+Open data
-Basic information
Entry | Database: PDB / ID: 7v8h | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of LRR domain from Shigella flexneri IpaH1.4 | ||||||||||||||||||
Components | RING-type E3 ubiquitin transferase | ||||||||||||||||||
Keywords | LIGASE / ubiquitin / innate immune | ||||||||||||||||||
Function / homology | Function and homology information modulation of process of another organism / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / host cell cytoplasm / protein ubiquitination / extracellular region / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Shigella flexneri 5a str. M90T (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||||||||||||||
Authors | Liu, J. / Wang, Y. / Pan, L. | ||||||||||||||||||
Funding support | China, 5items
| ||||||||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Mechanistic insights into the subversion of the linear ubiquitin chain assembly complex by the E3 ligase IpaH1.4 of Shigella flexneri. Authors: Liu, J. / Wang, Y. / Wang, D. / Wang, Y. / Xu, X. / Zhang, Y. / Li, Y. / Zhang, M. / Gong, X. / Tang, Y. / Shen, L. / Li, M. / Pan, L. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7v8h.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7v8h.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 7v8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/7v8h ftp://data.pdbj.org/pub/pdb/validation_reports/v8/7v8h | HTTPS FTP |
---|
-Related structure data
Related structure data | 7v8eC 7v8fC 7v8gC 5kh1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.909535870212, -0.0948495899864, 0.40465794948), (-0.0753447108192, -0.919853403415, -0.384958297452), (0.408739128723, -0.380622216253, 0.829493250814)Vector: 62. ...NCS oper: (Code: given Matrix: (-0.909535870212, -0.0948495899864, 0.40465794948), Vector: |
-Components
#1: Protein | Mass: 26991.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri 5a str. M90T (bacteria) Strain: M90T / Gene: ipaH1.4 / Plasmid: pRSF-Deut1-Trx / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9AFJ5, RING-type E3 ubiquitin transferase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.31 % |
---|---|
Crystal grow | Temperature: 289 K / Method: evaporation / pH: 4 / Details: 0.1 M sodium citrate (pH 4.0), 0.8 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.456→76.919 Å / Num. obs: 21136 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 24.6 % / Biso Wilson estimate: 37.05 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.067 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.456→2.498 Å / Redundancy: 25.4 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1091 / CC1/2: 0.81 / Rpim(I) all: 0.518 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KH1 Resolution: 2.46→60.82 Å / SU ML: 0.2194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7769 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→60.82 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.734799407111 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|