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Yorodumi- PDB-5cqc: Crystal structure of the legionella pneumophila effector protein RavZ -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cqc | ||||||
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Title | Crystal structure of the legionella pneumophila effector protein RavZ | ||||||
Components | putative RavZ protein | ||||||
Keywords | HYDROLASE / Ulp-family cysteine protease / autophagy inhibitor / PI3P binding domain / legionella pneumophila effector protein | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.985 Å | ||||||
Authors | Horenkamp, F.A. / Reinisch, K.M. | ||||||
Citation | Journal: Dev.Cell / Year: 2015 Title: The Legionella Anti-autophagy Effector RavZ Targets the Autophagosome via PI3P- and Curvature-Sensing Motifs. Authors: Horenkamp, F.A. / Kauffman, K.J. / Kohler, L.J. / Sherwood, R.K. / Krueger, K.P. / Shteyn, V. / Roy, C.R. / Melia, T.J. / Reinisch, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cqc.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cqc.ent.gz | 119 KB | Display | PDB format |
PDBx/mmJSON format | 5cqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cqc_validation.pdf.gz | 437.4 KB | Display | wwPDB validaton report |
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Full document | 5cqc_full_validation.pdf.gz | 447.5 KB | Display | |
Data in XML | 5cqc_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 5cqc_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/5cqc ftp://data.pdbj.org/pub/pdb/validation_reports/cq/5cqc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47118.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg1683 / Plasmid: pGex6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5ZUV9 |
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#2: Chemical | ChemComp-BA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.73 Å3/Da / Density % sol: 74.01 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 12% PEG 3350, 0.2 M BaCl2, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2014 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→110 Å / Num. all: 18551 / Num. obs: 18194 / % possible obs: 99.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.98→3.14 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 0.9 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.985→68.942 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.61 / 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: 2.985→68.942 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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