+Open data
-Basic information
Entry | Database: PDB / ID: 3c5v | ||||||
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Title | PP2A-specific methylesterase apo form (PME) | ||||||
Components | Protein phosphatase methylesterase 1 | ||||||
Keywords | HYDROLASE / demethylase / PP2A / Alternative splicing / Phosphoprotein / Serine esterase | ||||||
Function / homology | Function and homology information protein phosphatase methylesterase-1 / protein C-terminal methylesterase activity / protein methylesterase activity / protein demethylation / protein phosphatase regulator activity / lncRNA binding / protein phosphatase inhibitor activity / Cyclin A/B1/B2 associated events during G2/M transition / protein phosphatase 2A binding / G2/M transition of mitotic cell cycle ...protein phosphatase methylesterase-1 / protein C-terminal methylesterase activity / protein methylesterase activity / protein demethylation / protein phosphatase regulator activity / lncRNA binding / protein phosphatase inhibitor activity / Cyclin A/B1/B2 associated events during G2/M transition / protein phosphatase 2A binding / G2/M transition of mitotic cell cycle / protein phosphatase binding / cadherin binding / protein kinase binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Xing, Y. / Li, Z. / Chen, Y. / Stock, J. / Jeffrey, P.D. / Shi, Y. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2008 Title: Structural mechanism of demethylation and inactivation of protein phosphatase 2A. Authors: Xing, Y. / Li, Z. / Chen, Y. / Stock, J.B. / Jeffrey, P.D. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c5v.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c5v.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 3c5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/3c5v ftp://data.pdbj.org/pub/pdb/validation_reports/c5/3c5v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34743.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPME1, PME1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y570 |
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#2: Water | ChemComp-HOH / |
Sequence details | PME-1 WITH INTERNAL PROTEOLYTI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 26% v/v Jeffamine-2001, 200mM sodium chloride, 5mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→100 Å / Num. all: 25077 / Num. obs: 25077 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.074 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.293 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→19.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1749029.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.3381 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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