SASDW77

DGSt - Chimeric protein consisting of DCV, GFP and SpyTag domain

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2025-08-01T07:48:37.612084+02:00

Note: The experimentally determined protein mass (SEC-MALS) is overestimated due to the presence of a fluorescent protein in the sample. The light scattering laser operates at a wavelength that excites the fluorescent protein, leading to inaccurate signal measurements.

▼

1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · DGSt - Chimeric protein consisting of DCV, GFP and SpyTag domain

Concentration	— – 8.0	Buffer / pH	20 mM Tris, 150 mM NaCL, 3% glycerol / 7.5
Experimental temperature	20.0	Facility / beamline	PETRA III / EMBL P12
Wavelength	0.123985 nm	Exposure	1.0 s × 3000

Molecular Components

Component	Type / organism	UniProt and Construct	Oligomeric State	Molecular weight
DCV-GFP-St View sequence >DGSTMAKSGNYSYKRWVFTINNPTFEDYVHVLEFCTLDNCKFAIVGEEKGANGTPHLQGFLNLRSNARAAALEESLGGRAWLSRARGSDEDNEEYCAKESTYLRVGEPVSKGRSSSGKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATIGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGKYKTRAVVKFEGDTLVNRIELKGTDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFTVRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQTVLSKDPNEKRDHMVLHEYVNAAGITGSGGSGAHIVMVDAYKPTKGSGHHHHHHHH	proteinsynthetic construct	——–—	monomerMolecule count 1	41.266 kDa

Experimental Curves

Curve	Points / columns	q range	Uncertainty quality	Negative-intensity points	Source file
1	814[3]	0.16131–2.50088 1/nm	Has uncertainty columnMissing 0	0	sasbdb/entries/77/sasdw77/source/SASDW77.dat

▼

2. Measurements Reported by SASBDB Reported Results

Metric	Method	Value	Uncertainty	Unit
dmax	P(r)	9.1	0.2	nm
i0	Guinier	4166.37	—	arbitrary
i0	P(r)	4135.0	—	arbitrary
mw	Experimental	47.4	—	kDa
mw	Porod	33.0	—	kDa
porod_volume	Porod	54.0	—	nm³
rg	Guinier	2.82	0.022	nm
rg	P(r)	2.839	—	nm

These values are reported by SASBDB; SAXSdb did not recalculate them from the experimental curve.

▼

3. Source Fits and Models Source Fits & Models

Fit 1 · Pepsi-SAXS 3.0

χ²: 1.1095CorMap p: 0.0935Unit: 1/A

Fit data Fit log Fit plot Residual plot

Model	Name / Type	Software	Symmetry	Model MW	PDB Declaration	Source file
1	—atomic	MODELLER 10.5	—	41.26	—	Model Image

▶

4. Source File Index Source Files

Category	Path	Download status	Size
curve	sasbdb/entries/77/sasdw77/source/SASDW77.dat	downloaded	37526
full_entry_zip	sasbdb/entries/77/sasdw77/source/SASDW77.zip	downloaded	101220
pddf	sasbdb/entries/77/sasdw77/source/SASDW77.out	downloaded	74280
sascif	sasbdb/entries/77/sasdw77/source/SASDW77.sascif	not_available	—
summary	sasbdb/entries/77/sasdw77/source/summary.json	downloaded	7202

▶

5. Experiment Description and Publication Experiment & Publication

▼

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 name	20 mM Tris, 150 mM NaCL, 3% glycerol	Buffer concentration	—
pH	7.5	Additives	—
Buffer description	—
Purity measurement method	—	Extinction coefficient	—
Absorbance	—	Scattering contrast	—
Specific volume / dry volume	— / —	Mixture / deuteration	— / —

Acquisition Conditions and Instrument

Measurement date	2024-03-18	Storage / measurement temperature	5.0 / 20.0
Exposure time	1.0	Frames	3000
Wavelength	0.123985	Sample-to-detector distance	3.0
Source	X-ray synchrotron	Detector	Pilatus 6M
Facility / beamline	PETRA III / EMBL P12 · DESY; Hamburg, Germany
q range	0.161 – 2.501	Sample volume / flow rate	80.0 / 0.7

