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- PDB-3g02: Structure of enantioselective mutant of epoxide hydrolase from As... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g02 | ||||||
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Title | Structure of enantioselective mutant of epoxide hydrolase from Aspergillus niger generated by directed evolution | ||||||
![]() | Epoxide hydrolase | ||||||
![]() | HYDROLASE / EPOXIDE HYDROLASE / ALPHA/BETA HYDROLASE FOLD / enantioselective / mutant / directed evolution | ||||||
Function / homology | ![]() epoxide hydrolase / epoxide metabolic process / epoxide hydrolase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Naworyta, A. / Mowbray, S.L. | ||||||
![]() | ![]() Title: Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stage Authors: Reetz, M.T. / Bocola, M. / Wang, L.-W. / Sanchis, J. / Cronin, A. / Arand, M. / Zou, J. / Archelas, A. / Bottalla, A.-L. / Naworyta, A. / Mowbray, S.L. #1: ![]() Title: Structure of Aspergillus niger epoxide hydrolase at 1.8 A resolution: implications for the structure and function of the mammalian microsomal class of epoxide hydrolases Authors: Zou, J. / Hallberg, B.M. / Bergfors, T. / Oesch, F. / Arand, M. / Mowbray, S.L. / Jones, T.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.9 KB | Display | ![]() |
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PDB format | ![]() | 143 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.4 KB | Display | ![]() |
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Full document | ![]() | 454.2 KB | Display | |
Data in XML | ![]() | 34.5 KB | Display | |
Data in CIF | ![]() | 52.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3g0iC ![]() 1qo7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 46047.125 Da / Num. of mol.: 2 / Fragment: residues 5-398 Mutation: L215F, A217N, R219S, L249Y, T317W, T318V, M329P, L330Y, C350V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20% PEG 6000, 0.1M MES, pH 6.0, 0.1M unbuffered sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 31, 2007 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30.54 Å / Num. all: 209428 / Num. obs: 120696 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 7.2 / Num. unique all: 18142 / % possible all: 98.2 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QO7 Resolution: 1.5→28.91 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.877 / SU B: 1.201 / SU ML: 0.046 / SU R Cruickshank DPI: 0.082 / SU Rfree: 0.079 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.51 Å2 / Biso mean: 15.23 Å2 / Biso min: 3.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→28.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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