDSRL AGGYENVPTVDIHMKQVGYEDQWLQLLRTYVGPMTESLFPGYHTKARAVMNFVVRYRPDE QPSLRPHHDSSTFTLNVALNHKGLDYEGGGCRFLRYDCVISSPRKGWALLHPGRLTHYHE GLPTTWGTRYIMVSFVDP
experiment.sample.molecule[0].mw90.0
experiment.sample.molecule[0].total_mw180.0
experiment.sample.molecule[0].number_molecules2
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.name25 mM HEPES, 200 mM NaCl
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
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experiment.sample.nameProcollagen lysyl hydroxylase LH3 measured using SEC-SAXS
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
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experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressItaly
experiment.contributor[0].affiliation[0].full_nameUniversity of Pavia
experiment.contributor[0].affiliation[0].webpagehttp://wcm-3.unipv.it
experiment.contributor[0].contributor_nameFederico
experiment.contributor[0].contributor_surnameForneris
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2018-02-28
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time1.0
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experiment.wavelength0.09919
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pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionThe sample was injected at a load concentration of 3.5 mg/mL. The SEC column used was a Superdex 200 PC 3.2/300 Increase (GE Healthcare) at a flow rate 0.075 mL/min.
experiment_descriptionSynchrotron SAXS data from solutions of procollagen lysyl hydroxylase LH3 in 25 mM HEPES, 200 mM NaCl, pH 8 were measured at 20°C using SEC-SAXS collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) equipped with a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09919 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.50 mg/ml was injected onto the column. 75 successive 1 second frames were collected through the sample elution peak and processed using CHROMIXS that included the identification and subtraction of an appropriate solvent-blank.
tags[]
intensity_unitarbitrary
experimental_mw180.0
experimental_mw_errornull
guinier_i0_mw184.0
guinier_i0_mw_error6.0
porod_mw170.0
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pddf_i062.4
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guinier_i061.5
guinier_i0_error0.12
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pddf_rg_error0.02
guinier_rg5.05
guinier_rg_error0.07
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pddf_dmax_errornull
porod_volume268.0
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estimated_volumenull
estimated_volume_errornull
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pddf_point_firstnull
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i0_calibration_standard_datanull
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symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDDW4
statussuccess
started_at2026-08-11T14:32:50.827778+00:00
finished_at2026-08-11T14:32:59.773566+00:00
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View the complete summary.json source
{
  "code": "SASDDW4",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3.",
    "publication": {
      "title": "Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3.",
      "author_list": "Scietti L, Chiapparino A, De Giorgi F, Fumagalli M, Khoriauli L, Nergadze S, Basu S, Olieric V, Cucca L, Banushi B, Profumo A, Giulotto E, Gissen P, Forneris F",
      "journal": "Nat Commun",
      "doi": "10.1038/s41467-018-05631-5",
      "pmid": "30089812",
      "published_date": "2018 Aug 8"
    },
    "status": "released",
    "submitted_date": "2018-03-09",
    "released_date": "2018-08-13"
  },
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      "country": "France",
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    },
    "sample": {
      "molecule": [
        {
          "long_name": "Procollagen lysyl hydroxylase LH3",
          "short_name": "LH3",
          "sequence": "SSDRPRGRDPVNPEKLLVITVATAETEGYLRFLRSAEFFNYTVRTLGLGEEWRGGDVARTV\r\nGGGQKVRWLKKEMEKYADREDMIIMFVDSYDVILAGSPTELLKKFVQSGSRLLFSAESFC\r\nWPEWGLAEQYPEVGTGKRFLNSGGFIGFATTIHQIVRQWKYKDDDDDQLFYTRLYLDPGL\r\nREKLSLNLDHKSRIFQNLNGALDEVVLKFDRNRVRIRNVAYDTLPIVVHGNGPTKLQLNY\r\nLGNYVPNGWTPEGGCGFCNQDRRTLPGGQPPPRVFLAVFVEQPTPFLPRFLQRLLLLDYP\r\nPDRVTLFLHNNEVFHEPHIADSWPQLQDHFSAVKLVGPEEALSPGEARDMAMDLCRQDPE\r\nCEFYFSLDADAVLTNLQTLRILIEENRKVIAPMLSRHGKLWSNFWGALSPDEYYARSEDY\r\nVELVQRKRVGVWNVPYISQAYVIRGDTLRMELPQRDVFSGSDTDPDMAFCKSFRDKGIFL\r\nHLSNQHEFGRLLATSRYDTEHLHPDLWQIFDNPVDWKEQYIHENYSRALEGEGIVEQPCP\r\nDVYWFPLLSEQMCDELVAEMEHYGQWSGGRHEDSRLAGGYENVPTVDIHMKQVGYEDQWL\r\nQLLRTYVGPMTESLFPGYHTKARAVMNFVVRYRPDEQPSLRPHHDSSTFTLNVALNHKGL\r\nDYEGGGCRFLRYDCVISSPRKGWALLHPGRLTHYHEGLPTTWGTRYIMVSFVDPAAA",
