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Yorodumi- PDB-5by0: Crystal structure of magnesium-bound Duf89 protein Saccharomyces ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5by0 | ||||||
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Title | Crystal structure of magnesium-bound Duf89 protein Saccharomyces cerevisiae | ||||||
Components | Protein-glutamate O-methyltransferase | ||||||
Keywords | TRANSFERASE / DUF89 / Mg-bound / family of carbohydrate phosphatases | ||||||
Function / homology | Function and homology information fructose-1-phosphatase activity / fructose 6-phosphate aldolase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatase activity / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Nocek, B. / Cuff, M. / Cui, H. / Xu, X. / Savchenko, A. / Joachimiak, A. / Yakunin, A. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of magnesium-bound Duf89 protein Saccharomyces cerevisiae Authors: Nocek, B. / Cuff, M. / Cui, H. / Xu, X. / Savchenko, A. / Joachimiak, A. / Yakunin, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5by0.cif.gz | 209.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5by0.ent.gz | 173.2 KB | Display | PDB format |
PDBx/mmJSON format | 5by0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5by0_validation.pdf.gz | 426.2 KB | Display | wwPDB validaton report |
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Full document | 5by0_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 5by0_validation.xml.gz | 23 KB | Display | |
Data in CIF | 5by0_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/5by0 ftp://data.pdbj.org/pub/pdb/validation_reports/by/5by0 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 54720.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: YMR027W, YM9711.17 / Cell line (production host): BL21DE3 / Production host: Escherichia coli (E. coli) References: UniProt: Q04371, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 0.1 M MgCl2, 0.1 M Bis-Tris, 25% Peg3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2011 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34.4 Å / Num. obs: 46859 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→34.4 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→34.4 Å
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Refine LS restraints |
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LS refinement shell |
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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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