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- PDB-8wnh: Crystal structure of cis-epoxysuccinate hydrolase from Rhodococcu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8wnh | ||||||
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Title | Crystal structure of cis-epoxysuccinate hydrolase from Rhodococcus opacus | ||||||
![]() | Epoxide hydrolase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | hydrolase activity, acting on acid halide bonds, in C-halide compounds / L-2-Haloacid dehalogenase / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / FORMIC ACID / Epoxide hydrolase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Han, Y. / Kong, X.D. / Xu, J.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insights of a cis -Epoxysuccinate Hydrolase Facilitate the Development of Robust Biocatalysts for the Production of l-(+)-Tartrate. Authors: Han, Y. / Luo, Y. / Ma, B.D. / Li, J. / Xu, J.H. / Kong, X.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.9 KB | Display | ![]() |
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PDB format | ![]() | 85.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.4 KB | Display | ![]() |
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Full document | ![]() | 449.5 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wmtC ![]() 8wwsC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28165.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FMT / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 3.5 M sodium formate, 0.1 M BIS-TRIS propane, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 27, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→72.69 Å / Num. obs: 63411 / % possible obs: 96.6 % / Redundancy: 25.9 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.015 / Rrim(I) all: 0.077 / Χ2: 0.93 / Net I/σ(I): 27 / Num. measured all: 1644287 |
Reflection shell | Resolution: 1.77→1.87 Å / % possible obs: 100 % / Redundancy: 26.9 % / Rmerge(I) obs: 1.733 / Num. measured all: 253387 / Num. unique obs: 9416 / CC1/2: 0.868 / Rpim(I) all: 0.339 / Rrim(I) all: 1.766 / Χ2: 0.86 / Net I/σ(I) obs: 2.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.773→38.375 Å
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Refine LS restraints |
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LS refinement shell |
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