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Open data
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Basic information
Entry | Database: PDB / ID: 3ady | ||||||
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Title | Crystal structure of DotD from Legionella | ||||||
![]() | DotD | ||||||
![]() | PROTON TRANSPORT / 3-layer(bab) sandwich / MTH1598-like | ||||||
Function / homology | DotD protein / DotD protein / DotD superfamily / DotD protein / Phage tail protein beta-alpha-beta fold / 3-Layer(bab) Sandwich / Alpha Beta / DotD![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Imada, K. / Nakano, N. / Kubori, T. / Kinoshita, M. / Nagai, H. | ||||||
![]() | ![]() Title: Crystal structure of Legionella DotD: insights into the relationship between type IVB and type II/III secretion systems Authors: Nakano, N. / Kubori, T. / Kinoshita, M. / Imada, K. / Nagai, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.1 KB | Display | ![]() |
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PDB format | ![]() | 25 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.6 KB | Display | ![]() |
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Full document | ![]() | 426 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | AUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN. |
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Components
#1: Protein | Mass: 16191.568 Da / Num. of mol.: 1 / Fragment: periplasmic fragment, residues 20 -163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10 Details: 8% PEG 8000, 0.1M CHES-NaOH, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2008 |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97897 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.41 Å / Num. all: 12739 / Num. obs: 12739 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 29.39 Å2 / Rsym value: 0.072 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 1830 / Rsym value: 0.352 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.5225 Å2 / ksol: 0.327575 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→36.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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