+Open data
-Basic information
Entry | Database: PDB / ID: 4tvv | ||||||
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Title | Crystal structure of LppA from Legionella pneumophila | ||||||
Components | Tyrosine phosphatase II superfamily protein | ||||||
Keywords | HYDROLASE / bacterial effector protein / phytase / myo-inositol-hexakisphosphate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Weber, S. / Stirnimann, C. / Wieser, M. / Meier, R. / Engelhardt, S. / Li, X. / Capitani, G. / Kammerer, R. / Hilbi, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: A Type IV Translocated Legionella Cysteine Phytase Counteracts Intracellular Growth Restriction by Phytate. Authors: Weber, S. / Stirnimann, C.U. / Wieser, M. / Frey, D. / Meier, R. / Engelhardt, S. / Li, X. / Capitani, G. / Kammerer, R.A. / Hilbi, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tvv.cif.gz | 735.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tvv.ent.gz | 620.7 KB | Display | PDB format |
PDBx/mmJSON format | 4tvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/4tvv ftp://data.pdbj.org/pub/pdb/validation_reports/tv/4tvv | HTTPS FTP |
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-Related structure data
Related structure data | 3f41S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35984.852 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2819 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZRR1 |
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-Non-polymers , 5 types, 1479 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-TRS / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 40 mM KH2PO4 ph 4.1, 16% PEG 8000, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 264769 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.3 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F41 Resolution: 1.4→48.259 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→48.259 Å
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Refine LS restraints |
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LS refinement shell |
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