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- PDB-6cgk: Structure of the HAD domain of effector protein Lem4 (lpg1101) fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6cgk | ||||||
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Title | Structure of the HAD domain of effector protein Lem4 (lpg1101) from Legionella pneumophila (inactive mutant)with phosphate bound in the active site | ||||||
![]() | effector protein Lem4 (lpg1101) | ||||||
![]() | HYDROLASE / haloacid dehalogenase superfamily / tyrosine phosphatase / translocated bacterial effector | ||||||
Function / homology | ![]() host cell cytoplasmic vesicle / small GTPase binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Beyrakhova, K.A. / Xu, C. / Cygler, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Legionella pneumophilaeffector Lem4 is a membrane-associated protein tyrosine phosphatase. Authors: Beyrakhova, K. / Li, L. / Xu, C. / Gagarinova, A. / Cygler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.2 KB | Display | ![]() |
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PDB format | ![]() | 73.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.2 KB | Display | ![]() |
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Full document | ![]() | 443.3 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6cdwC ![]() 6cgjSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24704.826 Da / Num. of mol.: 1 / Mutation: D25N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg1101 / Plasmid: pMCSG7 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris 6.5, 22% PEG 3350, 0.2 M Mg acetate, 0.6 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 5, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.668→52.814 Å / Num. obs: 24546 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.024 / Rrim(I) all: 0.09 / Net I/σ(I): 19.7 / Num. measured all: 351125 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6CGJ Resolution: 1.668→47.238 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.74 Å2 / Biso mean: 40.5311 Å2 / Biso min: 19.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.668→47.238 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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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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