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Open data
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Basic information
Entry | Database: PDB / ID: 2iq1 | ||||||
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Title | Crystal structure of human PPM1K | ||||||
![]() | Protein phosphatase 2C kappa, PPM1K | ||||||
![]() | HYDROLASE / protein phosphatase 2C kappa / structural genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | ![]() [3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)]-phosphatase / 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 ...[3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)]-phosphatase / 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 / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bonanno, J.B. / Freeman, J. / Russell, M. / Bain, K.T. / Adams, J. / Pelletier, L. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Structural genomics of protein phosphatases Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.3 KB | Display | ![]() |
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PDB format | ![]() | 48.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.9 KB | Display | ![]() |
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Full document | ![]() | 429.5 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rxdC ![]() 2fh7C ![]() 2g59C ![]() 2hcmC ![]() 2hhlC ![]() 2hxpC ![]() 2hy3C ![]() 2i0oC ![]() 2i1yC ![]() 2i44C ![]() 2irmC ![]() 2isnC ![]() 2nv5C ![]() 2oycC ![]() 2p27C ![]() 2p4uC ![]() 2p69C ![]() 2p8eC ![]() 2pbnC ![]() 2q5eC ![]() 2qjcC ![]() 2r0bC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30199.197 Da / Num. of mol.: 1 / Fragment: Residues 89-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.46 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 8 Details: 100mM Hepes pH 8, 18% PEG 10K, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 11, 2006 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→51.674 Å / Num. all: 15773 / Num. obs: 15758 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 8 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2.5 / Num. measured all: 17878 / Num. unique all: 2247 / Rsym value: 0.848 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 51.645 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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