+Open data
-Basic information
Entry | Database: PDB / ID: 4iip | ||||||
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Title | Legionella pneumophila effector | ||||||
Components | Adenosine monophosphate-protein hydrolase SidD | ||||||
Keywords | HYDROLASE / beta sandwich / de-AMPylation / rab1 / legionella containing vacuole surface | ||||||
Function / homology | Function and homology information protein deadenylylation / protein adenylylhydrolase activity / protein adenylylation / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / regulation of GTPase activity / small GTPase binding / host cell perinuclear region of cytoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Tascon, I. / Chen, Y. / Neunuebel, M.R. / Rojas, A.L. / Machner, M.P. / Hierro, A. | ||||||
Citation | Journal: Plos Pathog. / Year: 2013 Title: Structural Basis for Rab1 De-AMPylation by the Legionella pneumophila Effector SidD Authors: Chen, Y. / Tascon, I. / Neunuebel, M.R. / Pallara, C. / Brady, J. / Kinch, L.N. / Fernandez-Recio, J. / Rojas, A.L. / Machner, M.P. / Hierro, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iip.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iip.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 4iip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/4iip ftp://data.pdbj.org/pub/pdb/validation_reports/ii/4iip | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36121.883 Da / Num. of mol.: 1 / Fragment: UNP residues 37-350 / Mutation: D110A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: sidD, lpg2465 / Production host: Escherichia coli (E. coli) References: UniProt: Q5ZSQ2, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases | ||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CL / #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: 2.64 Å3/Da / Density % sol: 53.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 1.6M NaCl, 0.1M Na acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→28.63 Å / Num. obs: 30812 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.066 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.097 / Net I/σ(I): 18.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.63 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1838 / WRfactor Rwork: 0.139 / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.9026 / SU B: 2.46 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1128 / SU Rfree: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.7 Å2 / Biso mean: 27.6487 Å2 / Biso min: 10.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→28.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.898→1.947 Å / Total num. of bins used: 20
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