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Open data
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Basic information
Entry | Database: PDB / ID: 5m0w | |||||||||||||||
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Title | N-terminal domain of mouse Shisa 3 | |||||||||||||||
![]() | Protein shisa-3 homolog | |||||||||||||||
![]() | SIGNALING PROTEIN / Single-pass transmembrane protein / tumor suppressor gene / Wnt-signaling pathway / disulfide | |||||||||||||||
Function / homology | Shisa family / Shisa, N-terminal domain / multicellular organism development / negative regulation of canonical Wnt signaling pathway / membrane => GO:0016020 / endoplasmic reticulum membrane / DI(HYDROXYETHYL)ETHER / Protein shisa-3 homolog![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Lohkamp, B. / Ojala, J.R.M. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Ab initio solution of macromolecular crystal structures without direct methods. Authors: McCoy, A.J. / Oeffner, R.D. / Wrobel, A.G. / Ojala, J.R. / Tryggvason, K. / Lohkamp, B. / Read, R.J. #1: ![]() Title: Ab initio solution of macromolecular crystal structures without direct methods Authors: McCoy, A.J. / Oeffner, R.D. / Wrobel, A. / Ojala, J.R.M. / Tryggvason, K. / Lohkamp, B. / Read, R.J. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.3 KB | Display | ![]() |
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PDB format | ![]() | 34.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.5 KB | Display | ![]() |
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Full document | ![]() | 479.1 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 9040.780 Da / Num. of mol.: 1 / Fragment: UNP residues 22-95 Source method: isolated from a genetically manipulated source Details: N-terminal domain with Strep tag / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 118 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MES / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2.0 M (NH4)2SO4, 100 mM MES pH 6.5, 4% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 4, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→29.88 Å / Num. obs: 18352 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 12.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 1.39→1.41 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.879 / % possible all: 88.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Single sulphur Resolution: 1.39→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.276 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.161 Å2
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Refinement step | Cycle: 1 / Resolution: 1.39→30 Å
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Refine LS restraints |
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