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Yorodumi- PDB-4c4y: Crystal structure of human bifunctional epoxide hydroxylase 2 com... -
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-Basic information
Entry | Database: PDB / ID: 4c4y | ||||||
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Title | Crystal structure of human bifunctional epoxide hydroxylase 2 complexed with A4 | ||||||
Components | BIFUNCTIONAL EPOXIDE HYDROLASE 2 | ||||||
Keywords | HYDROLASE / DRUG DESIGN | ||||||
Function / homology | Function and homology information lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / epoxide metabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) ...lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / epoxide metabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / regulation of cholesterol metabolic process / phosphatase activity / peroxisomal matrix / toxic substance binding / dephosphorylation / cholesterol homeostasis / Peroxisomal protein import / response to toxic substance / peroxisome / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Pilger, J. / Mazur, A. / Monecke, P. / Schreuder, H. / Elshorst, B. / Langer, T. / Schiffer, A. / Krimm, I. / Wegstroth, M. / Lee, D. ...Pilger, J. / Mazur, A. / Monecke, P. / Schreuder, H. / Elshorst, B. / Langer, T. / Schiffer, A. / Krimm, I. / Wegstroth, M. / Lee, D. / Hessler, G. / Wendt, K.-U. / Becker, S. / Griesinger, C. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: A Combination of Spin Diffusion Methods for the Determination of Protein-Ligand Complex Structural Ensembles. Authors: Pilger, J. / Mazur, A. / Monecke, P. / Schreuder, H. / Elshorst, B. / Bartoschek, S. / Langer, T. / Schiffer, A. / Krimm, I. / Wegstroth, M. / Lee, D. / Hessler, G. / Wendt, K. / Becker, S. / Griesinger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c4y.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c4y.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 4c4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/4c4y ftp://data.pdbj.org/pub/pdb/validation_reports/c4/4c4y | HTTPS FTP |
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-Related structure data
Related structure data | 4c4xC 4c4zC 4yxrC 4yxsC 3otqS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 37370.926 Da / Num. of mol.: 1 / Fragment: EPOXIDE HYDROXYLASE DOMAIN, RESIDUES 230-255 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase |
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#2: Chemical | ChemComp-7WI / |
#3: 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: 2.11 Å3/Da / Density % sol: 41.7 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: HANGING DROP. 1 UL PROTEIN SOLUTION (8 MG/ML SEH IN 100 MM NAPO2, PH 7.4, 5 MM DTT AND 15% GLYCEROL) WAS MIXED WITH 1 UL RESERVOIR SOLUTION (100 MM TRIS-HCL, PH 8.3, 26% PEG4000 AND 200 MM ...Details: HANGING DROP. 1 UL PROTEIN SOLUTION (8 MG/ML SEH IN 100 MM NAPO2, PH 7.4, 5 MM DTT AND 15% GLYCEROL) WAS MIXED WITH 1 UL RESERVOIR SOLUTION (100 MM TRIS-HCL, PH 8.3, 26% PEG4000 AND 200 MM LI2SO4 AND EQUILIBRATED AT 20C. CRYSTALS APPEARED IN ABOUT 2 WEEKS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→57.24 Å / Num. obs: 12191 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 42.14 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.41→2.54 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.6 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OTQ Resolution: 2.41→40.82 Å / Cor.coef. Fo:Fc: 0.8444 / Cor.coef. Fo:Fc free: 0.7755 / SU R Cruickshank DPI: 0.957 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.798 / SU Rfree Blow DPI: 0.37 / SU Rfree Cruickshank DPI: 0.363
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Displacement parameters | Biso mean: 37.02 Å2
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Refine analyze | Luzzati coordinate error obs: 0.477 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→40.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.64 Å / Total num. of bins used: 6
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