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Yorodumi- PDB-4c4x: Crystal structure of human bifunctional epoxide hydroxylase 2 com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c4x | ||||||
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Title | Crystal structure of human bifunctional epoxide hydroxylase 2 complexed with C9 | ||||||
Components | BIFUNCTIONAL EPOXIDE HYDROLASE 2 | ||||||
Keywords | HYDROLASE / DRUG DESIGN / MULTIPLE BINDING MODES | ||||||
Function / homology | Function and homology information lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / phospholipid dephosphorylation / epoxide metabolic process / lipid phosphatase activity / 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 / Biosynthesis of maresins / soluble epoxide hydrolase / phospholipid dephosphorylation / epoxide metabolic process / lipid phosphatase activity / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / regulation of cholesterol metabolic process / dephosphorylation / phosphatase activity / peroxisomal matrix / toxic substance binding / 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: 2.17 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 | 4c4x.cif.gz | 148.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c4x.ent.gz | 116.3 KB | Display | PDB format |
PDBx/mmJSON format | 4c4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c4x_validation.pdf.gz | 461.5 KB | Display | wwPDB validaton report |
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Full document | 4c4x_full_validation.pdf.gz | 468.1 KB | Display | |
Data in XML | 4c4x_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 4c4x_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/4c4x ftp://data.pdbj.org/pub/pdb/validation_reports/c4/4c4x | HTTPS FTP |
-Related structure data
Related structure data | 4c4yC 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
#1: Protein | Mass: 37370.926 Da / Num. of mol.: 2 / Fragment: EPOXIDE HYDROXYLASE DOMAIN RESIDUES 230-555 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 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.6 % / 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 / Detector: PIXEL / Date: Nov 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→44.31 Å / Num. obs: 35085 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 35.12 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.17→2.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OTQ Resolution: 2.17→29.63 Å / Cor.coef. Fo:Fc: 0.9089 / Cor.coef. Fo:Fc free: 0.879 / SU R Cruickshank DPI: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.319 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.21 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. THE INHIBITOR HAS BEEN MODELED IN TWO ORIENTATIONS
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Displacement parameters | Biso mean: 38.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.287 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→29.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.24 Å / Total num. of bins used: 17
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