Original SASBDB Plots

Downloadable Files

Category	File	Status	Size	Checksum	Download and View
curve	sasbdb/entries/77/sasdw77/source/SASDW77.dat	downloaded	37526	a655f60a5c810c0a55d2c4dc7bfacaa3aa683ef2a33582bb629b7f2221c5d7d0	DownloadView source fileSource site
full_entry_zip	sasbdb/entries/77/sasdw77/source/SASDW77.zip	downloaded	101220	07e802aa3f30b4684db2d266cc7357c233fe2735b385986272d206e8e00a0e43	DownloadView source fileSource site
pddf	sasbdb/entries/77/sasdw77/source/SASDW77.out	downloaded	74280	1e013f7b5224811a106f532bb10826b45318d241432c33ba3184a5dafdbbc7b6	DownloadView source fileSource site
sascif	sasbdb/entries/77/sasdw77/source/SASDW77.sascif	not_available	—	—	DownloadView source fileSource site
summary	sasbdb/entries/77/sasdw77/source/summary.json	downloaded	7202	206577092838bf02959193103e21a54e3b0f243b0780630731dce6f3cb2b2ec6	DownloadView source fileSource site

curve：source record

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full_entry_zip：source record and ZIP contents (4 items)

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pddf：source record

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sascif：source record

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summary：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：156 field values

