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- PDB-6exb: Crystal structure of DotM cytoplasmic domain (residues 153-380), ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6exb | ||||||
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Title | Crystal structure of DotM cytoplasmic domain (residues 153-380), native form | ||||||
![]() | IcmP (DotM) | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Meir, A. / Waksman, G. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.6 KB | Display | ![]() |
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PDB format | ![]() | 81.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
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Full document | ![]() | 453 KB | Display | |
Data in XML | ![]() | 21 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6exaC ![]() 6excC ![]() 6exdSC ![]() 6exeC 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: 26508.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: icmP, lpg0445 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.51 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate pH 5.0 a 15% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→102.7 Å / Num. obs: 46854 / % possible obs: 99.85 % / Redundancy: 10.1 % / Rsym value: 0.098 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.84→1.89 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.513 / Rsym value: 0.029 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6EXD Resolution: 1.84→102.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.836 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.137 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.467 Å2
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Refinement step | Cycle: 1 / Resolution: 1.84→102.7 Å
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Refine LS restraints |
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