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Yorodumi- PDB-3v0f: Crystal structure of Ciona intestinalis voltage sensor-containing... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v0f | ||||||
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Title | Crystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 241-576(C363S), form II | ||||||
Components | Voltage-sensor containing phosphatase | ||||||
Keywords | HYDROLASE / PTP / C2 / Phosphatase | ||||||
Function / homology | Function and homology information regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol dephosphorylation / protein tyrosine phosphatase activity / cell projection / cell motility / monoatomic ion channel activity / negative regulation of cell population proliferation / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Ciona intestinalis (vase tunicate) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Liu, L. / Kohout, S.C. / Xu, Q. / Muller, S. / Kimberlin, C. / Isacoff, E.Y. / Minor, D.L. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: A glutamate switch controls voltage-sensitive phosphatase function. Authors: Liu, L. / Kohout, S.C. / Xu, Q. / Muller, S. / Kimberlin, C.R. / Isacoff, E.Y. / Minor, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v0f.cif.gz | 321.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v0f.ent.gz | 263 KB | Display | PDB format |
PDBx/mmJSON format | 3v0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v0f_validation.pdf.gz | 450.7 KB | Display | wwPDB validaton report |
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Full document | 3v0f_full_validation.pdf.gz | 457.5 KB | Display | |
Data in XML | 3v0f_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 3v0f_validation.cif.gz | 54.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/3v0f ftp://data.pdbj.org/pub/pdb/validation_reports/v0/3v0f | HTTPS FTP |
-Related structure data
Related structure data | 3v0dSC 3v0eC 3v0gC 3v0hC 3v0iC 3v0jC 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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1 |
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2 |
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Unit cell |
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Details | Two molecules in the asymmetric unit |
-Components
#1: Protein | Mass: 38827.984 Da / Num. of mol.: 2 / Fragment: unp residues 241-576 / Mutation: C363S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Gene: Ci-VSP / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 pLysS / References: UniProt: Q4W8A1 #2: Chemical | #3: 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: 2.19 Å3/Da / Density % sol: 43.92 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 17.5-22.5% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl,pH 8.0; crystal were soaked in 30% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl, pH 8.0 to remove phosphate ...Details: 17.5-22.5% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl,pH 8.0; crystal were soaked in 30% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl, pH 8.0 to remove phosphate by serial dilution, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2010 / Details: Double Crystal Si(111) |
Radiation | Monochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→84 Å / Num. all: 163916 / Num. obs: 153889 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 7 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3.5 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB: 3V0D Resolution: 1.3→83.51 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.39 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.05 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.827 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→83.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.301→1.335 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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