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Yorodumi- PDB-7wbm: Crystal structure of Legionella pneumophila effector protein Lpg0081 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wbm | ||||||
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Title | Crystal structure of Legionella pneumophila effector protein Lpg0081 | ||||||
Components | Lpg0081 | ||||||
Keywords | HYDROLASE / MacroD-type ADP-ribose hydrolase | ||||||
Function / homology | Chem-AR6 / Dot/Icm T4SS effector Function and homology information | ||||||
Biological species | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Lee, J. / Kim, H. / Oh, B.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Reversible modification of mitochondrial ADP/ATP translocases by paired Legionella effector proteins. Authors: Kubori, T. / Lee, J. / Kim, H. / Yamazaki, K. / Nishikawa, M. / Kitao, T. / Oh, B.H. / Nagai, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wbm.cif.gz | 180.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wbm.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 7wbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/7wbm ftp://data.pdbj.org/pub/pdb/validation_reports/wb/7wbm | HTTPS FTP |
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-Related structure data
Related structure data | 7wbkSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47016.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Gene: lpg0081 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZZD0 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.65M Na,K tartrate, 0.2M lithium sulfate, 3% (w/v) sucrose, 0.1M CHES (pH 9.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 143455 / % possible obs: 97.93 % / Redundancy: 4.7 % / Biso Wilson estimate: 51.93 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.51 |
Reflection shell | Resolution: 2.7→2.796 Å / Num. unique obs: 9096 / CC1/2: 0.696 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WBK Resolution: 2.7→35.83 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.08 / 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: 2.7→35.83 Å
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Refine LS restraints |
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LS refinement shell |
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