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Yorodumi- PDB-4bx0: Crystal Structure of a Monomeric Variant of murine Chronophin (Py... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bx0 | |||||||||
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Title | Crystal Structure of a Monomeric Variant of murine Chronophin (Pyridoxal Phosphate phosphatase) | |||||||||
Components | PYRIDOXAL PHOSPHATE PHOSPHATASE | |||||||||
Keywords | HYDROLASE / PDXP / PLPP / HAD PHOSPHATASE / HAD-LIKE HYDROLASE / MONOMER | |||||||||
Function / homology | Function and homology information pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / contractile ring / positive regulation of actin filament depolymerization / cellular response to ATP / regulation of mitotic nuclear division / myosin phosphatase activity / protein-serine/threonine phosphatase ...pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / contractile ring / positive regulation of actin filament depolymerization / cellular response to ATP / regulation of mitotic nuclear division / myosin phosphatase activity / protein-serine/threonine phosphatase / growth factor binding / phosphoprotein phosphatase activity / cleavage furrow / lamellipodium membrane / dephosphorylation / heat shock protein binding / protein dephosphorylation / regulation of cytokinesis / ruffle membrane / cell-cell junction / actin cytoskeleton / midbody / magnesium ion binding / protein homodimerization activity / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Kestler, C. / Knobloch, G. / Gohla, A. / Schindelin, H. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Chronophin Dimerization is Required for Proper Positioning of its Substrate Specificity Loop Authors: Kestler, C. / Knobloch, G. / Tessmer, I. / Jeanclos, E. / Schindelin, H. / Gohla, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bx0.cif.gz | 179 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bx0.ent.gz | 144.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bx0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/4bx0 ftp://data.pdbj.org/pub/pdb/validation_reports/bx/4bx0 | HTTPS FTP |
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-Related structure data
Related structure data | 4bx2C 4bx3C 2oycS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31664.041 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P60487, pyridoxal phosphatase, phosphoserine phosphatase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GOL / |
#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: 2.01 Å3/Da / Density % sol: 38.85 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1M MES PH 6.5, 25% PEG-MME 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30.61 Å / Num. obs: 25533 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 19.09 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OYC Resolution: 1.75→28.404 Å / SU ML: 0.28 / σ(F): 1.37 / Phase error: 23.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.901 Å2 / ksol: 0.353 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→28.404 Å
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Refine LS restraints |
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LS refinement shell |
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