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- PDB-8wmt: Crystal structure of cis-epoxysuccinic hydrolase from Bradyrhizob... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8wmt | ||||||
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Title | Crystal structure of cis-epoxysuccinic hydrolase from Bradyrhizobium mercantei | ||||||
![]() | cis-epoxysuccinic hydrolase | ||||||
![]() | HYDROLASE / cis-epoxysuccinic 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 | ![]() | 118 KB | Display | ![]() |
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PDB format | ![]() | 89.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.3 KB | Display | ![]() |
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Full document | ![]() | 442.2 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 36.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28394.350 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.2 M Sodium citrate tribasic dihydrate, 0.1 M BIS-TRIS propane pH 6.0 |
-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: Sep 10, 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: 1.72→64.29 Å / Num. obs: 70748 / % possible obs: 99.9 % / Redundancy: 22.5 % / CC1/2: 1 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.015 / Rrim(I) all: 0.073 / Χ2: 0.97 / Net I/σ(I): 24.9 / Num. measured all: 1590008 |
Reflection shell | Resolution: 1.72→1.76 Å / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 1.402 / Num. measured all: 54749 / Num. unique obs: 5150 / CC1/2: 0.678 / Rpim(I) all: 0.442 / Rrim(I) all: 1.473 / Χ2: 0.82 / Net I/σ(I) obs: 1.7 |
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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: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→43.67 Å
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Refine LS restraints |
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LS refinement shell |
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