+Open data
-Basic information
Entry | Database: PDB / ID: 2oyc | ||||||
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Title | Crystal structure of human pyridoxal phosphate phosphatase | ||||||
Components | Pyridoxal phosphate phosphatase | ||||||
Keywords | HYDROLASE / Phosphatase / Structural Genomics / NYSGXRC / New York SGX Research Center for Structural Genomics / PSI-2 / Protein Structure Initiative | ||||||
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 / dephosphorylation ...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 / dephosphorylation / phosphoprotein phosphatase activity / lamellipodium membrane / heat shock protein binding / protein dephosphorylation / regulation of cytokinesis / ruffle membrane / cell-cell junction / cytoskeleton / magnesium ion binding / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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 | 2oyc.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oyc.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 2oyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oyc_validation.pdf.gz | 442.6 KB | Display | wwPDB validaton report |
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Full document | 2oyc_full_validation.pdf.gz | 446.9 KB | Display | |
Data in XML | 2oyc_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 2oyc_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/2oyc ftp://data.pdbj.org/pub/pdb/validation_reports/oy/2oyc | HTTPS FTP |
-Related structure data
Related structure data | 1rxdC 2fh7C 2g59C 2hcmC 2hhlC 2hxpC 2hy3C 2i0oC 2i1yC 2i44C 2iq1C 2irmC 2isnC 2nv5C 2p27C 2p4uC 2p69C 2p8eC 2pbnC 2q5eC 2qjcC 2r0bC 1zjjS 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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Components on special symmetry positions |
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Details | Probable 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-NA / |
#3: Chemical | ChemComp-WO4 / |
#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: 2.37 Å3/Da / Density % sol: 48.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 40% PEG4000, 0.1M Sodium citrate pH 5.6, 20% Isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. all: 35004 / Num. obs: 35004 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.069 / Rsym value: 0.058 / Χ2: 0.816 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 6 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.16 / Num. unique all: 6442 / Rsym value: 0.633 / Χ2: 0.514 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ZJJ Resolution: 1.72→26.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.36 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.111 / ESU R Free: 0.107 / 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: 31.002 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→26.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.767 Å / Total num. of bins used: 20
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