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Yorodumi- PDB-3f4a: Structure of Ygr203w, a yeast protein tyrosine phosphatase of the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f4a | ||||||
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Title | Structure of Ygr203w, a yeast protein tyrosine phosphatase of the Rhodanese family | ||||||
Components | Uncharacterized protein YGR203W | ||||||
Keywords | HYDROLASE / protein phosphatase / rhodanese-like family / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information thiosulfate sulfurtransferase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / dephosphorylation / phosphatase activity / protein tyrosine phosphatase activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Singer, A.U. / Xu, X. / Cui, H. / Osipiuk, J. / Joachimiak, A. / Edwards, A.M. / Yakunin, A.F. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structure of Ygr203w, a yeast protein tyrosine phosphatase of the Rhodanese family Authors: Proudfoot, M. / Brown, G. / Singer, A.U. / Xu, X. / Cui, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f4a.cif.gz | 84 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f4a.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 3f4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f4a_validation.pdf.gz | 456.5 KB | Display | wwPDB validaton report |
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Full document | 3f4a_full_validation.pdf.gz | 459.5 KB | Display | |
Data in XML | 3f4a_validation.xml.gz | 17 KB | Display | |
Data in CIF | 3f4a_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/3f4a ftp://data.pdbj.org/pub/pdb/validation_reports/f4/3f4a | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19986.533 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: protein was digested with limiting amounts of trypsin Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: G7731, YGR203W / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) References: UniProt: P42937, protein-serine/threonine phosphatase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-NH4 / | #5: 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 grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris 8,5, 1.5 M LiSO4 plus 0.015 mg/ml trypsin. Cryoprotected with N-paratone oil, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2008 / Details: Mirrors |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 27702 / Num. obs: 27354 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.682 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.6 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: none Resolution: 1.8→36.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.343 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.132 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.415 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→36.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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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