+Open data
-Basic information
Entry | Database: PDB / ID: 1rxd | ||||||
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Title | Crystal structure of human protein tyrosine phosphatase 4A1 | ||||||
Components | protein tyrosine phosphatase type IVA, member 1; Protein tyrosine phosphatase IVA1 | ||||||
Keywords | structural genomics / unknown function / NYSGXRC / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information protein tyrosine/serine/threonine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / spindle / early endosome / positive regulation of cell migration / cell cycle / endoplasmic reticulum ...protein tyrosine/serine/threonine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / spindle / early endosome / positive regulation of cell migration / cell cycle / endoplasmic reticulum / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Sun, J.P. / Fedorov, A.A. / Almo, S.C. / Zhang, Z.Y. / Burley, S.K. / 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 | 1rxd.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rxd.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/1rxd ftp://data.pdbj.org/pub/pdb/validation_reports/rx/1rxd | HTTPS FTP |
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-Related structure data
Related structure data | 2fh7C 2g59C 2hcmC 2hhlC 2hxpC 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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2 |
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3 |
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Unit cell |
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Details | The biological assemply is a monomer |
-Components
#1: Protein | Mass: 18427.883 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q93096 #2: 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: 3.216 Å3/Da / Density % sol: 60.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3350, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911, 0.97934, 0.97166 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 19, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→25 Å / Num. all: 48954 / Num. obs: 48954 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.132 / Net I/σ(I): 14.6 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3.2 / % possible all: 72.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→25 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.8521 Å2 / ksol: 0.358711 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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