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Yorodumi- PDB-5jpu: Structure of limonene epoxide hydrolase mutant - H-2-H5 complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jpu | ||||||
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Title | Structure of limonene epoxide hydrolase mutant - H-2-H5 complex with (S,S)-cyclohexane-1,2-diol | ||||||
Components | limonene epoxide hydrolase | ||||||
Keywords | HYDROLASE / Epoxide Hydrolase / Enantioselectivity / Complex | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Li, G. / Zhang, H. / Sun, Z. / Liu, X. / Reetz, M.T. | ||||||
Funding support | China, 1items
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Citation | Journal: To be published Title: Multi-Parameter Optimization in Directed Evolution: Engineering Thermostability, Enantioselectivity and Activity of an Epoxide Hydrolase Authors: Li, G. / Zhang, H. / Sun, Z. / Liu, X. / 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 | 5jpu.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jpu.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/5jpu ftp://data.pdbj.org/pub/pdb/validation_reports/jp/5jpu | HTTPS FTP |
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-Related structure data
Related structure data | 5jppC 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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Unit cell |
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-Components
#1: Protein | Mass: 17500.643 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ZAG3*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. | |
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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: 2.24 Å3/Da / Density % sol: 44.97 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES (pH 7.5), 2% v/v Polyethylene glycol 400, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 49387 / % possible obs: 100 % / Redundancy: 14.8 % / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 1.5→1.53 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NU3 Resolution: 1.5→24.363 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.94
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 43.377 Å2 / ksol: 0.383 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.5→24.363 Å
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Refine LS restraints |
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LS refinement shell |
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