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Yorodumi- PDB-4r9k: Structure of thermostable eightfold mutant of limonene epoxide hy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r9k | ||||||
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Title | Structure of thermostable eightfold mutant of limonene epoxide hydrolase from Rhodococcus erythropolis | ||||||
Components | Limonene-1,2-epoxide hydrolase | ||||||
Keywords | HYDROLASE / limonene epoxide hydrolase / NTF-2 fold / engineered / thermostable | ||||||
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 | Floor, R.J. / Wijma, H.J. / Jekel, P.A. / Terwisscha van Scheltinga, A.C. / Dijkstra, B.W. / Janssen, D.B. | ||||||
Citation | Journal: Proteins / Year: 2015 Title: X-ray crystallographic validation of structure predictions used in computational design for protein stabilization. Authors: Floor, R.J. / Wijma, H.J. / Jekel, P.A. / Terwisscha van Scheltinga, A.C. / Dijkstra, B.W. / Janssen, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r9k.cif.gz | 112 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r9k.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 4r9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/4r9k ftp://data.pdbj.org/pub/pdb/validation_reports/r9/4r9k | HTTPS FTP |
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-Related structure data
Related structure data | 4r9lC 1nwwS S: Starting model for refinement C: citing same article (ref.) |
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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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19482.072 Da / Num. of mol.: 3 / Mutation: S15P, A19K, E45K, T76K, T85V, N92K, Y96F, E124D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase #2: Chemical | ChemComp-GOL / #3: Chemical | #4: 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: 2.11 Å3/Da / Density % sol: 41.72 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 1.44 M tri-sodium citrate, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2012 | |||||||||||||||||||||
Radiation | Monochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.45→76.253 Å / Num. obs: 87794 / % possible obs: 99.9 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 9.9 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.024 / Net I/σ(I): 18 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NWW Resolution: 1.5→44 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.002 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.056 / ESU R Free: 0.058 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.991 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→44 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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