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- PDB-5ms7: Crystal structure of the legionella pneumophila effector protein ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ms7 | ||||||
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Title | Crystal structure of the legionella pneumophila effector protein RavZ_20-502 | ||||||
![]() | Legionella pneumophila effector protein RavZ | ||||||
![]() | HYDROLASE / Hydrolase / Autophagy / Legionella pneumophila effector protein / ATG8 deconjugating enzyme | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pantoom, S. / Vetter, I.R. / Wu, Y.W. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.5 KB | Display | ![]() |
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PDB format | ![]() | 133.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ms2C ![]() 5ms5C ![]() 5ms6C ![]() 5ms8C ![]() 5cqcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 54285.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lpg1683 / Plasmid: pOPIN / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.17 Å3/Da / Density % sol: 70.49 % |
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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: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2016 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97862 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.15 Å / Num. obs: 22921 / % possible obs: 100 % / Redundancy: 26.7 % / Biso Wilson estimate: 86.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1938 / Net I/σ(I): 15.14 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 26.3 % / Rmerge(I) obs: 1.951 / Mean I/σ(I) obs: 1.94 / CC1/2: 0.165 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CQC Resolution: 2.8→47.145 Å / SU ML: 0.48 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 30.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→47.145 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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