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Yorodumi- PDB-4xby: Crystal Structure of the L74F/M78V/I80V/L114F mutant of LEH compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xby | ||||||
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Title | Crystal Structure of the L74F/M78V/I80V/L114F mutant of LEH complexed with cyclopentene oxide | ||||||
Components | Limonene-1,2-epoxide hydrolase | ||||||
Keywords | HYDROLASE / epoxide hydrolase | ||||||
Function / homology | Function and homology information limonene-1,2-epoxide hydrolase / limonene-1,2-epoxide hydrolase activity Similarity search - Function | ||||||
Biological species | Rhodococcus erythropolis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Model details | A mutant of limonene 1,2-epoxide hydrolase | ||||||
Authors | Kong, X.D. / Sun, Z. / Xu, J.H. / Reetz, M.T. / Zhou, J. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution Authors: Sun, Z. / Lonsdale, R. / Kong, X.D. / Xu, J.H. / Zhou, J. / Reetz, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xby.cif.gz | 242.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xby.ent.gz | 194.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/4xby ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xby | HTTPS FTP |
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-Related structure data
Related structure data | 4xbtC 4xbxC 4xdvC 4xdwC 1nu3S 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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2 |
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3 |
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4 |
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Unit cell |
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Details | The biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D) |
-Components
#1: Protein | Mass: 17369.381 Da / Num. of mol.: 8 / Fragment: UNP residues 5-149 / Mutation: L74F/M78V/I80V/L114F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase #2: Chemical | ChemComp-3ZS / ( #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: 2.91 Å3/Da / Density % sol: 57.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.4 M citrate sodium |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 24, 2014 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 63084 / % possible obs: 95 % / Redundancy: 4.4 % / Biso Wilson estimate: 36.78 Å2 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.075 / Rrim(I) all: 0.163 / Χ2: 1.027 / Net I/av σ(I): 7.787 / Net I/σ(I): 8.5 / Num. measured all: 276030 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NU3 Resolution: 2.3→29.87 Å / FOM work R set: 0.7888 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.74 Å2 / Biso mean: 31.41 Å2 / Biso min: 9.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→29.87 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22
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