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Open data
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Basic information
Entry | Database: PDB / ID: 3via | ||||||
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Title | Crystal structure of the PH domain of Evectin-2 from human | ||||||
![]() | Pleckstrin homology domain-containing family B member 2 | ||||||
![]() | PROTEIN TRANSPORT / antiparallel BETA sheet | ||||||
Function / homology | ![]() regulation of cell differentiation / phosphatidylinositol-3,4,5-trisphosphate binding / recycling endosome membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okazaki, S. / Kato, R. / Wakatsuki, S. | ||||||
![]() | ![]() Title: Structural basis of the strict phospholipid binding specificity of the pleckstrin homology domain of human evectin-2 Authors: Okazaki, S. / Kato, R. / Uchida, Y. / Taguchi, T. / Arai, H. / Wakatsuki, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.7 KB | Display | ![]() |
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PDB format | ![]() | 44.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Components
#1: Protein | Mass: 13096.894 Da / Num. of mol.: 2 / Fragment: PH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.95 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG MME 5000, 0.1M bis-tris-HCl, 13% ethylene glycol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→100 Å / Num. all: 40506 / Num. obs: 21746 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 48 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 8.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.321 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→32.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.751→1.796 Å / Total num. of bins used: 20
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