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- PDB-4bx3: Crystal Structure of murine Chronophin (Pyridoxal Phosphate Phosp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bx3 | |||||||||
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Title | Crystal Structure of murine Chronophin (Pyridoxal Phosphate Phosphatase) | |||||||||
![]() | PYRIDOXAL PHOSPHATE PHOSPHATASE | |||||||||
![]() | HYDROLASE / PDXP / HAD PHOSPHATASE / HAD-LIKE HYDROLASE | |||||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Knobloch, G. / Gohla, A. / Schindelin, H. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 333.3 KB | Display | ![]() |
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PDB format | ![]() | 280.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.9 KB | Display | ![]() |
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Full document | ![]() | 461.6 KB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bx0C ![]() 4bx2C ![]() 2oycS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.08087, 0.9568, -0.2793), Vector: |
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Components
#1: Protein | Mass: 31614.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P60487, pyridoxal phosphatase, phosphoserine phosphatase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.53 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.1M IMIDAZOLE PH 8, 0.2M NACL, 1M SODIUM TARTRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 23, 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: 2.19→44.66 Å / Num. obs: 39743 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 47.02 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.19→2.31 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2OYC Resolution: 2.193→44.659 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 22.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.193→44.659 Å
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Refine LS restraints |
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LS refinement shell |
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