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- PDB-1jk7: CRYSTAL STRUCTURE OF THE TUMOR-PROMOTER OKADAIC ACID BOUND TO PRO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jk7 | |||||||||
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Title | CRYSTAL STRUCTURE OF THE TUMOR-PROMOTER OKADAIC ACID BOUND TO PROTEIN PHOSPHATASE-1 | |||||||||
![]() | SERINE/THREONINE PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT | |||||||||
![]() | HYDROLASE/TOXIN / HYDROLASE-INHIBITOR COMPLEX / HYDROLASE-TOXIN COMPLEX | |||||||||
Function / homology | ![]() PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / protein phosphatase 1 binding / lamin binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / microtubule organizing center / myosin phosphatase activity / protein serine/threonine phosphatase activity / glycogen metabolic process ...PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / protein phosphatase 1 binding / lamin binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / microtubule organizing center / myosin phosphatase activity / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / Triglyceride catabolism / Maturation of hRSV A proteins / entrainment of circadian clock by photoperiod / phosphatase activity / phosphoprotein phosphatase activity / cleavage furrow / blastocyst development / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of glial cell proliferation / Resolution of Sister Chromatid Cohesion / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / RHO GTPases Activate Formins / RAF activation / circadian regulation of gene expression / neuron differentiation / regulation of circadian rhythm / kinetochore / Separation of Sister Chromatids / MAPK cascade / Circadian Clock / presynapse / midbody / spermatogenesis / mitochondrial outer membrane / dendritic spine / nuclear speck / cell cycle / protein domain specific binding / cell division / focal adhesion / glutamatergic synapse / protein-containing complex binding / nucleolus / protein kinase binding / protein-containing complex / mitochondrion / RNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Maynes, J.T. / Bateman, K.S. / Cherney, M.M. / Das, A.K. / James, M.N. | |||||||||
![]() | ![]() Title: Crystal structure of the tumor-promoter okadaic acid bound to protein phosphatase-1. Authors: Maynes, J.T. / Bateman, K.S. / Cherney, M.M. / Das, A.K. / Luu, H.A. / Holmes, C.F. / James, M.N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.2 KB | Display | ![]() |
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PDB format | ![]() | 59.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.7 KB | Display | ![]() |
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Full document | ![]() | 781.9 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fjmS 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37030.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P36873, protein-serine/threonine phosphatase |
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-Non-polymers , 5 types, 185 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/OKA.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/OKA.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-OKA / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | The Okadaic Acid was obtained from DINOFLAGEL |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: LITHIUM SULPHATE, PEG 400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 15, 2000 / Details: MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 24439 / Num. obs: 24439 / % possible obs: 97.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5.46 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.33 % / Rmerge(I) obs: 0.358 / % possible all: 95.4 |
Reflection | *PLUS Num. measured all: 434544 |
Reflection shell | *PLUS % possible obs: 95.4 % / Mean I/σ(I) obs: 4.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FJM Resolution: 1.9→29.66 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2611346.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.6197 Å2 / ksol: 0.384153 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→29.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.8 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.243 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.218 |