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Yorodumi- PDB-5io3: Crystal structure of the legionella pneumophila effector protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5io3 | ||||||
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Title | Crystal structure of the legionella pneumophila effector protein RavZ - I422 | ||||||
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 str. Philadelphia 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.74 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 | 5io3.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5io3.ent.gz | 135.4 KB | Display | PDB format |
PDBx/mmJSON format | 5io3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5io3_validation.pdf.gz | 411.7 KB | Display | wwPDB validaton report |
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Full document | 5io3_full_validation.pdf.gz | 426.6 KB | Display | |
Data in XML | 5io3_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 5io3_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/5io3 ftp://data.pdbj.org/pub/pdb/validation_reports/io/5io3 | HTTPS FTP |
-Related 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: 56295.258 Da / Num. of mol.: 1 / Mutation: C258S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Strain: Philadelphia 1 / Gene: lpg1683 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5ZUV9 |
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#2: 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: 3.9 Å3/Da / Density % sol: 68.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 2.2M NaCl, 28% PEG 3350, 0.1M Imidazole pH6.5 |
-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 270 / 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: 2.74→39.25 Å / Num. obs: 23220 / % possible obs: 98 % / Redundancy: 10.6 % / Net I/σ(I): 20.3 |
-Processing
Software |
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Refinement | Resolution: 2.74→39.25 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 33.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.74→39.25 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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