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Yorodumi- PDB-5ms8: Crystal structure of the legionella pneumophila effector protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ms8 | ||||||
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Title | Crystal structure of the legionella pneumophila effector protein RavZ_1-487 | ||||||
Components | Legionella pneumophila effector protein RavZ | ||||||
Keywords | HYDROLASE / Hydrolase / Autophagy / Legionella pneumophila effector protein / ATG8 deconjugating enzyme | ||||||
Function / homology | Function and homology information host intracellular membrane-bounded organelle / symbiont-mediated suppression of host autophagy / protein delipidation / phosphatidylinositol-3-phosphate binding / cysteine-type peptidase activity / host cell cytoplasmic vesicle membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Legionella pneumophila subsp. pneumophila ATCC 33215 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Pantoom, S. / Vetter, I.R. / Wu, Y.W. | ||||||
Citation | Journal: Elife / Year: 2017 Title: Elucidation of the anti-autophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins. Authors: Yang, A. / Pantoom, S. / Wu, Y.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ms8.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ms8.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ms8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ms8_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
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Full document | 5ms8_full_validation.pdf.gz | 455.3 KB | Display | |
Data in XML | 5ms8_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 5ms8_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/5ms8 ftp://data.pdbj.org/pub/pdb/validation_reports/ms/5ms8 | HTTPS FTP |
-Related structure data
Related structure data | 5ms2C 5ms5C 5ms6C 5ms7C 5cqcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 54873.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila ATCC 33215 (bacteria) Gene: lpg1683 / Plasmid: pOPIN / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5ZUV9 | ||||
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#2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.9 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 16% PEG3350, 0.2 M BaCl2 and 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2015 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→47.05 Å / Num. obs: 21565 / % possible obs: 100 % / Redundancy: 26.7 % / Biso Wilson estimate: 86.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.2162 / Net I/σ(I): 14.09 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 27.9 % / Rmerge(I) obs: 1.927 / Mean I/σ(I) obs: 1.85 / CC1/2: 0.134 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CQC Resolution: 2.85→47.047 Å / SU ML: 0.55 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 30.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→47.047 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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