Field path	Raw value
code	SASDW77
status	Published
type_of_curve	SEC-SAS
angular_unit	1/nm
project.title	Programmable Protein-DNA Composite Nanostructures: from Nanostructure Construction to Protein-Induced Micro-Scale Material Self-Assembly and Functionalization.
project.publication.title	Programmable Protein-DNA Composite Nanostructures: from Nanostructure Construction to Protein-Induced Micro-Scale Material Self-Assembly and Functionalization.
project.publication.author_list	Zhou W, Strmšek Ž, Snoj J, Škarabot M, Jerala R
project.publication.journal	Small
project.publication.doi	10.1002/smll.202502060
project.publication.pmid	40442952
project.publication.published_date	2025 Jul
project.status	released
project.submitted_date	2025-02-06
project.released_date	2025-08-01
pddf_data	https://www.sasbdb.org/media/p_of_R_files/SASDW77.out
intensities_data	https://www.sasbdb.org/media/intensities_files/SASDW77.dat
intensities_log_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW77_dat_img.png
intensities_kratky_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW77_kratky_img.png
pddf_plot	https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDW77_pofr_img.png
intensities_guinier_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW77_guinier_img.png
sascif_data	https://www.sasbdb.org/media/sascif/sascif_files/SASDW77.sascif
experiment.instrument.detector.type	null
experiment.instrument.detector.name	Pilatus 6M
experiment.instrument.detector.resolution	null
experiment.instrument.name	PETRA III
experiment.instrument.city	DESY; Hamburg
experiment.instrument.country	Germany
experiment.instrument.beamline_name	EMBL P12
experiment.instrument.beam_geometry	null
experiment.instrument.type_of_source	X-ray synchrotron
experiment.instrument.point_source	null
experiment.instrument.line_collimation	null
experiment.instrument.sample_path_length	null
experiment.instrument.line_collimation_slitlength	null
experiment.instrument.line_collimation_integrationwidth	null
experiment.instrument.xray_energy	null
experiment.instrument.beam_profile_ah	null
experiment.instrument.beam_profile_al	null
experiment.sample.molecule[0].long_name	DCV-GFP-St
experiment.sample.molecule[0].short_name	DGSt
experiment.sample.molecule[0].sequence	>DGSt MAKSGNYSYKRWVFTINNPTFEDYVHVLEFCTLDNCKFAIVGEEKGANGTPHLQGFLNLRSNARAAALEESLGGRAWLSRARGSDEDNEEYCAKESTYLRVGEPVSKGRSSSGKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATIGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGKYKTRAVVKFEGDTLVNRIELKGTDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFTVRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQTVLSKDPNEKRDHMVLHEYVNAAGITGSGGSGAHIVMVDAYKPTKGSGHHHHHHHH
experiment.sample.molecule[0].organism	synthetic construct
experiment.sample.molecule[0].uniprot_code	null
experiment.sample.molecule[0].uniprot_range_first	null
experiment.sample.molecule[0].uniprot_range_last	null
experiment.sample.molecule[0].oligomerization	monomer
experiment.sample.molecule[0].molecular_type	protein
experiment.sample.molecule[0].uniprot_sequence
experiment.sample.molecule[0].mw	41.266
experiment.sample.molecule[0].total_mw	41.266
experiment.sample.molecule[0].number_molecules	1
experiment.sample.molecule[0].complex_state	False
experiment.sample.molecule[0].deuteration	null
experiment.sample.molecule[0].molecule_source	biological
experiment.sample.molecule[0].molecule_description	A chimeric protein consisting of DCV, GFP, and SpyTag domain. DCV is an endonuclease ssDNA binding domain originated from Muscovy duck circovirus. GFP is a green fluorescent protein.
experiment.sample.buffer.name	20 mM Tris, 150 mM NaCL, 3% glycerol
experiment.sample.buffer.concentration_unit	null
experiment.sample.buffer.comment	null
experiment.sample.buffer.additive	null
experiment.sample.buffer.concentration	null
experiment.sample.buffer.pka	null
experiment.sample.buffer.ph	7.5
experiment.sample.buffer.deuteration	null
experiment.sample.purity_method	null
experiment.sample.name	DGSt - Chimeric protein consisting of DCV, GFP and SpyTag domain
experiment.sample.ext_coefficient	null
experiment.sample.contrast	null
experiment.sample.specific_vol	null
experiment.sample.dry_vol	null
experiment.sample.absorbption	null
experiment.sample.deuteration	null
experiment.sample.mixture	null
experiment.contributor[0].affiliation[0].short_name	KI
experiment.contributor[0].affiliation[0].address	Ljubljana, Slovenia
experiment.contributor[0].affiliation[0].full_name	Kemijski inštitut
experiment.contributor[0].affiliation[0].webpage	null
experiment.contributor[0].contributor_name	Jaka
experiment.contributor[0].contributor_surname	Snoj
experiment.contributor[0].orcid	null
experiment.concentration_method	null
experiment.concentration_unit	null
experiment.date	2024-03-18
experiment.storage_temperature	5.0
experiment.cell_temperature	20.0
experiment.exposure_time	1.0
experiment.number_of_frames	3000
experiment.wavelength	0.123985
experiment.sample_detector_distance	3.0
experiment.concentration_min	null
experiment.concentration_max	8.0
experiment.sample_volume	80.0
experiment.flow_rate	0.7
experiment.s_min	0.161
experiment.s_max	2.501
experiment.total_exposure_time	null
experiment.seccolumn	47
fits[0].models[0].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDW77_fit1_model1_img.png
fits[0].models[0].software	MODELLER
fits[0].models[0].pdb_link	[]
fits[0].models[0].model_title	null
fits[0].models[0].type_of_model	atomic
fits[0].models[0].software_version	10.5
fits[0].models[0].model_data	https://www.sasbdb.org/media/pdb_file/SASDW77_fit1_model1.pdb
fits[0].models[0].model_mw	41.26
fits[0].models[0].bead_radius	null
fits[0].models[0].log	null
fits[0].models[0].symmetry	null
fits[0].models[0].comment	null
fits[0].models[0].user	1027
fits[0].fit_unit	1/A
fits[0].fit_plot	https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDW77_fit1_fixed_fit_img.png
fits[0].software	Pepsi-SAXS
fits[0].chi_square_value	1.1095
fits[0].p_value	0.0935
fits[0].fit_residual_plot	SASDW77_fit1_fitresiduals_img.png
fits[0].fit_data	https://www.sasbdb.org/media/fitting_files/SASDW77_fit1.fit
fits[0].fit_log	https://www.sasbdb.org/media/fitting_files/log_files/DCV_GFP_St_set_very_slow-201-1.log
fits[0].software_version	3.0
fits[0].description
estimated_volume_method	null
pddf_software	ATSAS GNOM
pddf_software_version	5.0
i0_calibration_standard	null
description	Note: The experimentally determined protein mass (SEC-MALS) is overestimated due to the presence of a fluorescent protein in the sample. The light scattering laser operates at a wavelength that excites the fluorescent protein, leading to inaccurate signal measurements.
experiment_description	null
tags	[]
intensity_unit	arbitrary
experimental_mw	47.4
experimental_mw_error	null
guinier_i0_mw	null
guinier_i0_mw_error	null
porod_mw	33.0
porod_mw_error	null
pddf_i0	4135.0
pddf_i0_error	null
guinier_i0	4166.37
guinier_i0_error	null
pddf_rg	2.839
pddf_rg_error	null
guinier_rg	2.82
guinier_rg_error	0.022
pddf_dmax	9.1
pddf_dmax_error	0.2
porod_volume	54.0
porod_volume_error	null
estimated_volume	null
estimated_volume_error	null
guinier_point_first	21
guinier_point_last	104
pddf_point_first	null
pddf_point_last	null
i0_calibration_standard_data	null
intensities_log_log_plot	SASDW77_datloglog_img.png
symmetry	null
last_modified	2025-08-01T07:48:37.612084+02:00
bragg_peak	[]

