+Open data
-Basic information
Entry | Database: PDB / ID: 7ew8 | ||||||
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Title | Legionella pneumophila effector AnkD | ||||||
Components | ANK_REP_REGION domain-containing protein | ||||||
Keywords | TOXIN / Legionella pneumophila effector / Lipid droplet / vesicle trafficking | ||||||
Function / homology | Ankyrin repeat profile. / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Uncharacterized protein Function and homology information | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.594 Å | ||||||
Authors | Chen, T.T. / Lin, Y.L. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Atypical Legionella GTPase effector hijacks host vesicular transport factor p115 to regulate host lipid droplet. Authors: Chen, T.T. / Lin, Y. / Zhang, S. / Liu, S. / Song, L. / Zhong, W. / Luo, Z.Q. / Han, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ew8.cif.gz | 182 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ew8.ent.gz | 142.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ew8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/7ew8 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/7ew8 | HTTPS FTP |
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-Related structure data
Related structure data | 7xqlC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 55163.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_12350, DI026_04400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F2G5 #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.42 Å3/Da / Density % sol: 49.12 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: magnesium chloride, Bis Tris, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. obs: 32269 / % possible obs: 92.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.59→2.63 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 15131 / CC1/2: 0.843 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.594→45.207 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.98 / 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: 115.1 Å2 / Biso mean: 49.8776 Å2 / Biso min: 11.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.594→45.207 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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