+Open data
-Basic information
Entry | Database: PDB / ID: 6omi | ||||||
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Title | Crystal structure of the Legionella effector protein MavL | ||||||
Components | MavL | ||||||
Keywords | HYDROLASE / ADP-ribosyltransferase (ART) / macrodomain / Secreted bacterial effector protein | ||||||
Function / homology | BROMIDE ION / Uncharacterized protein Function and homology information | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.643 Å | ||||||
Authors | Cygler, M. / Voth, K. | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the Legionella Effector protein MavL Authors: Cygler, M. / Voth, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6omi.cif.gz | 422.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6omi.ent.gz | 361.6 KB | Display | PDB format |
PDBx/mmJSON format | 6omi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6omi_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 6omi_full_validation.pdf.gz | 461.2 KB | Display | |
Data in XML | 6omi_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 6omi_validation.cif.gz | 51 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/6omi ftp://data.pdbj.org/pub/pdb/validation_reports/om/6omi | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 44423.336 Da / Num. of mol.: 3 / Fragment: residues 42-435 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2526 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZSJ1 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.02 Å3/Da / Density % sol: 59.23 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG8000, 0.2M Ammonium sulfate, 0.1M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 293.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.993054 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.993054 Å / Relative weight: 1 |
Reflection | Resolution: 2.643→48.77 Å / Num. obs: 41740 / % possible obs: 99.26 % / Redundancy: 1.998 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.53 |
Reflection shell | Resolution: 2.643→2.738 Å / Rmerge(I) obs: 1.387 / Num. unique obs: 4058 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.643→45.14 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.77 / 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: 2.643→48.77 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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