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Yorodumi- PDB-1rjd: Structure of PPM1, a leucine carboxy methyltransferase involved i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rjd | ||||||
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Title | Structure of PPM1, a leucine carboxy methyltransferase involved in the regulation of protein phosphatase 2A activity | ||||||
Components | carboxy methyl transferase for protein phosphatase 2A catalytic subunit | ||||||
Keywords | TRANSFERASE / SAM dependent methyltransferase | ||||||
Function / homology | Function and homology information Cyclin A/B1/B2 associated events during G2/M transition / [phosphatase 2A protein]-leucine-carboxy methyltransferase / protein C-terminal leucine carboxyl O-methyltransferase activity / C-terminal protein methylation / regulation of autophagy / protein-containing complex assembly Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Leulliot, N. / Quevillon-Cheruel, S. / Sorel, I. / Li de La Sierra-Gallay, I. / Collinet, B. / Graille, M. / Blondeau, K. / Bettache, N. / Poupon, A. / Janin, J. / van Tilbeurgh, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structure of protein phosphatase methyltransferase 1 (PPM1), a leucine carboxyl methyltransferase involved in the regulation of protein phosphatase 2A activity Authors: Leulliot, N. / Quevillon-Cheruel, S. / Sorel, I. / Li de La Sierra-Gallay, I. / Collinet, B. / Graille, M. / Blondeau, K. / Bettache, N. / Poupon, A. / Janin, J. / van Tilbeurgh, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rjd.cif.gz | 222.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rjd.ent.gz | 184.5 KB | Display | PDB format |
PDBx/mmJSON format | 1rjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/1rjd ftp://data.pdbj.org/pub/pdb/validation_reports/rj/1rjd | HTTPS FTP |
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-Related 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: 38567.438 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PPM1 / Plasmid: pET9 / Production host: Escherichia coli (E. coli) / Strain (production host): Xl-10 Gold References: UniProt: Q04081, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Chemical | ChemComp-BME / #4: Chemical | ChemComp-SO4 / | #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 | Density Matthews: 2.54 Å3/Da / Density % sol: 51.48 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 15% PEG 8000, 0.2M ammonium sulfate, 0.1M MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 4.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.94, 0.9792, 0.9795, 0.9184 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 14, 2002 | |||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→52 Å / Num. obs: 106254 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 100 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 52 Å / % possible obs: 100 % / Redundancy: 5.9 % / Num. measured all: 631127 / Rmerge(I) obs: 0.13 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→52.7 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.498 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.12 / ESU R Free: 0.117 / 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: 13.683 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→52.7 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 | *PLUS Lowest resolution: 52 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.214 / Rfactor Rwork: 0.172 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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