+Open data
-Basic information
Entry | Database: PDB / ID: 5xm6 | ||||||
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Title | the overall structure of VrEH2 | ||||||
Components | Epoxide hydrolase | ||||||
Keywords | HYDROLASE / epoxide hydrolase | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ether bonds; Ether hydrolases / epoxide hydrolase activity / hydrolase activity Similarity search - Function | ||||||
Biological species | Vigna radiata (mung bean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å | ||||||
Authors | Li, F.L. / Kong, X.D. / Yu, H.L. / Shang, Y.P. / Zhou, J.H. / Xu, J.H. | ||||||
Citation | Journal: Acs Catalysis / Year: 2018 Title: Regioselectivity Engineering of Epoxide Hydrolase: Near-Perfect Enantioconvergence through a Single Site Mutation Authors: Li, F.L. / Kong, X.D. / Chen, Q. / Zheng, Y.C. / Xu, Q. / Chen, F.F. / Fan, L.Q. / Lin, G.Q. / Zhou, J.H. / Yu, H.L. / Xu, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xm6.cif.gz | 212.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xm6.ent.gz | 168.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xm6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xm6_validation.pdf.gz | 452.4 KB | Display | wwPDB validaton report |
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Full document | 5xm6_full_validation.pdf.gz | 457.8 KB | Display | |
Data in XML | 5xm6_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 5xm6_validation.cif.gz | 58 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/5xm6 ftp://data.pdbj.org/pub/pdb/validation_reports/xm/5xm6 | HTTPS FTP |
-Related structure data
Related structure data | 5y6yC 5yb5C 2cjpS S: Starting model for refinement C: citing same article (ref.) |
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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: 39815.141 Da / Num. of mol.: 3 / Mutation: G3E, V4I, R114H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vigna radiata (mung bean) / Gene: Vreh3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0G3F3K2, UniProt: A0A0R5NGA4*PLUS, Hydrolases; Acting on ether bonds; Ether hydrolases #2: 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: 3.25 Å3/Da / Density % sol: 62.1 % / Description: rhombus |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 20000, PEG500MME, HEPES, Mops, sodium nitrate, ammonium sulfate, disodium hydrogen phosphate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 50435 / % possible obs: 100 % / Redundancy: 27.9 % / CC1/2: 0.987 / Rpim(I) all: 0.031 / Χ2: 1.022 / Net I/σ(I): 8.25 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 29.5 % / Num. unique obs: 4938 / CC1/2: 0.987 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CJP Resolution: 2.501→41.532 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.501→41.532 Å
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Refine LS restraints |
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LS refinement shell |
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