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Yorodumi- PDB-7xef: Crystal Structure of the Y53F/N55A mutant of LEH complexed with (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xef | ||||||
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Title | Crystal Structure of the Y53F/N55A mutant of LEH complexed with (R)-(1-benzyl-3-phenylpyrrolidin-3-yl)methanol | ||||||
Components | Limonene-1,2-epoxide hydrolase | ||||||
Keywords | HYDROLASE / limonene-1 / 2-epoxide hydrolase / mutant / Rhodococcus erythropolis | ||||||
Function / homology | limonene-1,2-epoxide hydrolase / limonene-1,2-epoxide hydrolase activity / Limonene-1,2-epoxide hydrolase / Limonene-1,2-epoxide hydrolase catalytic domain / NTF2-like domain superfamily / Chem-D0I / DI(HYDROXYETHYL)ETHER / Limonene-1,2-epoxide hydrolase Function and homology information | ||||||
Biological species | Rhodococcus erythropolis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.816 Å | ||||||
Authors | Qu, G. / Li, X. / Sun, Z.T. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Rational enzyme design for enabling biocatalytic Baldwin cyclization and asymmetric synthesis of chiral heterocycles. Authors: Li, J.K. / Qu, G. / Li, X. / Tian, Y. / Cui, C. / Zhang, F.G. / Zhang, W. / Ma, J.A. / Reetz, M.T. / Sun, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xef.cif.gz | 151.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xef.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 7xef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xef_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7xef_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7xef_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 7xef_validation.cif.gz | 46.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/7xef ftp://data.pdbj.org/pub/pdb/validation_reports/xe/7xef | HTTPS FTP |
-Related structure data
Related structure data | 7vwdC 7vwmC 7vx2C 7xeeC 1nwwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 17304.434 Da / Num. of mol.: 4 / Mutation: Y53F,N55A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase |
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-Non-polymers , 5 types, 719 molecules
#2: Chemical | ChemComp-D0I / [( #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.01 Å3/Da / Density % sol: 38.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NaCl, BIS-TRIS pH5.5, Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.816→43.7 Å / Num. obs: 45725 / % possible obs: 93.76 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.13 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.23 |
Reflection shell | Resolution: 1.816→1.881 Å / Num. unique obs: 4212 / CC1/2: 0.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NWW Resolution: 1.816→43.7 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 19.47 / 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: 67.93 Å2 / Biso mean: 14.633 Å2 / Biso min: 2.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.816→43.7 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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