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Yorodumi- PDB-2p69: Crystal Structure of Human Pyridoxal Phosphate Phosphatase with PLP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p69 | ||||||
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Title | Crystal Structure of Human Pyridoxal Phosphate Phosphatase with PLP | ||||||
Components | Pyridoxal phosphate phosphatase | ||||||
Keywords | HYDROLASE / Phosphatase / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / positive regulation of actin filament depolymerization / cellular response to ATP / regulation of mitotic nuclear division / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity ...pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / positive regulation of actin filament depolymerization / cellular response to ATP / regulation of mitotic nuclear division / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / lamellipodium membrane / dephosphorylation / heat shock protein binding / protein dephosphorylation / regulation of cytokinesis / ruffle membrane / cell-cell junction / cytoskeleton / magnesium ion binding / protein homodimerization activity / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Ramagopal, U.A. / Freeman, J. / Izuka, M. / Toro, R. / 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p69.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p69.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 2p69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/2p69 ftp://data.pdbj.org/pub/pdb/validation_reports/p6/2p69 | 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 2p8eC 2pbnC 2q5eC 2qjcC 2r0bC 2yocS 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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Unit cell |
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Details | The biological unit is a dimer |
-Components
#1: Protein | Mass: 33140.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDXP, PLP, PLPP / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96GD0, pyridoxal phosphatase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-PLP / |
#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: 2.38 Å3/Da / Density % sol: 48.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Citric acid pH 5.5, 20% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 16163 / Num. obs: 16163 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.09 / Χ2: 1.298 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.825 / Num. unique all: 1569 / Χ2: 0.563 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2YOC Resolution: 2.25→36.27 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.968 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.288 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.817 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→36.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.31 Å / Total num. of bins used: 20
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