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Yorodumi- PDB-5izv: Crystal structure of the legionella pneumophila effector protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5izv | ||||||
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Title | Crystal structure of the legionella pneumophila effector protein RavZ - F222 | ||||||
Components | Uncharacterized protein RavZ | ||||||
Keywords | HYDROLASE / Autophagy / Atg8 / deconjugating enzyme / protease / Atg4B | ||||||
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 strain Philadelphia 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.814 Å | ||||||
Authors | Kwon, D.H. / Kim, L. / Kim, B.-W. / Hong, S.B. / Song, H.K. | ||||||
Citation | Journal: Autophagy / Year: 2017 Title: The 1:2 complex between RavZ and LC3 reveals a mechanism for deconjugation of LC3 on the phagophore membrane Authors: Kwon, D.H. / Kim, S. / Jung, Y.O. / Roh, K.H. / Kim, L. / Kim, B.-W. / Hong, S.B. / Lee, I.Y. / Song, J.H. / Lee, W.C. / Choi, E.J. / Hwang, K.Y. / Song, H.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5izv.cif.gz | 310.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5izv.ent.gz | 256.2 KB | Display | PDB format |
PDBx/mmJSON format | 5izv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5izv_validation.pdf.gz | 450.7 KB | Display | wwPDB validaton report |
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Full document | 5izv_full_validation.pdf.gz | 475.1 KB | Display | |
Data in XML | 5izv_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 5izv_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/5izv ftp://data.pdbj.org/pub/pdb/validation_reports/iz/5izv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 56295.258 Da / Num. of mol.: 2 / Mutation: C258S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila strain Philadelphia 1 (bacteria) Strain: Philadelphia 1 / Gene: lpg1683 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZUV9 |
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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: 3.95 Å3/Da / Density % sol: 68.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2M NaCl, 20% PEG 3350, 0.1M MgCl2, 0.1M Imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.814→43.55 Å / Num. obs: 42566 / % possible obs: 98 % / Redundancy: 5 % / Net I/σ(I): 36.92 |
-Processing
Software |
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Refinement | Resolution: 2.814→43.55 Å / Cross valid method: FREE R-VALUE / σ(F): 2.62 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.814→43.55 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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