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Yorodumi- PDB-6exe: Crystal structure of DotM cytoplasmic domain (residues 153-380),R217E -
+Open data
-Basic information
Entry | Database: PDB / ID: 6exe | ||||||
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Title | Crystal structure of DotM cytoplasmic domain (residues 153-380),R217E | ||||||
Components | IcmP (DotM) | ||||||
Keywords | PROTEIN BINDING / Membrane protein / secretion system / type 4 secretion system / Legionella pneumophila / coupling complex | ||||||
Function / homology | : / protein transport / plasma membrane / Type 4 apparatus protein DotM Function and homology information | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Meir, A. / Waksman, G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Legionella DotM structure reveals a role in effector recruiting to the Type 4B secretion system. Authors: Meir, A. / Chetrit, D. / Liu, L. / Roy, C.R. / Waksman, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6exe.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6exe.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 6exe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6exe_validation.pdf.gz | 461.8 KB | Display | wwPDB validaton report |
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Full document | 6exe_full_validation.pdf.gz | 468.9 KB | Display | |
Data in XML | 6exe_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 6exe_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/6exe ftp://data.pdbj.org/pub/pdb/validation_reports/ex/6exe | HTTPS FTP |
-Related structure data
Related structure data | 6exaC 6exbSC 6excC 6exdC 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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Unit cell |
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-Components
#1: Protein | Mass: 26480.506 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Gene: icmP, lpg0445 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BLR / References: UniProt: Q5ZYC7 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MES / | #4: Water | ChemComp-HOH / | |
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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: 2.59 Å3/Da / Density % sol: 52.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium iodide 0.1 M MES pH 6.5 25% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2→53.45 Å / Num. obs: 34191 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rsym value: 0.181 / Net I/σ(I): 7.88 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.623 / Rsym value: 2.44 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EXB Resolution: 2→53.45 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.002 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.709 Å2
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Refinement step | Cycle: 1 / Resolution: 2→53.45 Å
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