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Yorodumi- PDB-2p8e: Crystal structure of the serine/threonine phosphatase domain of h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p8e | ||||||
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Title | Crystal structure of the serine/threonine phosphatase domain of human PPM1B | ||||||
Components | PPM1B beta isoform variant 6 | ||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information N-terminal protein myristoylation / negative regulation of defense response to virus / peptidyl-threonine dephosphorylation / negative regulation of interferon-beta production / negative regulation of non-canonical NF-kappaB signal transduction / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / negative regulation of canonical NF-kappaB signal transduction / protein dephosphorylation / ISG15 antiviral mechanism ...N-terminal protein myristoylation / negative regulation of defense response to virus / peptidyl-threonine dephosphorylation / negative regulation of interferon-beta production / negative regulation of non-canonical NF-kappaB signal transduction / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / negative regulation of canonical NF-kappaB signal transduction / protein dephosphorylation / ISG15 antiviral mechanism / positive regulation of canonical Wnt signaling pathway / manganese ion binding / nucleolus / magnesium ion binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.816 Å | ||||||
Authors | Bonanno, J.B. / Freeman, J. / Bain, K.T. / Lau, C. / Xu, W. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2007 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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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT A MONOMER IS PROBABLY THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p8e.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p8e.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 2p8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/2p8e ftp://data.pdbj.org/pub/pdb/validation_reports/p8/2p8e | HTTPS FTP |
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-Related structure data
Related structure data | 1rxdC 2fh7C 2g59C 2hcmC 2hhlC 2hxpC 2hy3C 2i0oC 2i1yC 2i44C 2iq1C 2irmC 2isnC 2nv5C 2oycC 2p27C 2p4uC 2p69C 2pbnC 2q5eC 2qjcC 2r0bC 1a6qS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | probable monomer |
-Components
#1: Protein | Mass: 34305.309 Da / Num. of mol.: 2 / Fragment: serine/threonine phosphatase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPM1B / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q4J6C0, UniProt: O75688*PLUS, protein-serine/threonine phosphatase #2: Chemical | #3: 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: 2.09 Å3/Da / Density % sol: 41.2 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7.5 Details: 100mM Hepes pH 7.5, 20% PEG 4000, 10% Isopropanol, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 15, 2007 |
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: 1.816→72.932 Å / Num. all: 49509 / Num. obs: 49509 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.184 / Rsym value: 0.184 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.816→1.91 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6430 / Rsym value: 0.842 / % possible all: 84.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1A6Q Resolution: 1.816→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.224 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 22.186 Å2
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Refinement step | Cycle: LAST / Resolution: 1.816→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.816→1.863 Å / Total num. of bins used: 20
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