[English] 日本語
Yorodumi- PDB-1rje: Structure of PPM1, a leucine carboxy methyltransferase involved i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rje | ||||||
---|---|---|---|---|---|---|---|
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 / regulation of autophagy / protein-containing complex assembly / methylation Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Leulliot, N. / Quevillon-Cheruel, S. / Sorel, I. / de La Sierra-Gallay, I.L. / 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. / de La Sierra-Gallay, I.L. / Collinet, B. / Graille, M. / Blondeau, K. / Bettache, N. / Poupon, A. / Janin, J. / van Tilbeurgh, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rje.cif.gz | 233.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rje.ent.gz | 186 KB | Display | PDB format |
PDBx/mmJSON format | 1rje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rje_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1rje_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1rje_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 1rje_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/1rje ftp://data.pdbj.org/pub/pdb/validation_reports/rj/1rje | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-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 | #4: Chemical | ChemComp-BME / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.46 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2002 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→24 Å / Num. obs: 76511 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2→2.11 Å / % possible all: 92 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 24 Å / Redundancy: 3.8 % / Num. measured all: 294159 / Rmerge(I) obs: 0.12 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.47 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.885 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.163 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 16.526 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→24.47 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 24 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.153 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|