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Open data
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Basic information
Entry | Database: PDB / ID: 4c8a | ||||||
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Title | mouse ZNRF3 ectodomain crystal form II | ||||||
![]() | E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zebisch, M. / Jones, E.Y. | ||||||
![]() | ![]() Title: Structural and Molecular Basis of Znrf3/Rnf43 Transmembrane Ubiquitin Ligase Inhibition by the Wnt Agonist R-Spondin. Authors: Zebisch, M. / Xu, Y. / Krastev, C. / Macdonald, B.T. / Chen, M. / Gilbert, R.J.C. / He, X. / Jones, E.Y. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.4 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4c84C ![]() 4c85C ![]() 4c86C ![]() 4c8cC ![]() 4c8fC ![]() 4c8pC ![]() 4c8tC ![]() 4c8uC ![]() 4c8vC ![]() 4c8wC ![]() 4c99C ![]() 4c9aC ![]() 4c9eC ![]() 4c9rC ![]() 4c9uC ![]() 4c9vC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 18203.557 Da / Num. of mol.: 3 / Fragment: ECTODOMAIN, RESIDUES 53-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q5SSZ7, ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.72 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→52.09 Å / Num. obs: 13223 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 85.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.6 |
Reflection shell | Highest resolution: 2.7 Å |
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Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure![]() Starting model: NONE Resolution: 2.7→52.15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.907 / SU B: 20.943 / SU ML: 0.424 / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / 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: 95.16 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→52.15 Å
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Refine LS restraints |
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