+Open data
-Basic information
Entry | Database: PDB / ID: 3via | ||||||
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Title | Crystal structure of the PH domain of Evectin-2 from human | ||||||
Components | Pleckstrin homology domain-containing family B member 2 | ||||||
Keywords | PROTEIN TRANSPORT / antiparallel BETA sheet | ||||||
Function / homology | Function and homology information regulation of cell differentiation / phosphatidylinositol-3,4,5-trisphosphate binding / recycling endosome membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Okazaki, S. / Kato, R. / Wakatsuki, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3via.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3via.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 3via.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/3via ftp://data.pdbj.org/pub/pdb/validation_reports/vi/3via | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Homo sapiens (human) / Gene: PLEKHB2 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q96CS7 #2: 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: 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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→32.77 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.891 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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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