manifest.json：34 field values

Field path	Raw value
code	SASDW77
status	success
started_at	2026-08-11T15:23:51.928495+00:00
finished_at	2026-08-11T15:23:59.711868+00:00
source_last_modified	2025-08-01T07:48:37.612084+02:00
files[0].status	downloaded
files[0].url	https://www.sasbdb.org/rest-api/entry/summary/SASDW77/
files[0].path	/data/saxsdb/sasbdb/entries/77/sasdw77/source/summary.json
files[0].size	7202
files[0].sha256	206577092838bf02959193103e21a54e3b0f243b0780630731dce6f3cb2b2ec6
files[1].status	downloaded
files[1].url	https://www.sasbdb.org/media/intensities_files/SASDW77.dat
files[1].path	/data/saxsdb/sasbdb/entries/77/sasdw77/source/SASDW77.dat
files[1].size	37526
files[1].sha256	a655f60a5c810c0a55d2c4dc7bfacaa3aa683ef2a33582bb629b7f2221c5d7d0
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files[3].status	not_available
files[3].url	https://www.sasbdb.org/media/sascif/sascif_files/SASDW77.sascif
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files[3].role	sascif
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files[4].zip_member_count	4
files[4].zip_validation	central_directory_readable

View the complete summary.json source

{
  "code": "SASDW77",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "Programmable Protein-DNA Composite Nanostructures: from Nanostructure Construction to Protein-Induced Micro-Scale Material Self-Assembly and Functionalization.",
    "publication": {
      "title": "Programmable Protein-DNA Composite Nanostructures: from Nanostructure Construction to Protein-Induced Micro-Scale Material Self-Assembly and Functionalization.",
      "author_list": "Zhou W, Strmšek Ž, Snoj J, Škarabot M, Jerala R",
      "journal": "Small",
      "doi": "10.1002/smll.202502060",
      "pmid": "40442952",
      "published_date": "2025 Jul"
    },
    "status": "released",
    "submitted_date": "2025-02-06",
    "released_date": "2025-08-01"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDW77.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDW77.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW77_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW77_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDW77_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDW77_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDW77.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": null,
        "name": "Pilatus 6M",
        "resolution": null
      },
      "name": "PETRA III",
      "city": "DESY; Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL P12",
      "beam_geometry": null,
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
      "sample_path_length": null,
      "line_collimation_slitlength": null,
      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
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          "long_name": "DCV-GFP-St",
          "short_name": "DGSt",
          "sequence": ">DGSt\r\nMAKSGNYSYKRWVFTINNPTFEDYVHVLEFCTLDNCKFAIVGEEKGANGTPHLQGFLNLRSNARAAALEESLGGRAWLSRARGSDEDNEEYCAKESTYLRVGEPVSKGRSSSGKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATIGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGKYKTRAVVKFEGDTLVNRIELKGTDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFTVRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQTVLSKDPNEKRDHMVLHEYVNAAGITGSGGSGAHIVMVDAYKPTKGSGHHHHHHHH",
          "organism": "synthetic construct",
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "",
          "mw": 41.266,
          "total_mw": 41.266,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": "A chimeric protein consisting of DCV, GFP, and SpyTag domain. DCV is an endonuclease ssDNA binding domain originated from Muscovy duck circovirus. GFP is a green fluorescent protein."
        }
      ],
      "buffer": {
        "name": "20 mM Tris, 150 mM NaCL, 3% glycerol",
        "concentration_unit": null,
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        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "DGSt - Chimeric protein consisting of DCV, GFP and SpyTag domain",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "KI",
            "address": "Ljubljana, Slovenia",
            "full_name": "Kemijski inštitut",
            "webpage": null
          }
        ],
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View the complete manifest.json source

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Title	Programmable Protein-DNA Composite Nanostructures: from Nanostructure Construction to Protein-Induced Micro-Scale Material Self-Assembly and Functionalization.
Authors	Zhou W, Strmšek Ž, Snoj J, Škarabot M, Jerala R
DOI / PMID	10.1002/smll.202502060 / 40442952