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Open data
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Basic information
Entry | Database: PDB / ID: 7xyw | ||||||||||||
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Title | Crystal structure of ZYG11B bound to AFLH degron | ||||||||||||
![]() | Protein zyg-11 homolog B | ||||||||||||
![]() | LIGASE / E3 | ||||||||||||
Function / homology | ![]() Cul2-RING ubiquitin ligase complex / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Dong, C. / Yan, X. / Li, Y. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: CRL2 ZER1/ZYG11B recognizes small N-terminal residues for degradation. Authors: Li, Y. / Zhao, Y. / Yan, X. / Ye, C. / Weirich, S. / Zhang, B. / Wang, X. / Song, L. / Jiang, C. / Jeltsch, A. / Dong, C. / Mi, W. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.2 KB | Display | ![]() |
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PDB format | ![]() | 168.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.5 KB | Display | ![]() |
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Full document | ![]() | 453.5 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xysC ![]() 7xytC ![]() 7xyuC ![]() 7xyvC ![]() 7xyxC ![]() 7ep1S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 28563.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES (pH 6.5), 1.6 M MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→61.45 Å / Num. obs: 21062 / % possible obs: 92.2 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.5→2.63 Å / Rmerge(I) obs: 1.413 / Num. unique obs: 3269 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7EP1 Resolution: 2.5→20.49 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.37 Å2 / Biso mean: 80.5187 Å2 / Biso min: 46.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→20.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: -37.7055 Å / Origin y: -39.7107 Å / Origin z: 10.2122 Å
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Refinement TLS group |
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