[English] 日本語
Yorodumi- PDB-1ek1: CRYSTAL STRUCTURE OF MURINE SOLUBLE EPOXIDE HYDROLASE COMPLEXED W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ek1 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF MURINE SOLUBLE EPOXIDE HYDROLASE COMPLEXED WITH CIU INHIBITOR | ||||||
Components | EPOXIDE HYDROLASE | ||||||
Keywords | HYDROLASE / HOMODIMER / ALPHA/BETA HYDROLASE FOLD / DISUBSTITUTED UREA INHIBITOR | ||||||
Function / homology | Function and homology information prostaglandin production involved in inflammatory response / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / Biosynthesis of maresins / lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / soluble epoxide hydrolase / epoxide metabolic process / lipid phosphatase activity ...prostaglandin production involved in inflammatory response / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / Biosynthesis of maresins / lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / soluble epoxide hydrolase / epoxide metabolic process / lipid phosphatase activity / lysophosphatidic acid phosphatase activity / Peroxisomal protein import / linoleic acid metabolic process / positive regulation of blood pressure / epoxide hydrolase activity / regulation of cholesterol metabolic process / phosphatase activity / toxic substance binding / dephosphorylation / cholesterol homeostasis / response to toxic substance / peroxisome / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å | ||||||
Authors | Argiriadi, M.A. / Morisseau, C. / Goodrow, M.H. / Dowdy, D.L. / Hammock, B.D. / Christianson, D.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Binding of alkylurea inhibitors to epoxide hydrolase implicates active site tyrosines in substrate activation. Authors: Argiriadi, M.A. / Morisseau, C. / Goodrow, M.H. / Dowdy, D.L. / Hammock, B.D. / Christianson, D.W. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Detoxification of environmental mutagens and carcinogens: Structure, mechanism, and evolution of liver epoxide hydrolase Authors: Argiriadi, M.A. / Morisseau, C. / Hammock, B.D. / Christianson, D.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ek1.cif.gz | 214.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ek1.ent.gz | 170.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ek1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ek1_validation.pdf.gz | 492.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ek1_full_validation.pdf.gz | 616.3 KB | Display | |
Data in XML | 1ek1_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 1ek1_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/1ek1 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/1ek1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | A domain-swapped homodimer constructed by chain A and B generated by two-fold symmetry. Inhibitor CIU bound in both molecules |
-Components
#1: Protein | Mass: 62582.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P34914, epoxide hydrolase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.72 % | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Ammonium sulfate, MES, ethanol, dithiothreitol, CIU (N-cyclohexyl-N'-(4-iodophenyl)urea) , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Argiriadi, M.A., (1999) Proc.Nat.Acad.Sci.USA, 96, 10637. | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.89 |
Detector | Type: OTHER / Detector: CCD / Date: Aug 30, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. all: 75620 / Num. obs: 73240 / % possible obs: 89.6 % / Observed criterion σ(F): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 3.1→20 Å / Redundancy: 2.22 % / Rmerge(I) obs: 0.253 / Num. unique all: 1866 / % possible all: 86.1 |
Reflection | *PLUS Num. obs: 19761 / Num. measured all: 73240 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3.1→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.194 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|