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Yorodumi- PDB-4da1: Crystal structure of branched-chain alpha-ketoacid dehydrogenase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4da1 | ||||||
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Title | Crystal structure of branched-chain alpha-ketoacid dehydrogenase phosphatase with Mg (II) ions at the active site | ||||||
Components | Protein phosphatase 1K, mitochondrial | ||||||
Keywords | HYDROLASE / metal-ion-assisted catalysis / dehydrogenase phosphatase / mitochondria | ||||||
Function / homology | Function and homology information [3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)]-phosphatase / [3-methyl-2-oxobutanoate dehydrogenase (lipoamide)]-phosphatase activity / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / regulation of mitochondrial membrane permeability involved in apoptotic process / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / manganese ion binding / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.383 Å | ||||||
Authors | Brautigam, C.A. / Chuang, J.L. / Chuang, D.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural and biochemical characterization of human mitochondrial branched-chain alpha-ketoacid dehydrogenase phosphatase. Authors: Wynn, R.M. / Li, J. / Brautigam, C.A. / Chuang, J.L. / Chuang, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4da1.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4da1.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 4da1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/4da1 ftp://data.pdbj.org/pub/pdb/validation_reports/da/4da1 | HTTPS FTP |
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-Related structure data
Related structure data | 2iq1S S: Starting model for refinement |
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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
#1: Protein | Mass: 43338.805 Da / Num. of mol.: 1 Fragment: truncated phosphatase protein (UNP residues 84-360) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPM1K, PP2CM / Production host: Escherichia coli (E. coli) References: UniProt: Q8N3J5, protein-serine/threonine phosphatase | ||||
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#2: Chemical | #3: Chemical | #4: 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: 3.22 Å3/Da / Density % sol: 61.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, 19% PEG3350, 0.2 M Magnesium chloride, 20 mM beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2010 |
Radiation | Monochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. obs: 22452 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.04 Å2 |
Reflection shell | Resolution: 2.38→2.42 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IQ1 Resolution: 2.383→43.942 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.287 Å2 / ksol: 0.372 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.34 Å2 / Biso mean: 51.3423 Å2 / Biso min: 23.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.383→43.942 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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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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