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- PDB-4cnm: Crystal structure of human 5T4 (Wnt-activated inhibitory factor 1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cnm | |||||||||
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Title | Crystal structure of human 5T4 (Wnt-activated inhibitory factor 1, Trophoblast glycoprotein) | |||||||||
![]() | TROPHOBLAST GLYCOPROTEIN | |||||||||
![]() | ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() mesenchymal cell migration / dendrite arborization / olfactory learning / positive regulation of chemotaxis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhao, Y. / Malinauskas, T. / Harlos, K. / Jones, E.Y. | |||||||||
![]() | ![]() Title: Structural Insights Into the Inhibition of Wnt Signaling by Cancer Antigen 5T4/Wnt-Activated Inhibitory Factor 1. Authors: Zhao, Y. / Malinauskas, T. / Harlos, K. / Jones, E.Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.4 KB | Display | ![]() |
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PDB format | ![]() | 101.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4cncC ![]() 3zyjS C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32900.395 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 60-345 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 2 types, 5 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-NAG / ![]() |
-Non-polymers , 3 types, 130 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PEG / ![]() #5: Chemical | ChemComp-CIT / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 34 % / Description: NONE |
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Crystal grow![]() | Details: THE CRYSTALLIZATION DROP CONTAINED 100 NL OF CONCENTRATED 5T4 (5.5 MG/ML), 100 NL OF 25% W/V POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M CITRATE PH 3.5, AND 0.5 NL OF 0.1 M NAOH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2013 Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.75→49.31 Å / Num. obs: 33062 / % possible obs: 99.8 % / Observed criterion σ(I): 3.1 / Redundancy: 9.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 3.1 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3ZYJ Resolution: 1.75→43.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.141 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: 35.524 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→43.94 Å
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Refine LS restraints |
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