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- SASDEY9: Collagen VI von Willebrand factor (VWA) double-domain fragment, N5N4 -

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Open data


ID or keywords:

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Basic information

Entry
Database: SASBDB / ID: SASDEY9
SampleCollagen VI von Willebrand factor (VWA) double-domain fragment, N5N4
  • Collagen, type VI, alpha 3 (protein), N5N4, Mus musculus
Function / homology
Function and homology information


collagen trimer / response to UV / extracellular matrix / phosphatidylinositol 3-kinase/protein kinase B signal transduction / serine-type endopeptidase inhibitor activity / sarcolemma / neuron apoptotic process / cell adhesion / extracellular space
Similarity search - Function
Collagen alpha-3(VI) chain, vWA domain / : / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Collagen alpha-3(VI) chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Contact author
  • Davide Comoletti (Department of Neuroscience and Cell Biology, Rutgers University., New Brunswick, NJ, United States)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

Model #2795
Type: dummy / Software: (DAMMIN) / Radius of dummy atoms: 2.50 A / Symmetry: P1
Comment: Refined individual model calculated from 10 spatially aligned models
Chi-square value: 1.027 / P-value: 0.852619
Model #2796
Type: dummy / Software: (5.0) / Radius of dummy atoms: 2.50 A / Symmetry: P1
Comment: Averaged spatial repersentation calculated from 10 aligned individual models
Chi-square value: 1.027 / P-value: 0.852619
Model #2797
Type: dummy / Radius of dummy atoms: 1.90 A / Chi-square value: 1.02 / P-value: 0.798665
Model #2798
Type: mix / Radius of dummy atoms: 1.90 A / Symmetry: P1
Comment: Generated using the crystal structure of N5 in combination with an ITASSER homology model of N4
Chi-square value: 1.018 / P-value: 0.180377

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Sample

SampleName: Collagen VI von Willebrand factor (VWA) double-domain fragment, N5N4
Specimen concentration: 12 mg/ml
BufferName: 20 mM TRIS, 150mM NaCl 3% v/v glycerol / pH: 7.4
Comment: The TRIS buffer is pH first, then add additional components are added without further pH adjustment
Entity #1458Name: N5N4 / Type: protein / Description: Collagen, type VI, alpha 3 / Formula weight: 44.274 / Num. of mol.: 1 / Source: Mus musculus / References: UniProt: D3YWD1
Sequence: GEKDVVFLID GSEGVRSGFP LLKDFVQRVV ESLDVGPDRV RVALVQYSDR TRPEFYLNSH MDQQGVISAI RRLTLLGGPT PNTGAALEFV LRNILTSSTG SRIAEGVPQL LIVLTAEPSG DDVRGPSVVL KQGGAVPIGI GIGNADISEM QTISFIPDFA VAIPTFRELG ...Sequence:
GEKDVVFLID GSEGVRSGFP LLKDFVQRVV ESLDVGPDRV RVALVQYSDR TRPEFYLNSH MDQQGVISAI RRLTLLGGPT PNTGAALEFV LRNILTSSTG SRIAEGVPQL LIVLTAEPSG DDVRGPSVVL KQGGAVPIGI GIGNADISEM QTISFIPDFA VAIPTFRELG TIQQVISERV IQLNREELSS LKPILTPSTG AGVGSKKDVV FLIDGSRNAG PEFQYIRTLI ERIVEYLDIG FDTTRVAVIQ FSEDSKMEFP LNAHFSKDEV QNAVRRLRPK GGSQVYIGNA LEYVLKNIFQ RPLGSRIEEG VPQFLVLISS GKSDDEVDDS AVELKQFGVA PLTIARHTDQ EELVKISLSP EYVYSVSTFR ELPRLEQKLL TPITTLTSQQ IHQILASTRY PPS

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Experimental information

BeamInstrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3 mm
DetectorName: Pilatus 6M
Scan
Title: Collagen VI von Willebrand factor (VWA) double-domain fragment, N5N4
Measurement date: Apr 20, 2018 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 18 / Unit: 1/nm /
MinMax
Q0.0681 6.9981
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1635 /
MinMax
Q0.0708301 4.58586
P(R) point1 1635
R0 9.85
Result
Type of curve: sec /
ExperimentalPorod
MW43 kDa41 kDa
Volume-66.2 nm3

P(R)GuinierGuinier error
Forward scattering, I0287.2 286.77 0.42
Radius of gyration, Rg2.895 nm2.85 nm0.01

MinMax
D-9.85
Guinier point1 122

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