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Yorodumi- PDB-6vve: Legionella pneumophila Lpg2603 kinase bound to IP6, Mn2+, and ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vve | |||||||||
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Title | Legionella pneumophila Lpg2603 kinase bound to IP6, Mn2+, and ADP | |||||||||
Components | Dot/Icm T4SS effector | |||||||||
Keywords | TRANSFERASE / phosphorylation / kinase / IP6 / ADP | |||||||||
Function / homology | Function and homology information host cell cytoplasmic vesicle / regulation of GTPase activity / small GTPase binding / nucleotide binding Similarity search - Function | |||||||||
Biological species | Legionella pneumophila (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Tomchick, D.R. / Tagliabracci, V.S. / Park, B.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: ALegionellaeffector kinase is activated by host inositol hexakisphosphate. Authors: Sreelatha, A. / Nolan, C. / Park, B.C. / Pawlowski, K. / Tomchick, D.R. / Tagliabracci, V.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vve.cif.gz | 231.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vve.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 6vve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vve_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6vve_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6vve_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 6vve_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/6vve ftp://data.pdbj.org/pub/pdb/validation_reports/vv/6vve | HTTPS FTP |
-Related structure data
Related structure data | 6vvcSC 6vvdC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 36508.906 Da / Num. of mol.: 1 / Fragment: UNP residues 21-322 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_13135, DI056_05180, DI105_03620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F2W2, UniProt: Q5ZSB6*PLUS |
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#2: Chemical | ChemComp-IHP / |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-MN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.1 M citric acid, 7% MKPD, 0.03 M sodium chloride, 0.5 mM IP6, 1 mM manganese chloride, 1 mM APS-PNP, 35% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5414 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 19, 2019 |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5414 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→29.85 Å / Num. obs: 22536 / % possible obs: 76.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.83 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.066 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.77→1.97 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2259 / Rpim(I) all: 0.395 / % possible all: 29 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6VVC Resolution: 1.85→29.85 Å / SU ML: 0.2609 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3101 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→29.85 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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