+Open data
-Basic information
Entry | Database: PDB / ID: 2hxp | ||||||
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Title | Crystal Structure of the human phosphatase (DUSP9) | ||||||
Components | Dual specificity protein phosphatase 9 | ||||||
Keywords | HYDROLASE / 8638a / Human Phosphatase / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / negative regulation of MAPK cascade / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity ...MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / negative regulation of MAPK cascade / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / JNK cascade / ERK1 and ERK2 cascade / protein dephosphorylation / protein-tyrosine-phosphatase / Negative regulation of MAPK pathway / MAPK cascade / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 Å | ||||||
Authors | Madegowda, M. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hxp.cif.gz | 44.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hxp.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/2hxp ftp://data.pdbj.org/pub/pdb/validation_reports/hx/2hxp | HTTPS FTP |
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-Related structure data
Related structure data | 1rxdC 2fh7C 2g59C 2hcmC 2hhlC 2hy3C 2i0oC 2i1yC 2i44C 2iq1C 2irmC 2isnC 2nv5C 2oycC 2p27C 2p4uC 2p69C 2p8eC 2pbnC 2q5eC 2qjcC 2r0bC 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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Unit cell |
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-Components
#1: Protein | Mass: 17680.049 Da / Num. of mol.: 1 / Fragment: residues 201-345 / Mutation: C290S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP9, MKP4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99956, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-PO4 / |
#3: 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: 2.49 Å3/Da / Density % sol: 50.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350, 0.1M Bis-Tris, 0.2M Ammonium Sulphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1, 1.7 | |||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 30, 2006 / Details: Mirrors | |||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.83→24.7 Å / Num. all: 15038 / Num. obs: 14920 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.022 / Net I/σ(I): 47.1 | |||||||||
Reflection shell | Resolution: 1.83→1.9 Å / Redundancy: 10 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 19 / Num. unique all: 1481 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.83→24.7 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 270810.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Residues listed in remark 465 were not modeled due to lack of or weak electron density. The residual density was modeled as phosphate, however it could equally well be sulfate.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.3294 Å2 / ksol: 0.371511 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.83→24.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.94 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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