+Open data
-Basic information
Entry | Database: PDB / ID: 7ya8 | ||||||
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Title | The crystal structure of IpaH2.5 LRR domain | ||||||
Components | RING-type E3 ubiquitin transferase | ||||||
Keywords | LIGASE / Shigella flexneri / Effector / IpaH2.5 / Ubiquitin ligase | ||||||
Function / homology | Function and homology information modulation of process of another organism / ligase activity / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / host cell cytoplasm / extracellular region Similarity search - Function | ||||||
Biological species | Shigella flexneri 5a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Hiragi, K. / Nishide, A. / Takagi, K. / Iwai, K. / Kim, M. / Mizushima, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Biochem. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ya8.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ya8.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 7ya8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/7ya8 ftp://data.pdbj.org/pub/pdb/validation_reports/ya/7ya8 | HTTPS FTP |
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-Related structure data
Related structure data | 7ya7SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27336.420 Da / Num. of mol.: 2 / Fragment: LRR domain(substrate recognision domain) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 5a (bacteria) / Strain: M90T / Gene: ipaH2.5, S0056, EKN05_023760, pWR501_0056 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q7BEH4, RING-type E3 ubiquitin transferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.74 Å3/Da / Density % sol: 81.74 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M succinic acid pH 6.6, 18.8% (w/v) polyethylene glycol (PEG)3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 22003 / % possible obs: 96 % / Redundancy: 6.6 % / Biso Wilson estimate: 56.82 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 22 |
Reflection shell | Resolution: 3.301→3.419 Å / Rmerge(I) obs: 0.053 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1436 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7YA7 Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.909 / SU B: 15.512 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.557 / ESU R Free: 0.356 / 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: 62.278 Å2
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Refinement step | Cycle: 1 / Resolution: 3.4→50 Å
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Refine LS restraints |
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