          "organism": "Homo sapiens",
          "uniprot_code": "O60568",
          "uniprot_range_first": 25,
          "uniprot_range_last": 738,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MTSSGPGPRFLLLLPLLLPPAASASDRPRGRDPVNPEKLLVITVATAETEGYLRFLRSAE\nFFNYTVRTLGLGEEWRGGDVARTVGGGQKVRWLKKEMEKYADREDMIIMFVDSYDVILAG\nSPTELLKKFVQSGSRLLFSAESFCWPEWGLAEQYPEVGTGKRFLNSGGFIGFATTIHQIV\nRQWKYKDDDDDQLFYTRLYLDPGLREKLSLNLDHKSRIFQNLNGALDEVVLKFDRNRVRI\nRNVAYDTLPIVVHGNGPTKLQLNYLGNYVPNGWTPEGGCGFCNQDRRTLPGGQPPPRVFL\nAVFVEQPTPFLPRFLQRLLLLDYPPDRVTLFLHNNEVFHEPHIADSWPQLQDHFSAVKLV\nGPEEALSPGEARDMAMDLCRQDPECEFYFSLDADAVLTNLQTLRILIEENRKVIAPMLSR\nHGKLWSNFWGALSPDEYYARSEDYVELVQRKRVGVWNVPYISQAYVIRGDTLRMELPQRD\nVFSGSDTDPDMAFCKSFRDKGIFLHLSNQHEFGRLLATSRYDTEHLHPDLWQIFDNPVDW\nKEQYIHENYSRALEGEGIVEQPCPDVYWFPLLSEQMCDELVAEMEHYGQWSGGRHEDSRL\nAGGYENVPTVDIHMKQVGYEDQWLQLLRTYVGPMTESLFPGYHTKARAVMNFVVRYRPDE\nQPSLRPHHDSSTFTLNVALNHKGLDYEGGGCRFLRYDCVISSPRKGWALLHPGRLTHYHE\nGLPTTWGTRYIMVSFVDP",
          "mw": 90.0,
          "total_mw": 180.0,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "25 mM HEPES, 200 mM NaCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 8.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Procollagen lysyl hydroxylase LH3 measured using SEC-SAXS",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Italy",
            "full_name": "University of Pavia",
            "webpage": "http://wcm-3.unipv.it"
          }
        ],
        "contributor_name": "Federico",
        "contributor_surname": "Forneris",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2018-02-28",
    "storage_temperature": 20.0,
    "cell_temperature": 20.0,
    "exposure_time": 1.0,
    "number_of_frames": 75,
    "wavelength": 0.09919,
    "sample_detector_distance": 2.87,
    "concentration_min": null,
    "concentration_max": 3.5,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.051,
    "s_max": 4.928,
    "total_exposure_time": null,
    "seccolumn": null
  },
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    {
      "models": [
        {
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          "software": "GASBOR",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDW4_fit3_model1.pdb",
          "model_mw": null,
          "bead_radius": 1.9,
          "log": null,
          "symmetry": null,
          "comment": null,
          "user": 294
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDW4_fit3_fit_img.png",
      "software": "GASBOR",
      "chi_square_value": 1.85,
      "p_value": 0.0,
      "fit_residual_plot": "SASDDW4_fit3_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDW4_fit3.fir",
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      "software_version": null,
      "description": null
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  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": "The sample was injected at a load concentration of 3.5 mg/mL. The SEC column used was a Superdex 200 PC 3.2/300 Increase (GE Healthcare) at a flow rate 0.075 mL/min.",
  "experiment_description": "Synchrotron SAXS data from solutions of procollagen lysyl hydroxylase LH3 in 25 mM HEPES, 200 mM NaCl, pH 8 were measured at 20°C using SEC-SAXS collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) equipped with a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09919 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.50 mg/ml was injected onto the column. 75 successive 1 second frames were collected through the sample elution peak and processed using CHROMIXS that included the identification and subtraction of an appropriate solvent-blank.",
  "tags": [],
  "intensity_unit": "arbitrary",
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  "experimental_mw_error": null,
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  "guinier_i0_mw_error": 6.0,
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  "guinier_rg_error": 0.07,
  "pddf_dmax": 20.96,
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  "porod_volume": 268.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 9,
  "guinier_point_last": 43,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDDW4_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}
View the complete manifest.json source
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