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Open data
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Basic information
Entry | Database: PDB / ID: 7ya7 | ||||||
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Title | The crystal structure of IpaH1.4 LRR domain | ||||||
![]() | RING-type E3 ubiquitin transferase | ||||||
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Function / homology | ![]() modulation of process of another organism / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / host cell cytoplasm / protein ubiquitination / extracellular region / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hiragi, K. / Nishide, A. / Takagi, K. / Iwai, K. / Kim, M. / Mizushima, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insight into the recognition of the linear ubiquitin assembly complex by Shigella E3 ligase IpaH1.4/2.5. Authors: Hiragi, K. / Nishide, A. / Takagi, K. / Iwai, K. / Kim, M. / Mizushima, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116 KB | Display | ![]() |
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PDB format | ![]() | 86.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ya8C ![]() 5b0nS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27322.393 Da / Num. of mol.: 2 / Fragment: LRR domain(substrate recognision domain) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9AFJ5, RING-type E3 ubiquitin transferase #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 50 mM imidazole (pH 8.0), 1.2 M NaCl. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.4→50 Å / Num. obs: 86206 / % possible obs: 98.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 33.9 |
Reflection shell | Resolution: 1.4→1.42 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4 / Num. unique obs: 8222 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5B0N Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.133 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.072 / 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: 17.799 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→50 Å
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Refine LS restraints |
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